Nabble - Perl - Bioperl-L

Gene critical region analysis -- visual display

2009-12-04T10:27:38Z

Background:
I have been involved in aging research off and on for ~16 years. My initial
focus was in the eventual decline of the "program" (because DNA has no ECC
and only limited redundancy) therefore my initial work (in the early 1990's
was focused on DNA repair genes (of which there about 150 in the human
genome) [1,2]. Most recently I have focused in on the DNA double strand
break repair processes (NHEJ) as a fundamental cause of aging because it may
fundamentally corrupt the genomes of individual cells. (And as most
programmers would agree -- break the code and you break the program).
Michael Lieber at UCLA has estimated that by the time a human is ~70 on the
order of several hundred genes in ones cells have been corrupted (which may
be an
indeterminate effect on the cells functioning).

Problem:
Just looking at the GenBank output for the human Artemis (DCLRE1C) gene
there are on the order of 18 SNPs and 8 possible phosphorylation sites (not
to mention other potential modification sites) -- this combined with the
fact that Methionine and Tryptophan and to a lesser extent Cysteine are more
susceptible to single base mutations (due the alteration of the codon->amino
acid coding even involving single base mutations/repairs) . There are
various programs to analyze such proteins for the critical sites -- SIFT and
the various programs pointed to by their sites. Now it seems to me that one
could attack this problem by integrating SNPs, mutations, etc. at the
critical sites (where "critical" may or may not be at normal SNPs -- which
presumably are primarily at non-critical sites -- and those proteins where
if you change the coding sequence to non-synomonous amino acids you
potentially break the protein (the real interpretation of which will not be
understood until population studies are done).

So, in the process of looking at the DCLRE1C protein I asked myself, "Why is
there not a BioPerl function which simply enables a visual interpretation of
the critical sites of the protein?" I.e. some color-coded representation of
the protein (which presumably has some augmented functionality to determine
things like probability or statistical information). I.e. hand the function
a .fasta file and it will give you an visual (colored) analysis of the
critical nature of specific a.a. -- i.e. something which could be used by
genomic or SNP analysis (such as I presume that being done by 23andme -- as
well as other organizations) to begin to separate out the variations in the
human genome (e.g. SNPs) from the mutations which may effect individuals.

I have the C programming and to a lesser extent Perl experience to
contribute to this -- I lack the BioPerl wisdom to make it generally
available.

If anyone has some suggestions as to what functions/modules might be of use
(in providing a "single-look" view of gene a.a. whose mutations may be more
or less detrimental) I would appreciate hearing from them.

Robert Bradbury

1. "DNA Repair and Mutagenesis", E.C. Friedberg et al, 2nd Ed., ASM Press
(2006)
2. "Aging of the Genome", J. Vijg, Oxford University Press (2007)
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Re: Regarding Organism based search in Remote blast

2009-12-04T06:59:17Z

Roopa,

At one point a couple of parameters differed between NCBI's web interface and our RemoteBlast-based BLAST interface to URLAPI (this should be indicated in your BLAST reports). See here:

http://thread.gmane.org/gmane.comp.lang.perl.bio.general/14155

Also, are the returned hits specific for the genome? You shoudl double-check; in some cases you have to set both HEADER and RETRIEVALHEADER to get the expected results (not sure why):

http://article.gmane.org/gmane.comp.lang.perl.bio.general/18737/match=remoteblast+ncbi

chris

On Dec 4, 2009, at 7:57 AM, Roopa Raghuveer wrote:

