tag:old.nabble.com,2006:forum-13596Nabble - BioPerl2009-11-11T15:48:33ZOfficially organized in 1995 and existing informally for several years prior, The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. BioPerl home is <a href="http://bio.perl.org/" target="_top" rel="nofollow">here</a>.tag:old.nabble.com,2006:post-26311041Maq assembly wrapper ready for beta testing2009-11-11T15:48:33Z2009-11-11T15:48:33ZMark A. JensenHi All-
<br><br>New modules are available in the core and in bioperl-run for
<br>working with Heng Li's short read assembler "maq"
<br>(<a href="http://maq.sourceforge.net/maq-man.shtml" target="_top" rel="nofollow">http://maq.sourceforge.net/maq-man.shtml</a>). Bio::Tools::Run::Maq
<br>allows a quick assembly call with a canned a maq pipeline, and also
<br>allows individual maq commands to be called separately.
<br>It uses Bio::Assembly::IO::maq (a read-only module) to deliver
<br>a Bio::Assembly::Scaffold from maq output.
<br><br>If you're interested, see
<br><a href="http://www.bioperl.org/wiki/HOWTO:Short-read_assemblies_with_maq" target="_top" rel="nofollow">http://www.bioperl.org/wiki/HOWTO:Short-read_assemblies_with_maq</a><br>and update your core and bioperl-run. The code inherits from Florent's
<br>excellent new Bio::Tools::Run::AssemblerBase -- kudos to him!!
<br><br>tests are in bioperl-run/trunk/t/Maq.t, see them for myriad examples
<br>send me the bugs
<br>MAJ
<br>_______________________________________________
<br>Bioperl-l mailing list
<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26311041&i=0" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26302791Re: [Fwd: Re: A question about iBio::Index: anditscorrect use]2009-11-11T07:01:18Z2009-11-11T07:01:18Zjluis.lavinHi once again,
<br>I have modified the script following the instructions Jason gave me (at
<br>last what I understood, remember it is my first time trying to learn a
<br>programming language...and I´m not the smartest guy in the class, hehe)but
<br>it seems I didn´t fix the problem...
<br>Here´s the new code I wrote:
<br><br>#!/c:/Perl -w
<br> use strict;
<br> use Bio::Index::Fasta;
<br> use Bio::DB::Fasta;
<br> use Bio::SeqIO;
<br> use IO::File;
<br><br># assign files to scalars
<br>my $index_file = 'PC91.fasta';
<br>my $id_list = 'LCS2.txt';
<br><br># open index file
<br>my $db = Bio::DB::Fasta->new($index_file) or die;
<br><br># open the id list
<br>my $in = IO::File->new($id_list) or die;
<br><br># open FASTA to write
<br>my $out = new Bio::SeqIO (-file => ">>index_extracted.fasta",
<br>-format => 'fasta');
<br><br># retrieve ids loop
<br>foreach my $id ($in) {
<br>if ($id eq ''){
<br>die ("empty list")
<br>}
<br>else {
<br>my $seqobj = my $inx->fetch($id);
<br>$out->write_seq($seqobj);
<br>}
<br>}
<br><br># parse fasta headers
<br>sub my_makeid {
<br>my $id = shift;
<br>if ( $id =~ /^>[^:]+:(\S+)/ ) {
<br>return $1;
<br>} elsif ($id =~ /^>(\S+)/) {
<br>return $1;
<br>} else {
<br>warn("cannot parse ID for $id\n");
<br>}
<br>}
<br>exit;
<br><br>Would anyone, please take a look at it ...
<br><br>Thanks in advance ;)
<br><br><br><br><br>El Mar, 10 de Noviembre de 2009, 19:47, Jason Stajich escribió:
<div class='shrinkable-quote'><br>> Page 44 has the custom ID info or look at documentation for
<br>> Bio::DB::Fasta - there is a similar syntax for Bio::Index::Fasta if
<br>> you read the perldoc for the module.
<br>>
<br>> <a href="http://jason.open-bio.org/Bioperl_Tutorials/ProgrammingBiology2008/ProgBiology_BioPerl_I.pdf" target="_top" rel="nofollow">http://jason.open-bio.org/Bioperl_Tutorials/ProgrammingBiology2008/ProgBiology_BioPerl_I.pdf</a><br>>
<br>> Don't re-opening SeqIO each time just do it once at the beginning
<br>> outside of the loop and then call write_seq within the loop.
<br>>
<br>> This is one nuance of doing OO programming vs procedural is that there
<br>> is some outside state information that can persist in an object, but
<br>> conceptually, you want to open a filehandle once and just keep writing
<br>> to it.
<br>>
<br>> -jason
<br>> On Nov 10, 2009, at 2:43 AM, <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=0" target="_top" rel="nofollow">jluis.lavin@...</a> wrote:
<br>>
<br>>> Hello again,
<br>>>
<br>>> I tried what Mark told me modifying the code line he told me but
<br>>> there´s
<br>>> still a problem that I believe must be due to the sequences name.
<br>>> My secuences header on the Fasta file have this format:
<br>>>
<br>>>> PleosPC9_1_103820|fgenesh1_pg.3_#_1
<br>>>
<br>>> Th part on the right of the pipe changes depending on the program
<br>>> used to
<br>>> create the gene model, for example:
<br>>>
<br>>>> PleosPC9_1_103820|fgenesh1_pg.3_#_1
<br>>>> PleosPC9_1_123413|genemark.2731_g
<br>>>> PleosPC9_1_52065|e_gw1.3.64.1
<br>>>
<br>>> So I guess I need to parse my ids somehow for thr program to detect
<br>>> only
<br>>> the first part of the fasta header (the "protein name") and not to get
<br>>> messed with the other side of the pipe...
<br>>>
<br>>> This is the corrected code I wrote following Mark´s indications, but I
<br>>> still don´t have any idea about the parsing issue...
<br>>>
<br>>> #!/c:/Perl -w
<br>>> use Bio::Index::Fasta;
<br>>> use strict;
<br>>> #PC9.fasta is my genomic file
<br>>> my $Index_File_Name ="PC9.fasta";
<br>>> my $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
<br>>> #LCS.txt is my sequences list
<br>>> @ARGV = <LCS.txt>;
<br>>> foreach my $id (@ARGV) {
<br>>> if ($id eq ''){
<br>>> die ("empty list")
<br>>> }
<br>>> else {
<br>>> my $seqobj = $inx->fetch($id);
<br>>> my $out = new Bio::SeqIO (-file => ">>index_extracted.fasta",
<br>>> -format => 'fasta');
<br>>> $out->write_seq($seqobj);
<br>>> }
<br>>> }
<br>>> exit;
<br>>> }
<br>>>
<br>>> Thanks in advance
<br>>>
<br>>> PD. May it be a faster way of extracting those sequences using plain
<br>>> PERL?
<br>>>
<br>>>
<br>>>
<br>>>
<br>>> El Jue, 5 de Noviembre de 2009, 17:39, Mark A. Jensen escribió:
<br>>>> Yes, these are files created by the SDBM, Perl's internal db
<br>>>> manager. You
<br>>>> should
<br>>>> be able to
<br>>>> open the index by simply
<br>>>> $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
<br>>>> and the dbm will know what to do--
<br>>>> cheers MAJ
<br>>>> ----- Original Message -----
<br>>>> From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=1" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>>>> To: "Mark A. Jensen" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=2" target="_top" rel="nofollow">maj@...</a>>
<br>>>> Cc: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=3" target="_top" rel="nofollow">jluis.lavin@...</a>>; <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=4" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>>>> Sent: Thursday, November 05, 2009 11:21 AM
<br>>>> Subject: Re: [Bioperl-l] [Fwd: Re: A question about iBio::Index:
<br>>>> and its
<br>>>> correct
<br>>>> use]
<br>>>>
<br>>>>
<br>>>>> Thank you very much Mark, that´s a good point :$
<br>>>>> I guess your correction is referred to the second script, isn´t it?
<br>>>>>
<br>>>>> If it is so, there is still a problem with the first script, it
<br>>>>> doesn´t
<br>>>>> create the PC9.fasta.idx file, instead it creates two files named:
<br>>>>> -PC9.fasta.idx.pag
<br>>>>> -PC9.fasta.idx.dir
<br>>>>>
<br>>>>> which seem to be clearly related with some kind of indexing
<br>>>>> process...but,
<br>>>>> unless the PC9.fasta.idx file is only virtual or remains hidden, I
<br>>>>> can´t
<br>>>>> find it anywhere...
<br>>>>> Forgive me if I´m talking nosense...
<br>>>>>
<br>>>>> Thank you very much again for your help ;)
<br>>>>>
<br>>>>>
<br>>>>> El Jue, 5 de Noviembre de 2009, 17:02, Mark A. Jensen escribió:
<br>>>>>> Hey José,
<br>>>>>> The first thing that jumps out it the index file name. Looks
<br>>>>>> like you create it as
<br>>>>>> PC9.fasta.idx
<br>>>>>> But you read it as
<br>>>>>> PC9.fasta
<br>>>>>> Not an unusual mistake. Do
<br>>>>>> my $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
<br>>>>>> and see if it works.
<br>>>>>> MAJ
<br>>>>>> ----- Original Message -----
<br>>>>>> From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=5" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>>>>>> To: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=6" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>>>>>> Sent: Thursday, November 05, 2009 10:46 AM
<br>>>>>> Subject: [Bioperl-l] [Fwd: Re: A question about iBio::Index: and
<br>>>>>> its
<br>>>>>> correct
<br>>>>>> use]
<br>>>>>>
<br>>>>>>
<br>>>>>>
<br>>>>>>
<br>>>>>> ---------------------------- Mensaje original
<br>>>>>> ----------------------------
<br>>>>>> Subject: Re: [Bioperl-l] A question about iBio::Index: and its
<br>>>>>> correct
<br>>>>>> use
<br>>>>>> From: <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=7" target="_top" rel="nofollow">jluis.lavin@...</a>
<br>>>>>> Fecha: Jue, 5 de Noviembre de 2009, 16:46
<br>>>>>> To: "Mark A. Jensen" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=8" target="_top" rel="nofollow">maj@...</a>>
<br>>>>>> --------------------------------------------------------------------------
<br>>>>>>
<br>>>>>> Hi Mark,
<br>>>>>>
<br>>>>>> I´ve actually got two scripts, the first one is to create the
<br>>>>>> index and
<br>>>>>> the second one is to retrieve the sequence lis from the indexed
<br>>>>>> file.
<br>>>>>>
<br>>>>>> 1)Here is the Index creation script:
<br>>>>>>
<br>>>>>> #!/c:/Perl -w
<br>>>>>> use strict;
<br>>>>>> use Bio::Index::Fasta;
<br>>>>>> use strict;
<br>>>>>>
<br>>>>>> print "Enter file for indexing: \n";
<br>>>>>> my $Index_File_Name = <STDIN>;
<br>>>>>> my $inx = Bio::Index::Fasta->new(-filename =>
<br>>>>>> $Index_File_Name.".idx",
<br>>>>>> -write_flag => 1);
<br>>>>>> $inx->make_index(my $File_Name);
<br>>>>>>
<br>>>>>> 2)And here is the sequence retrieval script:
<br>>>>>>
<br>>>>>> #!/c:/Perl -w
<br>>>>>> use Bio::Index::Fasta;
<br>>>>>> use strict;
<br>>>>>> #PC9.fasta is my genomic file
<br>>>>>> my $Index_File_Name ="PC9.fasta";
<br>>>>>> my $inx = Bio::Index::Fasta->new($Index_File_Name);
<br>>>>>> #LCS.txt is my sequences list
<br>>>>>> @ARGV = <lCS.txt>;
<br>>>>>> foreach my $id (@ARGV) {
<br>>>>>> if ($id eq ''){
<br>>>>>> die ("empty list")
<br>>>>>> }
<br>>>>>> else {
<br>>>>>> my $seqobj = $inx->fetch($id);
<br>>>>>> my $out = new Bio::SeqIO (-file => ">>extracted_seqs.fasta",
<br>>>>>> -format => 'fasta');
<br>>>>>> $out->write_seq($seqobj);
<br>>>>>> }
<br>>>>>> }
<br>>>>>> exit;
<br>>>>>> }
<br>>>>>>
<br>>>>>> I hope this code is not a total scum...
<br>>>>>>
<br>>>>>> Thanks in advance ;)
<br>>>>>>
<br>>>>>>
<br>>>>>>
<br>>>>>> El Jue, 5 de Noviembre de 2009, 16:39, Mark A. Jensen escribió:
<br>>>>>>> José -- It looks like this is a good solution to your problem.