> Hello all,
>
> I am working on Remote blast.Here,I am trying to get 2 parameters into the
> remote blast code.They are
>
> 1.The input sequence that has to be sent to blast
>
> 2.Organism (The organism which has to be searched for ex:-Trypanasoma brucei
> etc.,)
>
> When I tried to take the organism parameter as an input from the
> user,through a web page,the Remote blast was not giving any results i.e., it
> says that there are no alignments found.
>
> But,when I hard coded the organism in the code,it gives me the results i.e.,
> 3hits.
>
> I could not understand this problem.Could any body please help me in this
> regard?
>
> My code is
>
> sub blastcode
> {
>
> $input1= $_[0];
>
> $organ= $_[1];
>
> open(NUC,'>',$nuc);
> print NUC $input1;
> close(NUC);
>
> my $prog = 'blastn';
> my $db = 'refseq_rna';
> my $e_val= '1e-10';
> my $organism= $organ;
>
> $gb = new Bio::DB::GenBank;
>
> my @params = ( '-prog' => $prog,
> '-data' => $db,
> '-expect' => $e_val,
> '-readmethod' => 'SearchIO',
> '-Organism' => $organism );
>
> open(OUTFILE,'>',$debugfile);
> print OUTFILE @params;
> close(OUTFILE);
>
>
> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>
> #change a paramter
> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = '$organism[ORGN]';
> #change a paramter
> # $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = '$input2[ORGN]';
>
> my $v = 1;
> #$v is just to turn on and off the messages
>
> my $str = Bio::SeqIO->new(-file => $nuc , '-format' => 'fasta' ,
> '-Organism' => $organism );
>
> while (my $input = $str->next_seq())
>
> {
> #Blast a sequence against a database:
> #Alternatively, you could pass in a file with many
> #sequences rather than loop through sequence one at a time
> #Remove the loop starting 'while (my $input = $str->next_seq())'
> #and swap the two lines below for an example of that.
>
> my $r = $factory->submit_blast($input);
>
> # my $r = $factory->submit_blast('amino.fa');
>
> print STDERR "waiting...." if($v>0);
>
> while ( my @rids = $factory->each_rid ) {
>
> foreach my $rid ( @rids ) {
>
> my $rc = $factory->retrieve_blast($rid);
>
> if( !ref($rc) )
> {
> if( $rc < 0 )
> {
> $factory->remove_rid($rid);
> }
> print STDERR "." if ( $v > 0 );
> sleep 5;
> }
> else {
> my $result = $rc->next_result();
> #save the output
> $blastdebugfile = $serverpath."/blastdebug_".time().".txt";
>
> # open(BLASTDEBUGFILE,'>',$debugfile);
> # print BLASTDEBUGFILE $result->next_hit();
> # close(BLASTDEBUGFILE);
>
> my $filename =
> $serverpath."/blastdata_".time().$result->query_name()."\.out";
>
> # open(DEBUGFILE,'>',$debugfile);
> # open(new,'>',$filename);
> # @arra=<new>;
> # print DEBUGFILE @arra;
> # close(DEBUGFILE);
> # close(new);
> $factory->save_output($filename);
>
> # open(BLASTDEBUGFILE,'>',$debugfile);
> # print BLASTDEBUGFILE "Hello $rid";
> # close(BLASTDEBUGFILE);
>
> $factory->remove_rid($rid);
>
> open(BLASTDEBUGFILE,'>',$blastdebugfile);
> print BLASTDEBUGFILE $organism;
> close(BLASTDEBUGFILE);
>
> # open(OUTFILE,'>',$outfile);
> # print OUTFILE "Test2 $result->database_name()";
> # close(OUTFILE);
>
> #$hit = $result->next_hit;
> #open(new,'>',$debugfile);
> #print $hit;
> #close(new);
>
> while ( my $hit = $result->next_hit ) {
>
> next unless ( $v > 0);
>
> # open(OUTFILE,'>',$debugfile);
> # print OUTFILE "$hit in while hits";
> # close(OUTFILE);
>
> my $sequ = $gb->get_Seq_by_version($hit->name);
> my $dna = $sequ->seq(); # get the sequence as a string
> push(@seqs,$dna);
> }
> }
> }
> }
> }
>
> #open(OUTFILE,'>',$debugfile);
> #print OUTFILE $seqs[0];
> #close(OUTFILE);
>
> return(@seqs);
> }
>
> Regards,
> Roopa.
> _______________________________________________
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Regarding Organism based search in Remote blast

2009-12-04T05:57:21Z

Hello all,

I am working on Remote blast.Here,I am trying to get 2 parameters into the
remote blast code.They are

1.The input sequence that has to be sent to blast

2.Organism (The organism which has to be searched for ex:-Trypanasoma brucei
etc.,)

When I tried to take the organism parameter as an input from the
user,through a web page,the Remote blast was not giving any results i.e., it
says that there are no alignments found.