<br>>>>>>> Please
<br>>>>>>> send
<br>>>>>>> you
<br>>>>>>> script so we can look at it-
<br>>>>>>> cheers Mark
<br>>>>>>> ----- Original Message -----
<br>>>>>>> From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=9" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>>>>>>> To: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=10" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>>>>>>> Sent: Thursday, November 05, 2009 10:28 AM
<br>>>>>>> Subject: [Bioperl-l] A question about iBio::Index: and its
<br>>>>>>> correct use
<br>>>>>>>
<br>>>>>>>
<br>>>>>>>
<br>>>>>>> Hello to all,
<br>>>>>>>
<br>>>>>>> I´m trying to write a script to retrieve a list of sequences
<br>>>>>>> from a
<br>>>>>>> local
<br>>>>>>> FASTA file (for example a fasta archive where all the protein
<br>>>>>>> models
<br>>>>>>> of
<br>>>>>>> an
<br>>>>>>> organism are stored). This file would be used by me as some kind
<br>>>>>>> "local
<br>>>>>>> database" (sorry if I mistake a few concepts...)
<br>>>>>>> I´ve been reading the BioPerl HOWTOs and I came across the
<br>>>>>>> Bio::Index::Fasta tool.
<br>>>>>>> If I didn´t misunderstood what I read (which can be easy because
<br>>>>>>> my
<br>>>>>>> low
<br>>>>>>> level on programming) this Indexing tool should do the job.
<br>>>>>>> I wrote a couple of scripts based on the documentation i read
<br>>>>>>> about
<br>>>>>>> this
<br>>>>>>> tool, but I don´t seem to be able to create the index file to be
<br>>>>>>> used
<br>>>>>>> later (to retrieve the sequences from).
<br>>>>>>> -First of all, I want to ask the people in this forum if the
<br>>>>>>> Bio::Index::Fasta is the right one to chose for this tasks.
<br>>>>>>> -Then I´ll beg you to take a look at my scripts, because I don´t
<br>>>>>>> seem
<br>>>>>>> to
<br>>>>>>> catch the bug...
<br>>>>>>>
<br>>>>>>> Best wishes to you all and thanks in advance ;)
<br>>>>>>>
<br>>>>>>> --
<br>>>>>>> José Luis Lavín Trueba, PhD
<br>>>>>>>
<br>>>>>>> Dpto. de Producción Agraria
<br>>>>>>> Grupo de Genética y Microbiología
<br>>>>>>> Universidad Pública de Navarra
<br>>>>>>> 31006 Pamplona
<br>>>>>>> Navarra
<br>>>>>>> SPAIN
<br>>>>>>>
<br>>>>>>>
<br>>>>>>> _______________________________________________
<br>>>>>>> Bioperl-l mailing list
<br>>>>>>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=11" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>>>>>>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>>>>>>
<br>>>>>>>
<br>>>>>>>
<br>>>>>>
<br>>>>>>
<br>>>>>> --
<br>>>>>> Dr. José Luis Lavín Trueba
<br>>>>>>
<br>>>>>> Dpto. de Producción Agraria
<br>>>>>> Grupo de Genética y Microbiología
<br>>>>>> Universidad Pública de Navarra
<br>>>>>> 31006 Pamplona
<br>>>>>> Navarra
<br>>>>>> SPAIN
<br>>>>>>
<br>>>>>>
<br>>>>>>
<br>>>>>> --
<br>>>>>> Dr. José Luis Lavín Trueba
<br>>>>>>
<br>>>>>> Dpto. de Producción Agraria
<br>>>>>> Grupo de Genética y Microbiología
<br>>>>>> Universidad Pública de Navarra
<br>>>>>> 31006 Pamplona
<br>>>>>> Navarra
<br>>>>>> SPAIN
<br>>>>>>
<br>>>>>>
<br>>>>>> _______________________________________________
<br>>>>>> Bioperl-l mailing list
<br>>>>>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=12" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>>>>>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>>>>>
<br>>>>>>
<br>>>>>>
<br>>>>>
<br>>>>>
<br>>>>> --
<br>>>>> Dr. José Luis Lavín Trueba
<br>>>>>
<br>>>>> Dpto. de Producción Agraria
<br>>>>> Grupo de Genética y Microbiología
<br>>>>> Universidad Pública de Navarra
<br>>>>> 31006 Pamplona
<br>>>>> Navarra
<br>>>>> SPAIN
<br>>>>>
<br>>>>>
<br>>>>>
<br>>>>>
<br>>>>
<br>>>> _______________________________________________
<br>>>> Bioperl-l mailing list
<br>>>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=13" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>>>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>>>
<br>>>
<br>>>
<br>>> --
<br>>> Dr. José Luis Lavín Trueba
<br>>>
<br>>> Dpto. de Producción Agraria
<br>>> Grupo de Genética y Microbiología
<br>>> Universidad Pública de Navarra
<br>>> 31006 Pamplona
<br>>> Navarra
<br>>> SPAIN
<br>>>
<br>>>
<br>>> _______________________________________________
<br>>> Bioperl-l mailing list
<br>>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=14" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>
<br>> --
<br>> Jason Stajich
<br>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=15" target="_top" rel="nofollow">jason.stajich@...</a>
<br>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=16" target="_top" rel="nofollow">jason@...</a>
<br>>
<br>>
<br>> _______________________________________________
<br>> Bioperl-l mailing list
<br>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=17" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>
</div><br><br>--
<br>Dr. José Luis Lavín Trueba
<br><br>Dpto. de Producción Agraria
<br>Grupo de Genética y Microbiología
<br>Universidad Pública de Navarra
<br>31006 Pamplona
<br>Navarra
<br>SPAIN
<br><br><br>_______________________________________________
<br>Bioperl-l mailing list
<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26302791&i=18" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26289222Re: Bio::Index::GenBank - by organism?2009-11-10T10:50:00Z2009-11-10T10:50:00ZJason Stajich-3You might also look at what mygenbank does:
<br><a href="http://homepage.mac.com/iankorf/mygenbank.html" target="_top" rel="nofollow">http://homepage.mac.com/iankorf/mygenbank.html</a><br><br>On Nov 9, 2009, at 7:55 PM, Chris Fields wrote:
<br><div class='shrinkable-quote'><br>> On Nov 9, 2009, at 6:05 PM, Jay Hannah wrote:
<br>>
<br>>> Many thanks to Ewan Birney et. al. for Bio::Index::*
<br>>>
<br>>> I can throw away my awful grep based index-by-accession stuff. :)
<br>>>
<br>>> Any chance someone has also written an organism based index
<br>>> mechanism? Something like...
<br>>>
<br>>> while (my $seq = $inx−>get_Seq_by_organism('*Xanthomonas*')) {
<br>>> print $seq->display_id . "\n";
<br>>> }
<br>>>
<br>>> Thanks,
<br>>>
<br>>> j
<br>>
<br>> It should work via id_parser(); from Bio::Index::GenBank:
<br>>
<br>> $inx->id_parser(\&get_id);
<br>> # make the index
<br>> $inx->make_index($file_name);
<br>>
<br>> # here is where the retrieval key is specified
<br>> sub get_id {
<br>> my $line = shift;
<br>> $line =~ /clone="(\S+)"/;
<br>> $1;
<br>> }
<br>>
<br>> Change the code ref deal with the line you want and parse the name
<br>> out. Caveat: this may not be absolutely perfect (it only passes in
<br>> a line at a time, and some species lines will wrap). Also not sure
<br>> how this would work in cases where multiple sequences from the same
<br>> species are present.
<br>>
<br>> The other option is to preparse everything and tie a hash to store a
<br>> species->UID map, then use that along with your Bio::Index index to
<br>> grab what you need.
<br>>
<br>> chris
<br>> _______________________________________________
<br>> Bioperl-l mailing list
<br>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289222&i=0" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a></div><br>--
<br>Jason Stajich
<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289222&i=1" target="_top" rel="nofollow">jason.stajich@...</a>
<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289222&i=2" target="_top" rel="nofollow">jason@...</a>
<br><br><br>_______________________________________________
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26289183Re: [Fwd: Re: A question about iBio::Index: and itscorrect use]2009-11-10T10:47:02Z2009-11-10T10:47:02ZJason Stajich-3Page 44 has the custom ID info or look at documentation for
<br>Bio::DB::Fasta - there is a similar syntax for Bio::Index::Fasta if
<br>you read the perldoc for the module.
<br><br> <a href="http://jason.open-bio.org/Bioperl_Tutorials/ProgrammingBiology2008/ProgBiology_BioPerl_I.pdf" target="_top" rel="nofollow">http://jason.open-bio.org/Bioperl_Tutorials/ProgrammingBiology2008/ProgBiology_BioPerl_I.pdf</a><br><br>Don't re-opening SeqIO each time just do it once at the beginning
<br>outside of the loop and then call write_seq within the loop.
<br><br>This is one nuance of doing OO programming vs procedural is that there
<br>is some outside state information that can persist in an object, but
<br>conceptually, you want to open a filehandle once and just keep writing
<br>to it.
<br><br>-jason
<br>On Nov 10, 2009, at 2:43 AM, <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=0" target="_top" rel="nofollow">jluis.lavin@...</a> wrote:
<br><div class='shrinkable-quote'><br>> Hello again,
<br>>
<br>> I tried what Mark told me modifying the code line he told me but
<br>> there´s
<br>> still a problem that I believe must be due to the sequences name.
<br>> My secuences header on the Fasta file have this format:
<br>>
<br>>> PleosPC9_1_103820|fgenesh1_pg.3_#_1
<br>>
<br>> Th part on the right of the pipe changes depending on the program
<br>> used to
<br>> create the gene model, for example:
<br>>
<br>>> PleosPC9_1_103820|fgenesh1_pg.3_#_1
<br>>> PleosPC9_1_123413|genemark.2731_g
<br>>> PleosPC9_1_52065|e_gw1.3.64.1
<br>>
<br>> So I guess I need to parse my ids somehow for thr program to detect
<br>> only
<br>> the first part of the fasta header (the "protein name") and not to get
<br>> messed with the other side of the pipe...
<br>>
<br>> This is the corrected code I wrote following Mark´s indications, but I
<br>> still don´t have any idea about the parsing issue...
<br>>
<br>> #!/c:/Perl -w
<br>> use Bio::Index::Fasta;
<br>> use strict;
<br>> #PC9.fasta is my genomic file
<br>> my $Index_File_Name ="PC9.fasta";
<br>> my $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
<br>> #LCS.txt is my sequences list
<br>> @ARGV = <LCS.txt>;
<br>> foreach my $id (@ARGV) {
<br>> if ($id eq ''){
<br>> die ("empty list")
<br>> }
<br>> else {
<br>> my $seqobj = $inx->fetch($id);
<br>> my $out = new Bio::SeqIO (-file => ">>index_extracted.fasta",
<br>> -format => 'fasta');
<br>> $out->write_seq($seqobj);
<br>> }
<br>> }
<br>> exit;
<br>> }
<br>>
<br>> Thanks in advance
<br>>
<br>> PD. May it be a faster way of extracting those sequences using plain
<br>> PERL?
<br>>
<br>>
<br>>
<br>>
<br>> El Jue, 5 de Noviembre de 2009, 17:39, Mark A. Jensen escribió:
<br>>> Yes, these are files created by the SDBM, Perl's internal db
<br>>> manager. You
<br>>> should
<br>>> be able to
<br>>> open the index by simply
<br>>> $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
<br>>> and the dbm will know what to do--
<br>>> cheers MAJ
<br>>> ----- Original Message -----
<br>>> From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=1" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>>> To: "Mark A. Jensen" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=2" target="_top" rel="nofollow">maj@...</a>>
<br>>> Cc: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=3" target="_top" rel="nofollow">jluis.lavin@...</a>>; <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=4" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>>> Sent: Thursday, November 05, 2009 11:21 AM
<br>>> Subject: Re: [Bioperl-l] [Fwd: Re: A question about iBio::Index:
<br>>> and its
<br>>> correct
<br>>> use]
<br>>>
<br>>>
<br>>>> Thank you very much Mark, that´s a good point :$
<br>>>> I guess your correction is referred to the second script, isn´t it?
<br>>>>
<br>>>> If it is so, there is still a problem with the first script, it
<br>>>> doesn´t
<br>>>> create the PC9.fasta.idx file, instead it creates two files named:
<br>>>> -PC9.fasta.idx.pag
<br>>>> -PC9.fasta.idx.dir
<br>>>>
<br>>>> which seem to be clearly related with some kind of indexing
<br>>>> process...but,
<br>>>> unless the PC9.fasta.idx file is only virtual or remains hidden, I
<br>>>> can´t
<br>>>> find it anywhere...
<br>>>> Forgive me if I´m talking nosense...
<br>>>>
<br>>>> Thank you very much again for your help ;)
<br>>>>
<br>>>>
<br>>>> El Jue, 5 de Noviembre de 2009, 17:02, Mark A. Jensen escribió:
<br>>>>> Hey José,
<br>>>>> The first thing that jumps out it the index file name. Looks
<br>>>>> like you create it as
<br>>>>> PC9.fasta.idx
<br>>>>> But you read it as
<br>>>>> PC9.fasta
<br>>>>> Not an unusual mistake. Do
<br>>>>> my $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
<br>>>>> and see if it works.
<br>>>>> MAJ
<br>>>>> ----- Original Message -----
<br>>>>> From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=5" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>>>>> To: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=6" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>>>>> Sent: Thursday, November 05, 2009 10:46 AM
<br>>>>> Subject: [Bioperl-l] [Fwd: Re: A question about iBio::Index: and
<br>>>>> its
<br>>>>> correct
<br>>>>> use]
<br>>>>>
<br>>>>>
<br>>>>>
<br>>>>>
<br>>>>> ---------------------------- Mensaje original
<br>>>>> ----------------------------
<br>>>>> Subject: Re: [Bioperl-l] A question about iBio::Index: and its
<br>>>>> correct
<br>>>>> use
<br>>>>> From: <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=7" target="_top" rel="nofollow">jluis.lavin@...</a>
<br>>>>> Fecha: Jue, 5 de Noviembre de 2009, 16:46
<br>>>>> To: "Mark A. Jensen" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=8" target="_top" rel="nofollow">maj@...</a>>
<br>>>>> --------------------------------------------------------------------------
<br>>>>>
<br>>>>> Hi Mark,
<br>>>>>
<br>>>>> I´ve actually got two scripts, the first one is to create the
<br>>>>> index and
<br>>>>> the second one is to retrieve the sequence lis from the indexed
<br>>>>> file.
<br>>>>>
<br>>>>> 1)Here is the Index creation script:
<br>>>>>
<br>>>>> #!/c:/Perl -w
<br>>>>> use strict;
<br>>>>> use Bio::Index::Fasta;
<br>>>>> use strict;
<br>>>>>
<br>>>>> print "Enter file for indexing: \n";
<br>>>>> my $Index_File_Name = <STDIN>;
<br>>>>> my $inx = Bio::Index::Fasta->new(-filename =>
<br>>>>> $Index_File_Name.".idx",
<br>>>>> -write_flag => 1);
<br>>>>> $inx->make_index(my $File_Name);
<br>>>>>
<br>>>>> 2)And here is the sequence retrieval script:
<br>>>>>
<br>>>>> #!/c:/Perl -w
<br>>>>> use Bio::Index::Fasta;
<br>>>>> use strict;
<br>>>>> #PC9.fasta is my genomic file
<br>>>>> my $Index_File_Name ="PC9.fasta";
<br>>>>> my $inx = Bio::Index::Fasta->new($Index_File_Name);
<br>>>>> #LCS.txt is my sequences list
<br>>>>> @ARGV = <lCS.txt>;
<br>>>>> foreach my $id (@ARGV) {
<br>>>>> if ($id eq ''){
<br>>>>> die ("empty list")
<br>>>>> }
<br>>>>> else {
<br>>>>> my $seqobj = $inx->fetch($id);
<br>>>>> my $out = new Bio::SeqIO (-file => ">>extracted_seqs.fasta",
<br>>>>> -format => 'fasta');
<br>>>>> $out->write_seq($seqobj);
<br>>>>> }
<br>>>>> }
<br>>>>> exit;
<br>>>>> }
<br>>>>>
<br>>>>> I hope this code is not a total scum...
<br>>>>>
<br>>>>> Thanks in advance ;)
<br>>>>>
<br>>>>>
<br>>>>>
<br>>>>> El Jue, 5 de Noviembre de 2009, 16:39, Mark A. Jensen escribió:
<br>>>>>> José -- It looks like this is a good solution to your problem.
<br>>>>>> Please
<br>>>>>> send
<br>>>>>> you
<br>>>>>> script so we can look at it-
<br>>>>>> cheers Mark
<br>>>>>> ----- Original Message -----
<br>>>>>> From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=9" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>>>>>> To: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=10" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>>>>>> Sent: Thursday, November 05, 2009 10:28 AM
<br>>>>>> Subject: [Bioperl-l] A question about iBio::Index: and its
<br>>>>>> correct use
<br>>>>>>
<br>>>>>>
<br>>>>>>
<br>>>>>> Hello to all,
<br>>>>>>
<br>>>>>> I´m trying to write a script to retrieve a list of sequences
<br>>>>>> from a
<br>>>>>> local
<br>>>>>> FASTA file (for example a fasta archive where all the protein
<br>>>>>> models
<br>>>>>> of
<br>>>>>> an
<br>>>>>> organism are stored). This file would be used by me as some kind
<br>>>>>> "local
<br>>>>>> database" (sorry if I mistake a few concepts...)
<br>>>>>> I´ve been reading the BioPerl HOWTOs and I came across the
<br>>>>>> Bio::Index::Fasta tool.
<br>>>>>> If I didn´t misunderstood what I read (which can be easy because
<br>>>>>> my
<br>>>>>> low
<br>>>>>> level on programming) this Indexing tool should do the job.
<br>>>>>> I wrote a couple of scripts based on the documentation i read
<br>>>>>> about
<br>>>>>> this
<br>>>>>> tool, but I don´t seem to be able to create the index file to be
<br>>>>>> used
<br>>>>>> later (to retrieve the sequences from).
<br>>>>>> -First of all, I want to ask the people in this forum if the
<br>>>>>> Bio::Index::Fasta is the right one to chose for this tasks.
<br>>>>>> -Then I´ll beg you to take a look at my scripts, because I don´t
<br>>>>>> seem
<br>>>>>> to
<br>>>>>> catch the bug...
<br>>>>>>
<br>>>>>> Best wishes to you all and thanks in advance ;)
<br>>>>>>
<br>>>>>> --
<br>>>>>> José Luis Lavín Trueba, PhD
<br>>>>>>
<br>>>>>> Dpto. de Producción Agraria
<br>>>>>> Grupo de Genética y Microbiología
<br>>>>>> Universidad Pública de Navarra
<br>>>>>> 31006 Pamplona
<br>>>>>> Navarra
<br>>>>>> SPAIN
<br>>>>>>
<br>>>>>>
<br>>>>>> _______________________________________________
<br>>>>>> Bioperl-l mailing list
<br>>>>>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=11" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>>>>>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>>>>>
<br>>>>>>
<br>>>>>>
<br>>>>>
<br>>>>>
<br>>>>> --
<br>>>>> Dr. José Luis Lavín Trueba
<br>>>>>
<br>>>>> Dpto. de Producción Agraria
<br>>>>> Grupo de Genética y Microbiología
<br>>>>> Universidad Pública de Navarra
<br>>>>> 31006 Pamplona
<br>>>>> Navarra
<br>>>>> SPAIN
<br>>>>>
<br>>>>>
<br>>>>>
<br>>>>> --
<br>>>>> Dr. José Luis Lavín Trueba
<br>>>>>
<br>>>>> Dpto. de Producción Agraria
<br>>>>> Grupo de Genética y Microbiología
<br>>>>> Universidad Pública de Navarra
<br>>>>> 31006 Pamplona
<br>>>>> Navarra
<br>>>>> SPAIN
<br>>>>>
<br>>>>>
<br>>>>> _______________________________________________
<br>>>>> Bioperl-l mailing list
<br>>>>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=12" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>>>>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>>>>
<br>>>>>
<br>>>>>
<br>>>>
<br>>>>
<br>>>> --
<br>>>> Dr. José Luis Lavín Trueba
<br>>>>
<br>>>> Dpto. de Producción Agraria
<br>>>> Grupo de Genética y Microbiología
<br>>>> Universidad Pública de Navarra
<br>>>> 31006 Pamplona
<br>>>> Navarra
<br>>>> SPAIN
<br>>>>
<br>>>>
<br>>>>
<br>>>>
<br>>>
<br>>> _______________________________________________
<br>>> Bioperl-l mailing list
<br>>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=13" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>>
<br>>
<br>>
<br>> --
<br>> Dr. José Luis Lavín Trueba
<br>>
<br>> Dpto. de Producción Agraria
<br>> Grupo de Genética y Microbiología
<br>> Universidad Pública de Navarra
<br>> 31006 Pamplona
<br>> Navarra
<br>> SPAIN
<br>>
<br>>
<br>> _______________________________________________
<br>> Bioperl-l mailing list
<br>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26289183&i=14" target="_top" rel="nofollow">Bioperl-l@...</a>
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<br>Jason Stajich
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<br><div class='shrinkable-quote'><br>> Thanks again very much for your help and the script.
<br>> i've been trying it, however I fail to find any protein record
<br>> linked to a
<br>> record in the pcsubstance database.
<br>> Do you think that its is because no links have been defined between
<br>> the 2
<br>> databases, or that I am just unlucky and that no link exists for the
<br>> particular records I'm testing?
<br>> Thanks again
<br>>
<br>> saikari
</div><br>It's probably that no links have been defined. I have found similar
<br>problems in the past with pubchem, in that not all substances have
<br>proteins associated with them. Most proteins linked to are those with
<br>a deposited structure.
<br><br>There are a few other databases to check out; KEGG, the BioCyc dbs
<br>(like EcoCyc), come to mind. I don't think we have a generic remote
<br>query engine set up for any of those unfortunately (unless there is
<br>one I'm unaware of), but I know BioCyc comes with it's own set of
<br>tools (including perl- and java-based query tools) and can be set up
<br>locally, which is likely much faster and more in lines with what you
<br>need.
<br><br>chris
<br><br>...
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<br><div class='shrinkable-quote'><br>> Hi,
<br>>
<br>> I'm using Bioperl for my research and it is very useful! Thank you!
<br>>
<br>> Currently I have a problem with locations tags of sequences. I read
<br>> in seed alignments of Rfam (in stockholm format, but I think it is
<br>> similar to other formats).
<br>>
<br>> If the location is like:
<br>>
<br>> AB194432.1/908-846
<br>>
<br>> the start/end values are changed to
<br>>
<br>> $seq->start = 846
<br>> $seq->end = 908
<br>>
<br>> and therefore the new location (e.g.$seq->get_nse) is:
<br>>
<br>> AB194432.1/846-908
<br>>
<br>> The $seq->strand tag is correctly set to -1 in this case, but if the
<br>> alignment is written out again (clustal, stockholm,...) this strand
<br>> info is lost and the sequences have this "wrong" location. But this
<br>> information is important in respect to the sequence accession number.
<br>>
<br>> Is there a way to set the location back to the original one or is
<br>> this behavior desired? Any manually setting with $seq->start($val)
<br>> failed due to automatic checking.
<br>>
<br>> I'm using bioperl 1.6.1
<br>>
<br>> Thanks!
<br>>
<br>> steffen
</div><br>This is a definite bug. We recently discussed amending the NSE format
<br>due to this (the subject came up over the last few months or so); it's
<br>fallen through the cracks. Fortunaely it is very easy to fix (the
<br>relevant method is in LocatableSeq).
<br><br>Does anyone have a problem with me adding this in? It will change
<br>output for only those instances where the strand is -1, so
<br><br>AB194432.1/908-846
<br><br>would be start = 846, end = 908, strand = -1
<br><br>AB194432.1/846-908
<br><br>would be start = 846, end = 908, strand = 1
<br><br>chris
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26283374problem with alignments and sequence locations2009-11-10T04:55:06Z2009-11-10T04:55:06ZSteffen HeyneHi,
<br><br>I'm using Bioperl for my research and it is very useful! Thank you!
<br><br>Currently I have a problem with locations tags of sequences. I read in
<br>seed alignments of Rfam (in stockholm format, but I think it is similar
<br>to other formats).
<br><br>If the location is like:
<br><br>AB194432.1/908-846
<br><br>the start/end values are changed to
<br><br>$seq->start = 846
<br>$seq->end = 908
<br><br>and therefore the new location (e.g.$seq->get_nse) is:
<br><br>AB194432.1/846-908
<br><br>The $seq->strand tag is correctly set to -1 in this case, but if the
<br>alignment is written out again (clustal, stockholm,...) this strand info
<br>is lost and the sequences have this "wrong" location. But this
<br>information is important in respect to the sequence accession number.