But,when I hard coded the organism in the code,it gives me the results i.e.,
3hits.

I could not understand this problem.Could any body please help me in this
regard?

My code is

sub blastcode
{

$input1= $_[0];

$organ= $_[1];

open(NUC,'>',$nuc);
print NUC $input1;
close(NUC);

my $prog = 'blastn';
my $db = 'refseq_rna';
my $e_val= '1e-10';
my $organism= $organ;

$gb = new Bio::DB::GenBank;

my @params = ( '-prog' => $prog,
'-data' => $db,
'-expect' => $e_val,
'-readmethod' => 'SearchIO',
'-Organism' => $organism );

open(OUTFILE,'>',$debugfile);
print OUTFILE @params;
close(OUTFILE);

my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

#change a paramter
$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = '$organism[ORGN]';
#change a paramter
# $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = '$input2[ORGN]';

my $v = 1;
#$v is just to turn on and off the messages

my $str = Bio::SeqIO->new(-file => $nuc , '-format' => 'fasta' ,
'-Organism' => $organism );

while (my $input = $str->next_seq())

{
#Blast a sequence against a database:
#Alternatively, you could pass in a file with many
#sequences rather than loop through sequence one at a time
#Remove the loop starting 'while (my $input = $str->next_seq())'
#and swap the two lines below for an example of that.

my $r = $factory->submit_blast($input);

# my $r = $factory->submit_blast('amino.fa');

print STDERR "waiting...." if($v>0);

while ( my @rids = $factory->each_rid ) {

foreach my $rid ( @rids ) {

my $rc = $factory->retrieve_blast($rid);

if( !ref($rc) )
{
if( $rc < 0 )
{
$factory->remove_rid($rid);
}
print STDERR "." if ( $v > 0 );
sleep 5;
}
else {
my $result = $rc->next_result();
#save the output
$blastdebugfile = $serverpath."/blastdebug_".time().".txt";

# open(BLASTDEBUGFILE,'>',$debugfile);
# print BLASTDEBUGFILE $result->next_hit();
# close(BLASTDEBUGFILE);

my $filename =
$serverpath."/blastdata_".time().$result->query_name()."\.out";

# open(DEBUGFILE,'>',$debugfile);
# open(new,'>',$filename);
# @arra=<new>;
# print DEBUGFILE @arra;
# close(DEBUGFILE);
# close(new);
$factory->save_output($filename);

# open(BLASTDEBUGFILE,'>',$debugfile);
# print BLASTDEBUGFILE "Hello $rid";
# close(BLASTDEBUGFILE);

$factory->remove_rid($rid);

open(BLASTDEBUGFILE,'>',$blastdebugfile);
print BLASTDEBUGFILE $organism;
close(BLASTDEBUGFILE);

# open(OUTFILE,'>',$outfile);
# print OUTFILE "Test2 $result->database_name()";
# close(OUTFILE);

#$hit = $result->next_hit;
#open(new,'>',$debugfile);
#print $hit;
#close(new);

while ( my $hit = $result->next_hit ) {

next unless ( $v > 0);

# open(OUTFILE,'>',$debugfile);
# print OUTFILE "$hit in while hits";
# close(OUTFILE);

my $sequ = $gb->get_Seq_by_version($hit->name);
my $dna = $sequ->seq(); # get the sequence as a string
push(@seqs,$dna);
}
}
}
}
}

#open(OUTFILE,'>',$debugfile);
#print OUTFILE $seqs[0];
#close(OUTFILE);

return(@seqs);
}

Regards,
Roopa.
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Re: Merging separate sequence and quality files to FASTQ ?

2009-12-03T20:16:48Z

On Dec 3, 2009, at 10:30 AM, Dan Bolser wrote:

> 2009/12/3 Chris Fields <cjfields@...>:
>> Dan,
>>
>> On Dec 3, 2009, at 7:07 AM, Dan Bolser wrote:
>
> ...
>
>>> I'm wondering, because with the FlaggedRevs extension you could
>>> basically build a whole release in the wiki. Which would be fun if
>>> nothing else!
>>
>> I'm not following you there. Could you elaborate on why that would be beneficial? I could see (
>
> I never said it would be beneficial, only that it would be fun.
>
> http://www.mediawiki.org/wiki/Flaggedrevs

Ah, okay, that makes some sense.

Just to stay on subject, committed a fix (r16439) to bioperl-live that addresses the additional newline issue.

chris
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Re: problem with alignments and sequence locations

2009-12-03T10:26:57Z

Hi all,

Like Steffen, I've had a few burning questions too regarding
LocatableSeq lately.

I've had an occasional issue with LocatableSeq. Most assembly-related
modules use LocatableSeq objects. They specify the sequence start but
not the sequence end. This works in most cases, but I've recently
encountered very occasional error messages related to having not
explicitely set the end of the sequence. I've been unable to put
together a small test case to reproduce the bug easily.

My question is. If the start of the sequence is set, is it mandatory to
set the end of the sequence? If so, then maybe the documentation needs
to be explicit about it and maybe there needs to be a check that
enforces that the end is set. In fact, it seems like if I provide a
sequence and its start position, the LocatableSeq code should be able to
automatically calculate its end, no?

Florent

Steffen Heyne wrote:

> Hello,
>
> so I tried to fix the problem with the location. Currently it works for
> me with the following changes:
>
> LocatableSeq.pm
>
> sub get_nse{
>
> ...
>
> my $ret;
> if ($self->strand() >= 0) {
> $ret = $id . $v. $char1 . $st . $char2 . $end ;
> } else {
> $ret = $id . $v. $char1 . $end . $char2 . $st ;
> }
> return $ret;
> }
>
> Then I recognized during the usage of $aln->remove_seq() that it cannot
> remove a seq as it uses a wrong NSE to lookup sequences. I changed the
> following:
>
> SimpleAlign.pm
>
> sub remove_seq {
>
> ...
> $id = $seq->id();
> $start = $seq->start();
> $end = $seq->end();
>
> ## changed code:
>
> my $v = $seq->version ? '.'.$seq->version : '';
> if ($seq->strand >=0){
> $name = sprintf("%s%s/%d-%d",$id,$v,$start,$end);
> } elsif ($seq->strand == -1){
> $name = sprintf("%s%s/%d-%d",$id,$v,$end,$start);
> }
> ...
>
> }
>
> The above code in LocatableSeq.pm worked in the case if I read an
> alignment in stockholm format and write it out in clustalw format. But
> if I read an alignment in clustalw and write it out as stockholm (or
> something else) it didn't worked, as the strand is not correctly set in
> ClustalW::next_aln. It works with the following changes:
>
> ClustalW.pm
>
> sub next_aln{
>
> ...
>
> my ( $sname, $start, $end, $strand ); ## strand added
> $strand = 0; ## new, standard = 0???
> foreach my $name ( sort { $order{$a} <=> $order{$b} } keys
> %alignments ) {
> if ( $name =~ /(\S+):(\d+)-(\d+)/ ) {
> ( $sname, $start, $end ) = ( $1, $2, $3 );
> $strand = 1; ## new
> if ($start > $end) { ## new
> ($start, $end, $strand) = ($end, $start, -1); ##new
> } ## new
>
> }
> else {
> ( $sname, $start ) = ( $name, 1 );
> my $str = $alignments{$name};
> $str =~ s/[^A-Za-z]//g;
> $end = length($str);
> }
>
> my $seq = Bio::LocatableSeq->new(
> -seq => $alignments{$name},
> -id => $sname,
> -start => $start,
> -end => $end,
> -strand=> $strand ## new
> );
>
> ...
>
> }
>
> So I don't know if I changed things at their correct position. And I
> found them only because I used certain functions. I dont know how broad
> the effect of a changed NSE in LocatableSeq.pm is to other Modules and
> functions. But I'm happy with my changes (so far :-)...).
>
> Do you will change this to your proposed way in bioperl trunk?
>
> Thanks!
>
> steffen
>
>
> Chris Fields schrieb:
>
>> On Nov 10, 2009, at 6:55 AM, Steffen Heyne wrote:
>>
>>
>>> Hi,
>>>
>>> I'm using Bioperl for my research and it is very useful! Thank you!
>>>
>>> Currently I have a problem with locations tags of sequences. I read in
>>> seed alignments of Rfam (in stockholm format, but I think it is
>>> similar to other formats).
>>>
>>> If the location is like:
>>>
>>> AB194432.1/908-846
>>>
>>> the start/end values are changed to
>>>
>>> $seq->start = 846
>>> $seq->end = 908
>>>
>>> and therefore the new location (e.g.$seq->get_nse) is:
>>>
>>> AB194432.1/846-908
>>>
>>> The $seq->strand tag is correctly set to -1 in this case, but if the
>>> alignment is written out again (clustal, stockholm,...) this strand
>>> info is lost and the sequences have this "wrong" location. But this
>>> information is important in respect to the sequence accession number.
>>>
>>> Is there a way to set the location back to the original one or is this
>>> behavior desired? Any manually setting with $seq->start($val) failed
>>> due to automatic checking.
>>>
>>> I'm using bioperl 1.6.1
>>>
>>> Thanks!
>>>
>>> steffen
>>>
>> This is a definite bug. We recently discussed amending the NSE format
>> due to this (the subject came up over the last few months or so); it's
>> fallen through the cracks. Fortunaely it is very easy to fix (the
>> relevant method is in LocatableSeq).
>>
>> Does anyone have a problem with me adding this in? It will change
>> output for only those instances where the strand is -1, so
>>
>> AB194432.1/908-846
>>
>> would be start = 846, end = 908, strand = -1
>>
>> AB194432.1/846-908
>>
>> would be start = 846, end = 908, strand = 1
>>
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@...
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>