<br><br>Is there a way to set the location back to the original one or is this
<br>behavior desired? Any manually setting with $seq->start($val) failed due
<br>to automatic checking.
<br><br>I'm using bioperl 1.6.1
<br><br>Thanks!
<br><br>steffen
<br><br><br>--
<br>---
<br>Steffen Heyne, Dipl.-Bioinf.
<br>Lehrstuhl für Bioinformatik
<br>Institut für Informatik
<br>Albert-Ludwigs-Universität Freiburg
<br>Georges-Köhler-Allee 106
<br>79110 Freiburg, Germany
<br><br>Tel: (+49) 761 203 8239
<br>Fax: (+49) 761 203 7462
<br>Mail: <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26283374&i=0" target="_top" rel="nofollow">heyne@...</a>
<br>_______________________________________________
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26282055Re: [bioperl newbie] Retrieving link to protein from PubChem2009-11-10T03:41:11Z2009-11-10T03:41:11Zsaikari keiteleThanks again very much for your help and the script.
<br>i've been trying it, however I fail to find any protein record linked to a
<br>record in the pcsubstance database.
<br>Do you think that its is because no links have been defined between the 2
<br>databases, or that I am just unlucky and that no link exists for the
<br>particular records I'm testing?
<br>Thanks again
<br><br>saikari
<br><br>On Mon, Nov 9, 2009 at 4:41 PM, saikari keitele <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26282055&i=0" target="_top" rel="nofollow">saikari78@...</a>> wrote:
<br><div class='shrinkable-quote'><br>> Fabulous!. Huge help.
<br>> saikari
<br>>
<br>> On Mon, Nov 9, 2009 at 4:27 PM, Chris Fields <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26282055&i=1" target="_top" rel="nofollow">cjfields@...</a>>wrote:
<br>>
<br>>> On Nov 9, 2009, at 10:05 AM, saikari keitele wrote:
<br>>>
<br>>> Hi,
<br>>>>
<br>>>> I'm using Bioperl to retrieve records from PubChem.
<br>>>> I'm trying to find a way-but have been unsuccessful- to retrieve from a
<br>>>> compound record, the reference to the protein(s) that can synthesize the
<br>>>> compound.
<br>>>> Thanks very much.
<br>>>>
<br>>>> saikari
<br>>>>
<br>>>
<br>>> The below bioperl script returns the GI for proteins that correspond to
<br>>> the substance passed on the command line; invoke using 'perl
<br>>> pc_substance.pl substance_requested'. It probably needs more fiddling to
<br>>> catch everything but it should get you started.
<br>>>
<br>>> For other bits and pieces (such as how to retrieve the raw sequence
<br>>> files), please see the EUtilities HOWTO:
<br>>>
<br>>> <a href="http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook" target="_top" rel="nofollow">http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook</a><br>>>
<br>>> chris
<br>>>
<br>>> ----------------------------------------
<br>>>
<br>>> #!/usr/bin/perl -w
<br>>>
<br>>> use 5.010;
<br>>> use strict;
<br>>> use warnings;
<br>>> use Bio::DB::EUtilities;
<br>>>
<br>>> my $substance = shift;
<br>>>
<br>>> my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
<br>>> -db => 'pcsubstance',
<br>>> -term => $substance,
<br>>> -usehistory => 'y');
<br>>>
<br>>> my $hist = $eutil->next_History || die;
<br>>>
<br>>> $eutil->reset_parameters(-eutil => 'elink',
<br>>> -history => $hist,
<br>>> -db => 'protein',
<br>>> -dbfrom => 'pcsubstance',
<br>>> -retmax => 1000);
<br>>>
<br>>> say join(',',$eutil->get_ids);
<br>>>
<br>>
<br>>
</div>_______________________________________________
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<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26282055&i=2" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26281445Re: [Fwd: Re: A question about iBio::Index: and itscorrect use]2009-11-10T02:43:40Z2009-11-10T02:43:40Zjluis.lavinHello again,
<br><br>I tried what Mark told me modifying the code line he told me but there´s
<br>still a problem that I believe must be due to the sequences name.
<br>My secuences header on the Fasta file have this format:
<br><br>>PleosPC9_1_103820|fgenesh1_pg.3_#_1
<br><br>Th part on the right of the pipe changes depending on the program used to
<br>create the gene model, for example:
<br><br>>PleosPC9_1_103820|fgenesh1_pg.3_#_1
<br>>PleosPC9_1_123413|genemark.2731_g
<br>>PleosPC9_1_52065|e_gw1.3.64.1
<br><br>So I guess I need to parse my ids somehow for thr program to detect only
<br>the first part of the fasta header (the "protein name") and not to get
<br>messed with the other side of the pipe...
<br><br>This is the corrected code I wrote following Mark´s indications, but I
<br>still don´t have any idea about the parsing issue...
<br><br>#!/c:/Perl -w
<br>use Bio::Index::Fasta;
<br>use strict;
<br>#PC9.fasta is my genomic file
<br>my $Index_File_Name ="PC9.fasta";
<br>my $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
<br>#LCS.txt is my sequences list
<br>@ARGV = <LCS.txt>;
<br>foreach my $id (@ARGV) {
<br>if ($id eq ''){
<br>die ("empty list")
<br>}
<br>else {
<br>my $seqobj = $inx->fetch($id);
<br>my $out = new Bio::SeqIO (-file => ">>index_extracted.fasta",
<br>-format => 'fasta');
<br>$out->write_seq($seqobj);
<br>}
<br>}
<br>exit;
<br>}
<br><br>Thanks in advance
<br><br>PD. May it be a faster way of extracting those sequences using plain PERL?
<br><br><br><br><br>El Jue, 5 de Noviembre de 2009, 17:39, Mark A. Jensen escribió:
<div class='shrinkable-quote'><br>> Yes, these are files created by the SDBM, Perl's internal db manager. You
<br>> should
<br>> be able to
<br>> open the index by simply
<br>> $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
<br>> and the dbm will know what to do--
<br>> cheers MAJ
<br>> ----- Original Message -----
<br>> From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=0" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>> To: "Mark A. Jensen" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=1" target="_top" rel="nofollow">maj@...</a>>
<br>> Cc: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=2" target="_top" rel="nofollow">jluis.lavin@...</a>>; <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=3" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>> Sent: Thursday, November 05, 2009 11:21 AM
<br>> Subject: Re: [Bioperl-l] [Fwd: Re: A question about iBio::Index: and its
<br>> correct
<br>> use]
<br>>
<br>>
<br>>> Thank you very much Mark, that´s a good point :$
<br>>> I guess your correction is referred to the second script, isn´t it?
<br>>>
<br>>> If it is so, there is still a problem with the first script, it doesn´t
<br>>> create the PC9.fasta.idx file, instead it creates two files named:
<br>>> -PC9.fasta.idx.pag
<br>>> -PC9.fasta.idx.dir
<br>>>
<br>>> which seem to be clearly related with some kind of indexing
<br>>> process...but,
<br>>> unless the PC9.fasta.idx file is only virtual or remains hidden, I can´t
<br>>> find it anywhere...
<br>>> Forgive me if I´m talking nosense...
<br>>>
<br>>> Thank you very much again for your help ;)
<br>>>
<br>>>
<br>>> El Jue, 5 de Noviembre de 2009, 17:02, Mark A. Jensen escribió:
<br>>>> Hey José,
<br>>>> The first thing that jumps out it the index file name. Looks
<br>>>> like you create it as
<br>>>> PC9.fasta.idx
<br>>>> But you read it as
<br>>>> PC9.fasta
<br>>>> Not an unusual mistake. Do
<br>>>> my $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
<br>>>> and see if it works.
<br>>>> MAJ
<br>>>> ----- Original Message -----
<br>>>> From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=4" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>>>> To: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=5" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>>>> Sent: Thursday, November 05, 2009 10:46 AM
<br>>>> Subject: [Bioperl-l] [Fwd: Re: A question about iBio::Index: and its
<br>>>> correct
<br>>>> use]
<br>>>>
<br>>>>
<br>>>>
<br>>>>
<br>>>> ---------------------------- Mensaje original
<br>>>> ----------------------------
<br>>>> Subject: Re: [Bioperl-l] A question about iBio::Index: and its correct
<br>>>> use
<br>>>> From: <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=6" target="_top" rel="nofollow">jluis.lavin@...</a>
<br>>>> Fecha: Jue, 5 de Noviembre de 2009, 16:46
<br>>>> To: "Mark A. Jensen" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=7" target="_top" rel="nofollow">maj@...</a>>
<br>>>> --------------------------------------------------------------------------
<br>>>>
<br>>>> Hi Mark,
<br>>>>
<br>>>> I´ve actually got two scripts, the first one is to create the index and
<br>>>> the second one is to retrieve the sequence lis from the indexed file.
<br>>>>
<br>>>> 1)Here is the Index creation script:
<br>>>>
<br>>>> #!/c:/Perl -w
<br>>>> use strict;
<br>>>> use Bio::Index::Fasta;
<br>>>> use strict;
<br>>>>
<br>>>> print "Enter file for indexing: \n";
<br>>>> my $Index_File_Name = <STDIN>;
<br>>>> my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name.".idx",
<br>>>> -write_flag => 1);
<br>>>> $inx->make_index(my $File_Name);
<br>>>>
<br>>>> 2)And here is the sequence retrieval script:
<br>>>>
<br>>>> #!/c:/Perl -w
<br>>>> use Bio::Index::Fasta;
<br>>>> use strict;
<br>>>> #PC9.fasta is my genomic file
<br>>>> my $Index_File_Name ="PC9.fasta";
<br>>>> my $inx = Bio::Index::Fasta->new($Index_File_Name);
<br>>>> #LCS.txt is my sequences list
<br>>>> @ARGV = <lCS.txt>;
<br>>>> foreach my $id (@ARGV) {
<br>>>> if ($id eq ''){
<br>>>> die ("empty list")
<br>>>> }
<br>>>> else {
<br>>>> my $seqobj = $inx->fetch($id);
<br>>>> my $out = new Bio::SeqIO (-file => ">>extracted_seqs.fasta",
<br>>>> -format => 'fasta');
<br>>>> $out->write_seq($seqobj);
<br>>>> }
<br>>>> }
<br>>>> exit;
<br>>>> }
<br>>>>
<br>>>> I hope this code is not a total scum...
<br>>>>
<br>>>> Thanks in advance ;)
<br>>>>
<br>>>>
<br>>>>
<br>>>> El Jue, 5 de Noviembre de 2009, 16:39, Mark A. Jensen escribió:
<br>>>>> José -- It looks like this is a good solution to your problem. Please
<br>>>>> send
<br>>>>> you
<br>>>>> script so we can look at it-
<br>>>>> cheers Mark
<br>>>>> ----- Original Message -----
<br>>>>> From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=8" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>>>>> To: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=9" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>>>>> Sent: Thursday, November 05, 2009 10:28 AM
<br>>>>> Subject: [Bioperl-l] A question about iBio::Index: and its correct use
<br>>>>>
<br>>>>>
<br>>>>>
<br>>>>> Hello to all,
<br>>>>>
<br>>>>> I´m trying to write a script to retrieve a list of sequences from a
<br>>>>> local
<br>>>>> FASTA file (for example a fasta archive where all the protein models
<br>>>>> of
<br>>>>> an
<br>>>>> organism are stored). This file would be used by me as some kind
<br>>>>> "local
<br>>>>> database" (sorry if I mistake a few concepts...)
<br>>>>> I´ve been reading the BioPerl HOWTOs and I came across the
<br>>>>> Bio::Index::Fasta tool.
<br>>>>> If I didn´t misunderstood what I read (which can be easy because my
<br>>>>> low
<br>>>>> level on programming) this Indexing tool should do the job.
<br>>>>> I wrote a couple of scripts based on the documentation i read about
<br>>>>> this
<br>>>>> tool, but I don´t seem to be able to create the index file to be used
<br>>>>> later (to retrieve the sequences from).
<br>>>>> -First of all, I want to ask the people in this forum if the
<br>>>>> Bio::Index::Fasta is the right one to chose for this tasks.
<br>>>>> -Then I´ll beg you to take a look at my scripts, because I don´t seem
<br>>>>> to
<br>>>>> catch the bug...