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Re: Merging separate sequence and quality files to FASTQ ?

2009-12-03T08:30:44Z

2009/12/3 Chris Fields <cjfields@...>:
> Dan,
>
> On Dec 3, 2009, at 7:07 AM, Dan Bolser wrote:

...

>> I'm wondering, because with the FlaggedRevs extension you could
>> basically build a whole release in the wiki. Which would be fun if
>> nothing else!
>
> I'm not following you there. Could you elaborate on why that would be beneficial? I could see (

I never said it would be beneficial, only that it would be fun.

http://www.mediawiki.org/wiki/Flaggedrevs

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Re: Merging separate sequence and quality files to FASTQ ?

2009-12-03T08:29:11Z

2009/12/3 Peter <biopython@...>:
> On Thu, Dec 3, 2009 at 2:39 PM, Chris Fields <cjfields@...> wrote:
>> Okay I will try to look into it today (it should be an easy fix). There are two issues, correct?

...

>> 2) missing description
>
> This is just a trivial bug/omission in the wiki example,

...

> Look - I seem to be learning Perl by osmosis ;)

Yay!

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Re: Merging separate sequence and quality files to FASTQ ?

2009-12-03T06:56:39Z

On Thu, Dec 3, 2009 at 2:39 PM, Chris Fields <cjfields@...> wrote:
> Okay I will try to look into it today (it should be an easy fix). There are two issues, correct?
>
> 1) extra blank line.

Which seems to be a bug in BioPerl SeqIO itself.

> 2) missing description

This is just a trivial bug/omission in the wiki example,
http://www.bioperl.org/wiki/Merging_separate_sequence_and_quality_files_to_FASTQ

You just need to replace this:

my $bsq_obj =
Bio::Seq::Quality->
new( -id => $seq_obj->id,
-seq => $seq_obj->seq,
-qual => $qual_obj->qual,
);

With:

my $bsq_obj =
Bio::Seq::Quality->
new( -id => $seq_obj->id,
-description => $seq_obj->description,
-seq => $seq_obj->seq,
-qual => $qual_obj->qual,
);

Look - I seem to be learning Perl by osmosis ;)

Peter

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Re: Merging separate sequence and quality files to FASTQ ?