<br>>>>>
<br>>>>> Best wishes to you all and thanks in advance ;)
<br>>>>>
<br>>>>> --
<br>>>>> José Luis Lavín Trueba, PhD
<br>>>>>
<br>>>>> Dpto. de Producción Agraria
<br>>>>> Grupo de Genética y Microbiología
<br>>>>> Universidad Pública de Navarra
<br>>>>> 31006 Pamplona
<br>>>>> Navarra
<br>>>>> SPAIN
<br>>>>>
<br>>>>>
<br>>>>> _______________________________________________
<br>>>>> Bioperl-l mailing list
<br>>>>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=10" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>>>>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>>>>
<br>>>>>
<br>>>>>
<br>>>>
<br>>>>
<br>>>> --
<br>>>> Dr. José Luis Lavín Trueba
<br>>>>
<br>>>> Dpto. de Producción Agraria
<br>>>> Grupo de Genética y Microbiología
<br>>>> Universidad Pública de Navarra
<br>>>> 31006 Pamplona
<br>>>> Navarra
<br>>>> SPAIN
<br>>>>
<br>>>>
<br>>>>
<br>>>> --
<br>>>> Dr. José Luis Lavín Trueba
<br>>>>
<br>>>> Dpto. de Producción Agraria
<br>>>> Grupo de Genética y Microbiología
<br>>>> Universidad Pública de Navarra
<br>>>> 31006 Pamplona
<br>>>> Navarra
<br>>>> SPAIN
<br>>>>
<br>>>>
<br>>>> _______________________________________________
<br>>>> Bioperl-l mailing list
<br>>>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=11" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>>>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>>>
<br>>>>
<br>>>>
<br>>>
<br>>>
<br>>> --
<br>>> Dr. José Luis Lavín Trueba
<br>>>
<br>>> Dpto. de Producción Agraria
<br>>> Grupo de Genética y Microbiología
<br>>> Universidad Pública de Navarra
<br>>> 31006 Pamplona
<br>>> Navarra
<br>>> SPAIN
<br>>>
<br>>>
<br>>>
<br>>>
<br>>
<br>> _______________________________________________
<br>> Bioperl-l mailing list
<br>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=12" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>
</div><br><br>--
<br>Dr. José Luis Lavín Trueba
<br><br>Dpto. de Producción Agraria
<br>Grupo de Genética y Microbiología
<br>Universidad Pública de Navarra
<br>31006 Pamplona
<br>Navarra
<br>SPAIN
<br><br><br>_______________________________________________
<br>Bioperl-l mailing list
<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26281445&i=13" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26278416Re: how to get the protein sequences from DNA sequences around novel SNPs?2009-11-09T20:58:32Z2009-11-09T20:58:32ZChris Fields-5On Nov 9, 2009, at 3:15 PM, Robert Bradbury wrote:
<br><div class='shrinkable-quote'><br>> On Mon, Nov 9, 2009 at 1:08 PM, Guangchun Song <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26278416&i=0" target="_top" rel="nofollow">gc11song@...</a>>
<br>> wrote:
<br>>>
<br>>> I'm new bioperl user. I' working on a project: To determine the
<br>>> status of all tutative SNPs such as non-synonymous vs. synonymous,
<br>>> and
<br>>> predict the tranlational effect of non-synonymous mutations as benign
<br>>> or malicious. I'm trying to use bioperl to get the DNA sequence and
<br>>> translate to protein sequence for the SNPs that are in gene's coding
<br>>> region. Could someone tell me how to do it?
<br>>>
<br>>>
<br>> I too would like to know if this information is available. I've
<br>> recently
<br>> been working with the dbSNP results from NCBI but they display the
<br>> results
<br>> in a graphical format rather than data that one can play with and ask
<br>> questions of like "What is the most disease causing gene in the Human
<br>> Genome?" or "What are the critical proteins damaged by gene defects
<br>> in the
<br>> Human Genome?" ... "In terms of premature deaths, extended health care
<br>> requirements, loss of quality of life, etc.?"
<br>>
<br>> The same types of questions can be applied to the dog and cat
<br>> genomes where
<br>> there is emotional value or the cow, horse, pig, etc. genomes where
<br>> there is
<br>> economic value?
<br>>
<br>> The value of BioPerl would increase significantly if there were
<br>> functionality that would allow easy access to "these mutations may
<br>> have
<br>> negative/positive impact" (which means you need a function that
<br>> qualifies
<br>> mutations by degree) and allow for impact to be subjectively
<br>> determined
<br>> (implying there must be some callback function to provide a user
<br>> quality/impact rating).
<br>>
<br>> For example:
<br>> $/@differences = protein_compare($mygene, $refseq_gene,
<br>> @critical_aa,
<br>> @critical_domain, $callback)
<br>> Where $callback could "rate" differences about the protein and
<br>> position and
<br>> the "type of interest" (e.g. metal binding amino acids, structural
<br>> changing
<br>> amino acids, critical catalysis amino acids, etc.).
<br>>
<br>> A default callback would be based on some evolving definition of
<br>> "critical"
<br>> changes which result in human disease for example.
<br>>
<br>> This is a "required" capability to be able to determine things like
<br>> the
<br>> "adaptability" of a species -- those with fewest critical mutation
<br>> points
<br>> may have better adaptability to mutation increasing circumstances.
<br>>
<br>> Please pardon any errors in perl syntax/usage its been a while since
<br>> I've
<br>> written perl and I'd really rather be coding in C.
<br>>
<br>> Robert
</div><br>I will say that most of the information from the SNP database is
<br>available in various formats (see following link under 'Retrieval
<br>Types'):
<br><br><a href="http://www.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html" target="_top" rel="nofollow">http://www.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html</a><br><br>You can access this information, as well as the full XML, using
<br>something like the following script.
<br><br>chris
<br><br>------------------------------------------------
<br><br>#!/usr/bin/perl -w
<br><br>use 5.010;
<br>use strict;
<br>use warnings;
<br>use Bio::DB::EUtilities;
<br><br>my $term = shift;
<br>my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
<br> -db => 'snp',
<br> -term => $term,
<br> -usehistory => 'y',
<br> -retmax => 100);
<br><br>my $hist = $eutil->next_History || die "No history returned";
<br><br># for SNP XML, change retmode to 'xml'
<br>$eutil->set_parameters(-eutil => 'efetch',
<br> -history => $hist,
<br> -retmode => 'text',
<br> -rettype => 'flt');
<br><br># dumps to STDOUT
<br>say $eutil->get_Response->content;
<br><br><br>_______________________________________________
<br>Bioperl-l mailing list
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26278092Re: Bio::Index::GenBank - by organism?2009-11-09T19:55:01Z2009-11-09T19:55:01ZChris Fields-5On Nov 9, 2009, at 6:05 PM, Jay Hannah wrote:
<br><div class='shrinkable-quote'><br>> Many thanks to Ewan Birney et. al. for Bio::Index::*
<br>>
<br>> I can throw away my awful grep based index-by-accession stuff. :)
<br>>
<br>> Any chance someone has also written an organism based index
<br>> mechanism? Something like...
<br>>
<br>> while (my $seq = $inx−>get_Seq_by_organism('*Xanthomonas*')) {
<br>> print $seq->display_id . "\n";
<br>> }
<br>>
<br>> Thanks,
<br>>
<br>> j
</div><br>It should work via id_parser(); from Bio::Index::GenBank:
<br><br> $inx->id_parser(\&get_id);
<br> # make the index
<br> $inx->make_index($file_name);
<br><br> # here is where the retrieval key is specified
<br> sub get_id {
<br> my $line = shift;
<br> $line =~ /clone="(\S+)"/;
<br> $1;
<br> }
<br><br>Change the code ref deal with the line you want and parse the name
<br>out. Caveat: this may not be absolutely perfect (it only passes in a
<br>line at a time, and some species lines will wrap). Also not sure how
<br>this would work in cases where multiple sequences from the same
<br>species are present.
<br><br>The other option is to preparse everything and tie a hash to store a
<br>species->UID map, then use that along with your Bio::Index index to
<br>grab what you need.
<br><br>chris
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<br><div class='shrinkable-quote'><br>>>>>>> Chris Fields writes:
<br>>
<br>>> Alex, Not sure why ExtUtils::Manifest can't be bundled as a separate
<br>>> perl package alone. It is part of perl core but it's also available
<br>>> on CPAN separately from perl itself:
<br>>
<br>>> <a href="http://search.cpan.org/~rkobes/ExtUtils-Manifest-1.57/lib/ExtUtils/Manifest.pm" target="_top" rel="nofollow">http://search.cpan.org/~rkobes/ExtUtils-Manifest-1.57/lib/ExtUtils/Manifest.pm</a><br>>
<br>> Hi Chris,
<br>>
<br>> Yes, in principle it would be possible to have this split out as a
<br>> separate package (currently it's a "subpackage" under the main perl
<br>> package), unfortunately that's just not the way it's currently done in
<br>> Fedora (probably because it's part of the core set and they like to
<br>> update all relevant packages in one step) and I have little control
<br>> over
<br>> that.
<br>>
<br>> As I suspected, the perl maintainer is not at all enthusiastic for
<br>> updating the whole of perl just for that package (except for rawhide
<br>> which would mean that bioperl 1.6.1 would not be available until F-13,
<br>> about 6 months from now). See:
<br>>
<br>> <a href="http://bugzilla.redhat.com/show_bug.cgi?id=533562#c1" target="_top" rel="nofollow">http://bugzilla.redhat.com/show_bug.cgi?id=533562#c1</a><br>>
<br>> Obviously I am not happy with this situation either, because it will
<br>> freeze bioperl on Fedora at 1.6.0 for about 6 months, so can you
<br>> recommend any temporary workarounds in the meantime?
</div><br>Well, if you don't absolutely require the MANIFEST for the final
<br>package you can forego the requirement. The file in question that
<br>triggered the requirement is a data file used only for testing:
<br><br>t/data/test 2.txt
<br><div class='shrinkable-quote'><br>>> This is the commit message for that BTW. This allows spaces in file
<br>>> names for the MANIFEST. v1.52 is a bug fix and is required.
<br>>
<br>>> <a href="http://code.open-bio.org/svnweb/index.cgi/bioperl/revision/?rev=15673" target="_top" rel="nofollow">http://code.open-bio.org/svnweb/index.cgi/bioperl/revision/?rev=15673</a><br>>
<br>> Perhaps I could create a patch that renamed files with spaces in
<br>> them to
<br>> ones with no spaces and then rename them again upon installation.
<br>>
<br>> Can you point me to which files are the problematic ones that
<br>> triggered
<br>> the dependency for 1.52? Perhaps I can figure a workaround.
<br>>
<br>> Meanwhile I will press the maintainer of perl in Fedora to perhaps
<br>> reconsider his position (e.g. if another update for perl is going out
<br>> for another reason, like a security update, perhaps he could roll in
<br>> the
<br>> 1.52 update at the same time).
<br>>
<br>> Cheers,
<br>> Alex
</div><br>I would point out that this is a fairly significant bug fix for
<br>ExtUtils::Manifest. A newer point release of perl is now available
<br>(5.10.1) that contains the fix and has a fix for a performance
<br>regression that popped up in 5.10.0.
<br><br>chris
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<br><br>I can throw away my awful grep based index-by-accession stuff. :)
<br><br>Any chance someone has also written an organism based index mechanism?
<br>Something like...
<br><br>while (my $seq = $inx−>get_Seq_by_organism('*Xanthomonas*')) {
<br> print $seq->display_id . "\n";
<br>}
<br><br>Thanks,
<br><br>j
<br><br><br><br><br>_______________________________________________
<br>Bioperl-l mailing list
<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26276605&i=0" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26275912Re: version of ExtUtils::Manifest too strict?2009-11-09T15:44:07Z2009-11-09T15:44:07ZAlex Lancaster>>>>> Chris Fields writes:
<br><br>> Alex, Not sure why ExtUtils::Manifest can't be bundled as a separate
<br>> perl package alone. It is part of perl core but it's also available
<br>> on CPAN separately from perl itself:
<br><br>> <a href="http://search.cpan.org/~rkobes/ExtUtils-Manifest-1.57/lib/ExtUtils/Manifest.pm" target="_top" rel="nofollow">http://search.cpan.org/~rkobes/ExtUtils-Manifest-1.57/lib/ExtUtils/Manifest.pm</a><br><br>Hi Chris,
<br><br>Yes, in principle it would be possible to have this split out as a
<br>separate package (currently it's a "subpackage" under the main perl
<br>package), unfortunately that's just not the way it's currently done in
<br>Fedora (probably because it's part of the core set and they like to
<br>update all relevant packages in one step) and I have little control over
<br>that.
<br><br>As I suspected, the perl maintainer is not at all enthusiastic for
<br>updating the whole of perl just for that package (except for rawhide
<br>which would mean that bioperl 1.6.1 would not be available until F-13,
<br>about 6 months from now). See:
<br><br><a href="http://bugzilla.redhat.com/show_bug.cgi?id=533562#c1" target="_top" rel="nofollow">http://bugzilla.redhat.com/show_bug.cgi?id=533562#c1</a><br><br>Obviously I am not happy with this situation either, because it will
<br>freeze bioperl on Fedora at 1.6.0 for about 6 months, so can you
<br>recommend any temporary workarounds in the meantime?
<br><br>> This is the commit message for that BTW. This allows spaces in file
<br>> names for the MANIFEST. v1.52 is a bug fix and is required.
<br><br>> <a href="http://code.open-bio.org/svnweb/index.cgi/bioperl/revision/?rev=15673" target="_top" rel="nofollow">http://code.open-bio.org/svnweb/index.cgi/bioperl/revision/?rev=15673</a><br><br>Perhaps I could create a patch that renamed files with spaces in them to
<br>ones with no spaces and then rename them again upon installation.
<br><br>Can you point me to which files are the problematic ones that triggered
<br>the dependency for 1.52? Perhaps I can figure a workaround.
<br><br>Meanwhile I will press the maintainer of perl in Fedora to perhaps
<br>reconsider his position (e.g. if another update for perl is going out
<br>for another reason, like a security update, perhaps he could roll in the
<br>1.52 update at the same time).
<br><br>Cheers,
<br>Alex
<br>_______________________________________________
<br>Bioperl-l mailing list
<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26275912&i=0" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26275008Re: how to get the protein sequences from DNA sequencesaround novel SNPs?2009-11-09T13:56:24Z2009-11-09T13:56:24ZMark A. JensenI agree that BioPerl would significantly increase in value with
<br>such a module; in fact, the BioTeam would probably buy us out.
<br>My opinion is that the entire GWAS enterprise is the search for
<br>such a callback function, for humans anyway. For those engaged
<br>in this quest, if BioPerl doesn't provide a Maserati, it at least provides
<br>good italian-made (among others) parts.
<br>MAJ
<br>----- Original Message -----
<br>From: "Robert Bradbury" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26275008&i=0" target="_top" rel="nofollow">robert.bradbury@...</a>>
<br>To: "Guangchun Song" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26275008&i=1" target="_top" rel="nofollow">gc11song@...</a>>
<br>Cc: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26275008&i=2" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>Sent: Monday, November 09, 2009 4:15 PM
<br>Subject: Re: [Bioperl-l] how to get the protein sequences from DNA
<br>sequencesaround novel SNPs?
<br><br><div class='shrinkable-quote'><br>> On Mon, Nov 9, 2009 at 1:08 PM, Guangchun Song <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26275008&i=3" target="_top" rel="nofollow">gc11song@...</a>> wrote:
<br>>>
<br>>> I'm new bioperl user. I' working on a project: To determine the
<br>>> status of all tutative SNPs such as non-synonymous vs. synonymous, and
<br>>> predict the tranlational effect of non-synonymous mutations as benign
<br>>> or malicious. I'm trying to use bioperl to get the DNA sequence and
<br>>> translate to protein sequence for the SNPs that are in gene's coding
<br>>> region. Could someone tell me how to do it?
<br>>>
<br>>>
<br>> I too would like to know if this information is available. I've recently
<br>> been working with the dbSNP results from NCBI but they display the results
<br>> in a graphical format rather than data that one can play with and ask
<br>> questions of like "What is the most disease causing gene in the Human
<br>> Genome?" or "What are the critical proteins damaged by gene defects in the
<br>> Human Genome?" ... "In terms of premature deaths, extended health care
<br>> requirements, loss of quality of life, etc.?"
<br>>
<br>> The same types of questions can be applied to the dog and cat genomes where
<br>> there is emotional value or the cow, horse, pig, etc. genomes where there is
<br>> economic value?
<br>>
<br>> The value of BioPerl would increase significantly if there were
<br>> functionality that would allow easy access to "these mutations may have
<br>> negative/positive impact" (which means you need a function that qualifies
<br>> mutations by degree) and allow for impact to be subjectively determined
<br>> (implying there must be some callback function to provide a user
<br>> quality/impact rating).
<br>>
<br>> For example:
<br>> $/@differences = protein_compare($mygene, $refseq_gene, @critical_aa,
<br>> @critical_domain, $callback)
<br>> Where $callback could "rate" differences about the protein and position and
<br>> the "type of interest" (e.g. metal binding amino acids, structural changing
<br>> amino acids, critical catalysis amino acids, etc.).
<br>>
<br>> A default callback would be based on some evolving definition of "critical"
<br>> changes which result in human disease for example.
<br>>
<br>> This is a "required" capability to be able to determine things like the
<br>> "adaptability" of a species -- those with fewest critical mutation points
<br>> may have better adaptability to mutation increasing circumstances.
<br>>
<br>> Please pardon any errors in perl syntax/usage its been a while since I've
<br>> written perl and I'd really rather be coding in C.
<br>>
<br>> Robert
<br>> _______________________________________________
<br>> Bioperl-l mailing list
<br>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26275008&i=4" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>
<br>>
</div><br>_______________________________________________
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26273879Re: how to get the protein sequences from DNA sequences around novel SNPs?2009-11-09T13:15:33Z2009-11-09T13:15:33ZRobertBradburyOn Mon, Nov 9, 2009 at 1:08 PM, Guangchun Song <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26273879&i=0" target="_top" rel="nofollow">gc11song@...</a>> wrote:
<br>>
<br>> I'm new bioperl user. I' working on a project: To determine the
<br>> status of all tutative SNPs such as non-synonymous vs. synonymous, and
<br>> predict the tranlational effect of non-synonymous mutations as benign
<br>> or malicious. I'm trying to use bioperl to get the DNA sequence and
<br>> translate to protein sequence for the SNPs that are in gene's coding
<br>> region. Could someone tell me how to do it?
<br>>
<br>>
<br>I too would like to know if this information is available. I've recently
<br>been working with the dbSNP results from NCBI but they display the results
<br>in a graphical format rather than data that one can play with and ask
<br>questions of like "What is the most disease causing gene in the Human
<br>Genome?" or "What are the critical proteins damaged by gene defects in the
<br>Human Genome?" ... "In terms of premature deaths, extended health care
<br>requirements, loss of quality of life, etc.?"
<br><br>The same types of questions can be applied to the dog and cat genomes where
<br>there is emotional value or the cow, horse, pig, etc. genomes where there is
<br>economic value?
<br><br>The value of BioPerl would increase significantly if there were
<br>functionality that would allow easy access to "these mutations may have
<br>negative/positive impact" (which means you need a function that qualifies
<br>mutations by degree) and allow for impact to be subjectively determined
<br>(implying there must be some callback function to provide a user
<br>quality/impact rating).
<br><br>For example:
<br> $/@differences = protein_compare($mygene, $refseq_gene, @critical_aa,
<br>@critical_domain, $callback)
<br>Where $callback could "rate" differences about the protein and position and
<br>the "type of interest" (e.g. metal binding amino acids, structural changing
<br>amino acids, critical catalysis amino acids, etc.).
<br><br>A default callback would be based on some evolving definition of "critical"
<br>changes which result in human disease for example.
<br><br>This is a "required" capability to be able to determine things like the
<br>"adaptability" of a species -- those with fewest critical mutation points
<br>may have better adaptability to mutation increasing circumstances.
<br><br>Please pardon any errors in perl syntax/usage its been a while since I've
<br>written perl and I'd really rather be coding in C.
<br><br>Robert
<br>_______________________________________________
<br>Bioperl-l mailing list
<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26273879&i=1" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26271080how to get the protein sequences from DNA sequences around novel SNPs?2009-11-09T10:08:48Z2009-11-09T10:08:48ZGuangchun SongHello,
<br><br>I'm new bioperl user. I' working on a project: To determine the
<br>status of all tutative SNPs such as non-synonymous vs. synonymous, and
<br>predict the tranlational effect of non-synonymous mutations as benign
<br>or malicious. I'm trying to use bioperl to get the DNA sequence and
<br>translate to protein sequence for the SNPs that are in gene's coding
<br>region. Could someone tell me how to do it?
<br><br>Thanks,
<br><br>-Guangchun Song
<br>_______________________________________________
<br>Bioperl-l mailing list
<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26271080&i=0" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26269519Re: [bioperl newbie] Retrieving link to protein from PubChem2009-11-09T08:41:20Z2009-11-09T08:41:20Zsaikari keiteleFabulous!. Huge help.
<br>saikari
<br><br>On Mon, Nov 9, 2009 at 4:27 PM, Chris Fields <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26269519&i=0" target="_top" rel="nofollow">cjfields@...</a>> wrote:
<br><div class='shrinkable-quote'><br>> On Nov 9, 2009, at 10:05 AM, saikari keitele wrote:
<br>>
<br>> Hi,
<br>>>
<br>>> I'm using Bioperl to retrieve records from PubChem.
<br>>> I'm trying to find a way-but have been unsuccessful- to retrieve from a
<br>>> compound record, the reference to the protein(s) that can synthesize the
<br>>> compound.
<br>>> Thanks very much.
<br>>>
<br>>> saikari
<br>>>
<br>>
<br>> The below bioperl script returns the GI for proteins that correspond to the
<br>> substance passed on the command line; invoke using 'perl pc_substance.plsubstance_requested'. It probably needs more fiddling to catch everything
<br>> but it should get you started.
<br>>
<br>> For other bits and pieces (such as how to retrieve the raw sequence files),
<br>> please see the EUtilities HOWTO:
<br>>
<br>> <a href="http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook" target="_top" rel="nofollow">http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook</a><br>>
<br>> chris
<br>>
<br>> ----------------------------------------
<br>>
<br>> #!/usr/bin/perl -w
<br>>
<br>> use 5.010;
<br>> use strict;
<br>> use warnings;
<br>> use Bio::DB::EUtilities;
<br>>
<br>> my $substance = shift;
<br>>
<br>> my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
<br>> -db => 'pcsubstance',
<br>> -term => $substance,
<br>> -usehistory => 'y');
<br>>
<br>> my $hist = $eutil->next_History || die;
<br>>
<br>> $eutil->reset_parameters(-eutil => 'elink',
<br>> -history => $hist,
<br>> -db => 'protein',
<br>> -dbfrom => 'pcsubstance',
<br>> -retmax => 1000);
<br>>
<br>> say join(',',$eutil->get_ids);
<br>>
</div>_______________________________________________
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<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26269519&i=1" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26269316Re: [bioperl newbie] Retrieving link to protein from PubChem2009-11-09T08:27:10Z2009-11-09T08:27:10ZChris Fields-5On Nov 9, 2009, at 10:05 AM, saikari keitele wrote:
<br><div class='shrinkable-quote'><br>> Hi,
<br>>
<br>> I'm using Bioperl to retrieve records from PubChem.
<br>> I'm trying to find a way-but have been unsuccessful- to retrieve
<br>> from a
<br>> compound record, the reference to the protein(s) that can synthesize
<br>> the
<br>> compound.
<br>> Thanks very much.
<br>>
<br>> saikari
</div><br>The below bioperl script returns the GI for proteins that correspond
<br>to the substance passed on the command line; invoke using 'perl
<br>pc_substance.pl substance_requested'. It probably needs more fiddling
<br>to catch everything but it should get you started.
<br><br>For other bits and pieces (such as how to retrieve the raw sequence
<br>files), please see the EUtilities HOWTO:
<br><br><a href="http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook" target="_top" rel="nofollow">http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook</a><br><br>chris
<br><br>----------------------------------------
<br><br>#!/usr/bin/perl -w
<br><br>use 5.010;
<br>use strict;
<br>use warnings;
<br>use Bio::DB::EUtilities;
<br><br>my $substance = shift;
<br><br>my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
<br> -db => 'pcsubstance',
<br> -term => $substance,
<br> -usehistory => 'y');
<br><br>my $hist = $eutil->next_History || die;
<br><br>$eutil->reset_parameters(-eutil => 'elink',
<br> -history => $hist,
<br> -db => 'protein',
<br> -dbfrom => 'pcsubstance',
<br> -retmax => 1000);
<br><br>say join(',',$eutil->get_ids);
<br>_______________________________________________
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<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26269316&i=0" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26268988[bioperl newbie] Retrieving link to protein from PubChem2009-11-09T08:05:57Z2009-11-09T08:05:57Zsaikari keiteleHi,
<br><br>I'm using Bioperl to retrieve records from PubChem.
<br>I'm trying to find a way-but have been unsuccessful- to retrieve from a
<br>compound record, the reference to the protein(s) that can synthesize the
<br>compound.
<br>Thanks very much.
<br><br>saikari
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<br><br>I'm using Bioperl to retrieve records from PubChem.