2009-12-03T06:39:35Z

On Dec 3, 2009, at 8:20 AM, Peter wrote:

> On Thu, Dec 3, 2009 at 1:47 PM, Chris Fields <cjfields@...> wrote:
>>
>> FASTQ parsing had undergone a major revision prior to
>> 1.6.1 (the latest release in CPAN). Basically, it now parses
>> all three FASTQ variants. However, Peter indicates there
>> may still be a problem, and it's likely he's running 1.6.1.
>> Peter can you confirm that?
>
> I had BioPerl from SVN circa 1.6.1 (not sure if this was before
> or after the release of 1.6.1 now):
>
> $ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
> 1.0069
> $ perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION,"\n"'
> 1.0069
>
> If the tuples mean anything to you:
>
> $ perl -MBio::Root::Version -e 'printf "%vd\n", $Bio::Root::Version::VERSION'
> 49.46.48.48.54.57
> $ perl -MBio::SeqIO -e 'printf "%vd\n", $Bio::SeqIO::VERSION'
> 49.46.48.48.54.57
>
> I just updated to revision 16435, and retested. I get the same
> BioPerl version numbers, and the same extra blank line in the
> sequence FASTQ output as Dan reported.
>
> Peter

Okay I will try to look into it today (it should be an easy fix). There are two issues, correct?

1) extra blank line.
2) missing description

Dan, could you go ahead and submit this as a bug, just in case (so we don't lose track)? Otherwise it might get lost on the mail list or wiki.

chris
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Re: Merging separate sequence and quality files to FASTQ ?

2009-12-03T06:20:32Z

On Thu, Dec 3, 2009 at 1:47 PM, Chris Fields <cjfields@...> wrote:
>
> FASTQ parsing had undergone a major revision prior to
> 1.6.1 (the latest release in CPAN). Basically, it now parses
> all three FASTQ variants. However, Peter indicates there
> may still be a problem, and it's likely he's running 1.6.1.
> Peter can you confirm that?

I had BioPerl from SVN circa 1.6.1 (not sure if this was before
or after the release of 1.6.1 now):

$ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
1.0069
$ perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION,"\n"'
1.0069

If the tuples mean anything to you:

$ perl -MBio::Root::Version -e 'printf "%vd\n", $Bio::Root::Version::VERSION'
49.46.48.48.54.57
$ perl -MBio::SeqIO -e 'printf "%vd\n", $Bio::SeqIO::VERSION'
49.46.48.48.54.57

I just updated to revision 16435, and retested. I get the same
BioPerl version numbers, and the same extra blank line in the
sequence FASTQ output as Dan reported.

Peter

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Re: Merging separate sequence and quality files to FASTQ ?

2009-12-03T05:47:32Z

Dan,

On Dec 3, 2009, at 7:07 AM, Dan Bolser wrote:

> 2009/12/3 Peter <biopython@...>:
>> On Thu, Dec 3, 2009 at 11:44 AM, Dan Bolser <dan.bolser@...> wrote:
>>> Hi, can someone test the script here on zero length fasta / qual files?
>>>
>>> http://www.bioperl.org/wiki/Merging_separate_sequence_and_quality_files_to_FASTQ
>>>
>>> It seems the output has an extra newline in the sequence part of the
>>> output (which throws off scripts that rely on the 'four lines per
>>> record' structure of the fastq (although I'm not sure if it's illegal
>>> fastq).
>>
>> Hi Dan,
>>
>> The OBF consensus was FASTQ records with a zero length
>> sequence might be useful, and should be output as exactly
>> four lines (one blank sequence line, one blank quality line).
>> However for parsing, any number of blank lines should be OK.
>> http://lists.open-bio.org/pipermail/open-bio-l/2009-July/000522.html
>>
>> I can confirm the perl script currently outputs a FASTQ file
>> with TWO blank lines for the sequence, giving five lines in
>> total for the zero length record. That does suggest a bug.
>> What version of BioPerl are you running?
>
> Hi Peter,
>
> Basically, I'm not running the 'latest' version of BP, which is why I
> asked this question of the list rather than filing a bug report. What
> version are you running? ;-)
>
> Sounds like 5 lines instead of the expected 4 is a minor bug. (Thanks
> for the info).