<br>I'm trying to find a way-but have been unsuccessful- to retrieve from a
<br>compound record, the reference to the protein(s) that can synthesize the
<br>compound.
<br>Thanks very much.
<br><br>saikari
<br>_______________________________________________
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26255313Re: GuessSeqFormat: fastq?2009-11-08T08:20:55Z2009-11-08T08:20:55ZMark A. JensenNever mind; got it covered-- MAJ
<br>----- Original Message -----
<br>From: "Mark A. Jensen" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26255313&i=0" target="_top" rel="nofollow">maj@...</a>>
<br>To: "bioperl-l" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26255313&i=1" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>Sent: Sunday, November 08, 2009 11:09 AM
<br>Subject: [Bioperl-l] GuessSeqFormat: fastq?
<br><br><br>> Hi All-
<br>> Any plans in the works for a _possibly_fastq sequence guesser?
<br>> MAJ
<br>> _______________________________________________
<br>> Bioperl-l mailing list
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<br>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>
<br>>
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26255129GuessSeqFormat: fastq?2009-11-08T08:09:43Z2009-11-08T08:09:43ZMark A. JensenHi All-
<br>Any plans in the works for a _possibly_fastq sequence guesser?
<br>MAJ
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26254590arguments to call back functions in GBrowse22009-11-08T06:50:48Z2009-11-08T06:50:48ZDaniel Lang-3-----BEGIN PGP SIGNED MESSAGE-----
<br>Hash: SHA1
<br><br>Hi Lincoln,
<br><br>a while back (May 29, 2009; 09:08pm) you replied to an even older thread
<br>("Re: Access the parent of a Bio::DB::SeqFeature within a gbrowse config
<br>callback function").
<br><br>I missed your reply and did follow it up back then, sorry!
<br><br>I'm currently facing the same issue again with gbrowse2. I have a
<br>callback function for "balloon click". Following your last reply I
<br>expected 5 arguments, but I am getting only three: $feature,$panel,$track.
<br><br>In principle, I am using the latest releases/checkouts...
<br>Which modules do I need to look at/update for this functionality?
<br><br>Furthermore, is there a possibility to share global variables between
<br>gbrowse2 and slaves? Should this work via init_code?
<br>Should modules initialized in a conf be in the scope of a slave?
<br><br>If not can I introduce modules via the slave config files, or do I need
<br>to alter the slave scripts?
<br><br><br>Thanks, again!
<br><br>Cheers,
<br>Daniel
<br><br><br>PS: gbrowse2 rocks!
<br>-----BEGIN PGP SIGNATURE-----
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<br>FiUAn16nQNemDGSy8nJBS5dUHQMnDgrP
<br>=ODxn
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<br>_______________________________________________
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<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26254590&i=0" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26241123Re: Parsing BLAST out file to HTML. How to change thedescription's name of each hit?2009-11-06T16:40:17Z2009-11-06T16:40:17ZMark A. JensenXiaoyu-
<br>That method should work to change the description; are you doing
<br><br>$hit->description('This is my new description');
<br><br>This method returns the old description when you change the value:
<br><br>$hit->description('old');
<br>$str = $hit->description('new'); # $str eq 'old'
<br>$str = $hit->description; # $str eq 'new'
<br><br>MAJ
<br><br>----- Original Message -----
<br>From: "Xiaoyu Liang" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26241123&i=0" target="_top" rel="nofollow">veronica.xiaoyu@...</a>>
<br>To: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26241123&i=1" target="_top" rel="nofollow">Bioperl-l@...</a>>
<br>Sent: Friday, November 06, 2009 5:25 PM
<br>Subject: [Bioperl-l] Parsing BLAST out file to HTML. How to change
<br>thedescription's name of each hit?
<br><br><div class='shrinkable-quote'><br>> Hi,
<br>>
<br>> I'm using Bio::SearchIO::Writer HTMLResultWriter help me parse BLAST out
<br>> file into HTML.
<br>>
<br>> Anybody knows how to parse and change the description name of each hit?
<br>>
<br>> By using hit->description can call hits' description, but it is not allowed
<br>> to be modified.
<br>>
<br>> Thank you very much,
<br>> Xiaoyu
<br>> _______________________________________________
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<br>>
</div><br>_______________________________________________
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26239584Parsing BLAST out file to HTML. How to change the description's name of each hit?2009-11-06T14:25:04Z2009-11-06T14:25:04ZXiaoyu LiangHi,
<br><br>I'm using Bio::SearchIO::Writer HTMLResultWriter help me parse BLAST out
<br>file into HTML.
<br><br>Anybody knows how to parse and change the description name of each hit?
<br><br>By using hit->description can call hits' description, but it is not allowed
<br>to be modified.
<br><br>Thank you very much,
<br>Xiaoyu
<br>_______________________________________________
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<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26239584&i=0" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26230896StandAloneBlast Unallowed parameter2009-11-06T12:58:04Z2009-11-06T12:58:04ZkleenixI'm not sure if i'm doing this wrong. I am trying to use the -m parameter in blastall using the StandAloneBlast bioperl class.
<br>when i add 'm'=>0 to @params i get Unallowed parameter: error.
<br>Am I adding the parameter wrong? i'm using StandAloneBlast version 1.51
<br><br>Thanks
<br><br>-Nevo<p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26235758Function that determines serious mutations2009-11-06T09:35:22Z2009-11-06T09:35:22ZRobertBradburyIs there a function in the library (or has someone written one) that can
<br>take a genbank entry and determine which mutations are harmful?
<br><br>It would be used to produce a table summary of:
<br> GENE # SNP # BadSNP
<br><br>One kind of gets this from NCBI if you lookup in the "GENE" db a gene name
<br>and then go to the "GeneView" om dbSNP page it has the information I want
<br>but largely in a graphical format while I simply want numbers I can dump
<br>into a spreadsheet.
<br><br>I don't think it would be hard, fetch the gene, run through the features for
<br>the SNP database, figure out whether they are good or bad SNPs, accumulate
<br>the statistics and dump it. I think the functions available are flexible
<br>enough to do it but I can't believe nobody has already done it. It could be
<br>a bit more complex in that one could do an analysis to see if the mutations
<br>are in a conserved domain or mutations that code for Cysteine or Methionine
<br>(or othe potentially "critical" amino acids) but since "critical" is in the
<br>eye of the beholder there would have to be some kind of callback to a
<br>scoring function.
<br><br>Thanks,
<br>Robert
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26231685Re: Bioperl2009-11-06T04:45:01Z2009-11-06T04:45:01ZMark A. JensenHi Resmi-
<br>You should look at <a href="http://bioperl.org/" target="_top" rel="nofollow">http://bioperl.org/</a> under "Installation" for
<br>information on getting and installing BioPerl. An introduction
<br>to working with trees in BioPerl is at this link:
<br><a href="http://www.bioperl.org/wiki/HOWTO:Trees" target="_top" rel="nofollow">http://www.bioperl.org/wiki/HOWTO:Trees</a><br>cheers,
<br>Mark
<br><br>----- Original Message -----
<br> From: Resmi S.
<br> To: <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26231685&i=0" target="_top" rel="nofollow">maj@...</a>
<br> Sent: Friday, November 06, 2009 7:27 AM
<br> Subject: Bioperl
<br><br><br><br><br> Respected Sir,
<br> I am Resmi S studying II MSc Bioinformatics.Now am doing my project in Phylogenetic Tree Construction using BioPerl.I am not much familiar on BioPerl modules.So could please send me the names of the Bioperl modules needed for my project.I also need to know , from where i will get these modules.If that is from CPAN,then send me the location or link.I kindly request you to send me the details soon.
<br><br> Yours Sincerely,
<br> Resmi S,
<br> II MSc Bioinformatics,
<br> School of Biotechnology,
<br> Amrita Vishwa Vidyapeetham,
<br> Email : <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26231685&i=1" target="_top" rel="nofollow">amm08bi019@...</a>
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<br><br>_______________________________________________
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26228554Re: A question about iBio::Index: and its correct use2009-11-06T00:44:45Z2009-11-06T00:44:45Zjluis.lavinThank you for the info Florent!
<br>I´ll try to read al the information on the link you provided and try to
<br>figure out how to make it work and if it is worthy for me, I mean, I work
<br>with several sequence files that come from multiple databases (JGI, BROAD,
<br>Genolevures or NCBI). Protein IDs from each of those databases is
<br>different from NCBI. Maybe it could be easier to write a script that
<br>allows me to enter a fasta file with all the protein models of a single
<br>organism, parse it and then extract the sequences of a given list (using
<br>the "ID style" of the particular database) than creating a BLAST index for
<br>each organism I need to work with...Did I explain the issue correctly?
<br>Anyway, since I don´t know anything about this tool Hans and you provided
<br>me, I can easily be wrong...
<br>Thank you for showing me the local BLAST Index tool, I´ll read the
<br>documentation carefully and study all its possibilities.
<br><br>Best wishes
<br><br>JL
<br><br><br>El Jue, 5 de Noviembre de 2009, 19:00, Florent Angly escribió:
<div class='shrinkable-quote'><br>> Hans-Rudolf was talking about a way to retrieve sequences from a BLAST
<br>> database. If you use BLAST locally, then your database is local too.
<br>> More info here:
<br>> <a href="http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/formatdb_fastacmd.html" target="_top" rel="nofollow">http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/formatdb_fastacmd.html</a><br>> Florent
<br>>
<br>>
<br>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26228554&i=0" target="_top" rel="nofollow">jluis.lavin@...</a> wrote:
<br>>> Thanks a lot for your help Hans,
<br>>> It's a little bit to hard to understand and turn into script this
<br>>> awesome
<br>>> information you've just given me...I hope I can use it in a near future
<br>>> anyway ;)
<br>>> The issue here is that the sequences I,m indexing are not generated by
<br>>> the
<br>>> NCBI nor stored there...although I belive you´re just refering to the
<br>>> tool
<br>>> itself and not to a retrieval from the NCBI.
<br>>>
<br>>> Thanks again you´re all great giving advice to newbies like me ;)
<br>>>
<br>>> Best wishes to you all
<br>>>
<br>>>
<br>>> El Jue, 5 de Noviembre de 2009, 17:02, Hotz, Hans-Rudolf escribió:
<br>>>
<br>>>>
<br>>>> Jluis
<br>>>>
<br>>>>
<br>>>>> -Then I´ll beg you to take a look at my scripts, because I don´t seem
<br>>>>> to
<br>>>>> catch the bug...
<br>>>>>
<br>>>> you haven't attached/included any scripts, have you?
<br>>>>
<br>>>>
<br>>>> Anyway, have you considered using BLAST indices (created with the
<br>>>> additional
<br>>>> flag "-o") together with the tool 'fastacmd' (which also included in
<br>>>> the
<br>>>> NCBI blast binaries) as a simple (and very fast) alternative for
<br>>>> fetching
<br>>>> sequences.
<br>>>>
<br>>>>
<br>>>> Regards, Hans
<br>>>>
<br>>>>
<br>>>>
<br>>>>
<br>>>
<br>>>
<br>>>
<br>>
<br>>
</div><br><br>--
<br>Dr. José Luis Lavín Trueba
<br><br>Dpto. de Producción Agraria
<br>Grupo de Genética y Microbiología
<br>Universidad Pública de Navarra
<br>31006 Pamplona
<br>Navarra
<br>SPAIN
<br><br><br>_______________________________________________
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26228303Bio::SeqIO::genbank.pm2009-11-06T00:06:48Z2009-11-06T00:06:48ZGabriel Valiente<br><br>There is a line in Bio::SeqIO::genbank.pm to convert data in classification lines into a classification array by splitting only
<br>on ';' or '.' so that a classification that is 2
<br>or more words will still get
<br>matched,my @class = map { s/^\s+//; s/\s+$//; s/\s{2,}/ /g; $_; } split /(?<!subgen)[;\.]+/, $class_lines;but this
<br>will break organism names that have a dot inside, such as "Salmonella
<br>enterica subsp. enterica serovar Typhimurium", which is now
<br>being broken into "Salmonella enterica subsp" and "enterica serovar
<br>Typhimurium".Changing [;\.]
<br>to [;] solves this issue,my @class = map { s/^\s+//; s/\s+$//; s/\s{2,}/ /g; $_; } split /(?<!subgen)[;]+/,
<br>$class_lines;Does anybody want to further
<br>test it before I commit this change? Thanks,Gabriel
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<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26219503Re: A question about iBio::Index: and its correct use2009-11-05T10:00:19Z2009-11-05T10:00:19ZFlorent AnglyHans-Rudolf was talking about a way to retrieve sequences from a BLAST
<br>database. If you use BLAST locally, then your database is local too.
<br>More info here:
<br><a href="http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/formatdb_fastacmd.html" target="_top" rel="nofollow">http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/formatdb_fastacmd.html</a><br>Florent
<br><br><br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26219503&i=0" target="_top" rel="nofollow">jluis.lavin@...</a> wrote:
<div class='shrinkable-quote'><br>> Thanks a lot for your help Hans,
<br>> It's a little bit to hard to understand and turn into script this awesome
<br>> information you've just given me...I hope I can use it in a near future
<br>> anyway ;)
<br>> The issue here is that the sequences I,m indexing are not generated by the
<br>> NCBI nor stored there...although I belive you´re just refering to the tool
<br>> itself and not to a retrieval from the NCBI.
<br>>
<br>> Thanks again you´re all great giving advice to newbies like me ;)
<br>>
<br>> Best wishes to you all
<br>>
<br>>
<br>> El Jue, 5 de Noviembre de 2009, 17:02, Hotz, Hans-Rudolf escribió:
<br>>
<br>>>
<br>>> Jluis
<br>>>
<br>>>
<br>>>> -Then I´ll beg you to take a look at my scripts, because I don´t seem to
<br>>>> catch the bug...
<br>>>>
<br>>> you haven't attached/included any scripts, have you?
<br>>>
<br>>>
<br>>> Anyway, have you considered using BLAST indices (created with the
<br>>> additional
<br>>> flag "-o") together with the tool 'fastacmd' (which also included in the
<br>>> NCBI blast binaries) as a simple (and very fast) alternative for fetching
<br>>> sequences.
<br>>>
<br>>>
<br>>> Regards, Hans
<br>>>
<br>>>
<br>>>
<br>>>
<br>>
<br>>
<br>>
</div><br>_______________________________________________
<br>Bioperl-l mailing list
<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26219503&i=1" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26219286Re: A question about iBio::Index: and its correct use2009-11-05T09:48:12Z2009-11-05T09:48:12Zjluis.lavinThanks a lot for your help Hans,
<br>It's a little bit to hard to understand and turn into script this awesome
<br>information you've just given me...I hope I can use it in a near future
<br>anyway ;)
<br>The issue here is that the sequences I,m indexing are not generated by the
<br>NCBI nor stored there...although I belive you´re just refering to the tool
<br>itself and not to a retrieval from the NCBI.
<br><br>Thanks again you´re all great giving advice to newbies like me ;)
<br><br>Best wishes to you all
<br><br><br>El Jue, 5 de Noviembre de 2009, 17:02, Hotz, Hans-Rudolf escribió:
<div class='shrinkable-quote'><br>>
<br>>
<br>>
<br>> Jluis
<br>>
<br>>> -Then I´ll beg you to take a look at my scripts, because I don´t seem to
<br>>> catch the bug...
<br>>
<br>> you haven't attached/included any scripts, have you?
<br>>
<br>>
<br>> Anyway, have you considered using BLAST indices (created with the
<br>> additional
<br>> flag "-o") together with the tool 'fastacmd' (which also included in the
<br>> NCBI blast binaries) as a simple (and very fast) alternative for fetching
<br>> sequences.
<br>>
<br>>
<br>> Regards, Hans
<br>>
<br>>
<br>>
</div><br><br>--
<br>Dr. José Luis Lavín Trueba
<br><br>Dpto. de Producción Agraria
<br>Grupo de Genética y Microbiología
<br>Universidad Pública de Navarra
<br>31006 Pamplona
<br>Navarra
<br>SPAIN
<br><br><br>_______________________________________________
<br>Bioperl-l mailing list
<br><a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26219286&i=0" target="_top" rel="nofollow">Bioperl-l@...</a>
<br><a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br><p>From forum: <a href="http://old.nabble.com/Perl---Bioperl-L-f13598.html" embed="fixTarget[13598]" target="_top" >Perl - Bioperl-L</a></p>tag:old.nabble.com,2006:post-26218109Re: [Fwd: Re: A question about iBio::Index: and its correct use]2009-11-05T08:39:09Z2009-11-05T08:39:09ZMark A. JensenYes, these are files created by the SDBM, Perl's internal db manager. You should
<br>be able to
<br>open the index by simply
<br>$inx = Bio::Index::Fasta->new('PC9.fasta.idx');
<br>and the dbm will know what to do--
<br>cheers MAJ
<br>----- Original Message -----
<br>From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=0" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>To: "Mark A. Jensen" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=1" target="_top" rel="nofollow">maj@...</a>>
<br>Cc: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=2" target="_top" rel="nofollow">jluis.lavin@...</a>>; <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=3" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>Sent: Thursday, November 05, 2009 11:21 AM
<br>Subject: Re: [Bioperl-l] [Fwd: Re: A question about iBio::Index: and its correct
<br>use]
<br><br><div class='shrinkable-quote'><br>> Thank you very much Mark, that´s a good point :$
<br>> I guess your correction is referred to the second script, isn´t it?
<br>>
<br>> If it is so, there is still a problem with the first script, it doesn´t
<br>> create the PC9.fasta.idx file, instead it creates two files named:
<br>> -PC9.fasta.idx.pag
<br>> -PC9.fasta.idx.dir
<br>>
<br>> which seem to be clearly related with some kind of indexing process...but,
<br>> unless the PC9.fasta.idx file is only virtual or remains hidden, I can´t
<br>> find it anywhere...
<br>> Forgive me if I´m talking nosense...
<br>>
<br>> Thank you very much again for your help ;)
<br>>
<br>>
<br>> El Jue, 5 de Noviembre de 2009, 17:02, Mark A. Jensen escribió:
<br>>> Hey José,
<br>>> The first thing that jumps out it the index file name. Looks
<br>>> like you create it as
<br>>> PC9.fasta.idx
<br>>> But you read it as
<br>>> PC9.fasta
<br>>> Not an unusual mistake. Do
<br>>> my $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
<br>>> and see if it works.
<br>>> MAJ
<br>>> ----- Original Message -----
<br>>> From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=4" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>>> To: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=5" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>>> Sent: Thursday, November 05, 2009 10:46 AM
<br>>> Subject: [Bioperl-l] [Fwd: Re: A question about iBio::Index: and its
<br>>> correct
<br>>> use]
<br>>>
<br>>>
<br>>>
<br>>>
<br>>> ---------------------------- Mensaje original ----------------------------
<br>>> Subject: Re: [Bioperl-l] A question about iBio::Index: and its correct use
<br>>> From: <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=6" target="_top" rel="nofollow">jluis.lavin@...</a>
<br>>> Fecha: Jue, 5 de Noviembre de 2009, 16:46
<br>>> To: "Mark A. Jensen" <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=7" target="_top" rel="nofollow">maj@...</a>>
<br>>> --------------------------------------------------------------------------
<br>>>
<br>>> Hi Mark,
<br>>>
<br>>> I´ve actually got two scripts, the first one is to create the index and
<br>>> the second one is to retrieve the sequence lis from the indexed file.
<br>>>
<br>>> 1)Here is the Index creation script:
<br>>>
<br>>> #!/c:/Perl -w
<br>>> use strict;
<br>>> use Bio::Index::Fasta;
<br>>> use strict;
<br>>>
<br>>> print "Enter file for indexing: \n";
<br>>> my $Index_File_Name = <STDIN>;
<br>>> my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name.".idx",
<br>>> -write_flag => 1);
<br>>> $inx->make_index(my $File_Name);
<br>>>
<br>>> 2)And here is the sequence retrieval script:
<br>>>
<br>>> #!/c:/Perl -w
<br>>> use Bio::Index::Fasta;
<br>>> use strict;
<br>>> #PC9.fasta is my genomic file
<br>>> my $Index_File_Name ="PC9.fasta";
<br>>> my $inx = Bio::Index::Fasta->new($Index_File_Name);
<br>>> #LCS.txt is my sequences list
<br>>> @ARGV = <lCS.txt>;
<br>>> foreach my $id (@ARGV) {
<br>>> if ($id eq ''){
<br>>> die ("empty list")
<br>>> }
<br>>> else {
<br>>> my $seqobj = $inx->fetch($id);
<br>>> my $out = new Bio::SeqIO (-file => ">>extracted_seqs.fasta",
<br>>> -format => 'fasta');
<br>>> $out->write_seq($seqobj);
<br>>> }
<br>>> }
<br>>> exit;
<br>>> }
<br>>>
<br>>> I hope this code is not a total scum...
<br>>>
<br>>> Thanks in advance ;)
<br>>>
<br>>>
<br>>>
<br>>> El Jue, 5 de Noviembre de 2009, 16:39, Mark A. Jensen escribió:
<br>>>> José -- It looks like this is a good solution to your problem. Please
<br>>>> send
<br>>>> you
<br>>>> script so we can look at it-
<br>>>> cheers Mark
<br>>>> ----- Original Message -----
<br>>>> From: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=8" target="_top" rel="nofollow">jluis.lavin@...</a>>
<br>>>> To: <<a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=9" target="_top" rel="nofollow">bioperl-l@...</a>>
<br>>>> Sent: Thursday, November 05, 2009 10:28 AM
<br>>>> Subject: [Bioperl-l] A question about iBio::Index: and its correct use
<br>>>>
<br>>>>
<br>>>>
<br>>>> Hello to all,
<br>>>>
<br>>>> I´m trying to write a script to retrieve a list of sequences from a
<br>>>> local
<br>>>> FASTA file (for example a fasta archive where all the protein models of
<br>>>> an
<br>>>> organism are stored). This file would be used by me as some kind "local
<br>>>> database" (sorry if I mistake a few concepts...)
<br>>>> I´ve been reading the BioPerl HOWTOs and I came across the
<br>>>> Bio::Index::Fasta tool.
<br>>>> If I didn´t misunderstood what I read (which can be easy because my low
<br>>>> level on programming) this Indexing tool should do the job.
<br>>>> I wrote a couple of scripts based on the documentation i read about this
<br>>>> tool, but I don´t seem to be able to create the index file to be used
<br>>>> later (to retrieve the sequences from).
<br>>>> -First of all, I want to ask the people in this forum if the
<br>>>> Bio::Index::Fasta is the right one to chose for this tasks.
<br>>>> -Then I´ll beg you to take a look at my scripts, because I don´t seem to
<br>>>> catch the bug...
<br>>>>
<br>>>> Best wishes to you all and thanks in advance ;)
<br>>>>
<br>>>> --
<br>>>> José Luis Lavín Trueba, PhD
<br>>>>
<br>>>> Dpto. de Producción Agraria
<br>>>> Grupo de Genética y Microbiología
<br>>>> Universidad Pública de Navarra
<br>>>> 31006 Pamplona
<br>>>> Navarra
<br>>>> SPAIN
<br>>>>
<br>>>>
<br>>>> _______________________________________________
<br>>>> Bioperl-l mailing list
<br>>>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=10" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>>>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>>>
<br>>>>
<br>>>>
<br>>>
<br>>>
<br>>> --
<br>>> Dr. José Luis Lavín Trueba
<br>>>
<br>>> Dpto. de Producción Agraria
<br>>> Grupo de Genética y Microbiología
<br>>> Universidad Pública de Navarra
<br>>> 31006 Pamplona
<br>>> Navarra
<br>>> SPAIN
<br>>>
<br>>>
<br>>>
<br>>> --
<br>>> Dr. José Luis Lavín Trueba
<br>>>
<br>>> Dpto. de Producción Agraria
<br>>> Grupo de Genética y Microbiología
<br>>> Universidad Pública de Navarra
<br>>> 31006 Pamplona
<br>>> Navarra
<br>>> SPAIN
<br>>>
<br>>>
<br>>> _______________________________________________
<br>>> Bioperl-l mailing list
<br>>> <a href="http://old.nabble.com/user/SendEmail.jtp?type=post&post=26218109&i=11" target="_top" rel="nofollow">Bioperl-l@...</a>
<br>>> <a href="http://lists.open-bio.org/mailman/listinfo/bioperl-l" target="_top" rel="nofollow">http://lists.open-bio.org/mailman/listinfo/bioperl-l</a><br>>>
<br>>>
<br>>>
<br>>
<br>>
<br>> --
<br>> Dr. José Luis Lavín Trueba
<br>>
<br>> Dpto. de Producción Agraria
<br>> Grupo de Genética y Microbiología
<br>> Universidad Pública de Navarra
<br>> 31006 Pamplona
<br>> Navarra
<br>> SPAIN
<br>>
<br>>
<br>>
<br>>
</div><br>_______________________________________________
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