FASTQ parsing had undergone a major revision prior to 1.6.1 (the latest release in CPAN). Basically, it now parses all three FASTQ variants. However, Peter indicates there may still be a problem, and it's likely he's running 1.6.1. Peter can you confirm that?

>> Peter
>>
>> P.S. The script is throwing away any description after the
>> identifier.
>
> That's probably bad. Feel free to edit the script on the wiki. Sadly,
> MediaWiki's diff features are less than optimal, so developing scripts
> on the wiki isn't ideal. Anyone know how to plug git-hub into a script
> apparently hosted on a wiki?
>
> Or is git-hub basically designed to be 'wiki for code'?

It's more an integrated solution for hosting code via git, with a wiki, bug queue, etc. Think Soourceforge, but a lot nicer and with no ads ;>

BitBucket/Hg is another (very nice) solution along the same lines, developed in Python (Github is Ruby-centric).

> I'm wondering, because with the FlaggedRevs extension you could
> basically build a whole release in the wiki. Which would be fun if
> nothing else!

I'm not following you there. Could you elaborate on why that would be beneficial? I could see (

chris

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Re: problem with alignments and sequence locations

2009-12-03T05:19:51Z

Hello,

so I tried to fix the problem with the location. Currently it works for
me with the following changes:

LocatableSeq.pm

sub get_nse{

...

my $ret;
if ($self->strand() >= 0) {
$ret = $id . $v. $char1 . $st . $char2 . $end ;
} else {
$ret = $id . $v. $char1 . $end . $char2 . $st ;
}
return $ret;
}

Then I recognized during the usage of $aln->remove_seq() that it cannot
remove a seq as it uses a wrong NSE to lookup sequences. I changed the
following:

SimpleAlign.pm

sub remove_seq {

...
$id = $seq->id();
$start = $seq->start();
$end = $seq->end();

## changed code:

my $v = $seq->version ? '.'.$seq->version : '';
if ($seq->strand >=0){
$name = sprintf("%s%s/%d-%d",$id,$v,$start,$end);
} elsif ($seq->strand == -1){
$name = sprintf("%s%s/%d-%d",$id,$v,$end,$start);
}
...

}

The above code in LocatableSeq.pm worked in the case if I read an
alignment in stockholm format and write it out in clustalw format. But
if I read an alignment in clustalw and write it out as stockholm (or
something else) it didn't worked, as the strand is not correctly set in
ClustalW::next_aln. It works with the following changes:

ClustalW.pm

sub next_aln{

...

my ( $sname, $start, $end, $strand ); ## strand added
$strand = 0; ## new, standard = 0???
foreach my $name ( sort { $order{$a} <=> $order{$b} } keys
%alignments ) {
if ( $name =~ /(\S+):(\d+)-(\d+)/ ) {
( $sname, $start, $end ) = ( $1, $2, $3 );
$strand = 1; ## new
if ($start > $end) { ## new
($start, $end, $strand) = ($end, $start, -1); ##new
} ## new

}
else {
( $sname, $start ) = ( $name, 1 );
my $str = $alignments{$name};
$str =~ s/[^A-Za-z]//g;
$end = length($str);
}

my $seq = Bio::LocatableSeq->new(
-seq => $alignments{$name},
-id => $sname,
-start => $start,
-end => $end,
-strand=> $strand ## new
);

...

}

So I don't know if I changed things at their correct position. And I
found them only because I used certain functions. I dont know how broad
the effect of a changed NSE in LocatableSeq.pm is to other Modules and
functions. But I'm happy with my changes (so far :-)...).

Do you will change this to your proposed way in bioperl trunk?

Thanks!

steffen

Chris Fields schrieb:

> On Nov 10, 2009, at 6:55 AM, Steffen Heyne wrote:
>
>> Hi,
>>
>> I'm using Bioperl for my research and it is very useful! Thank you!
>>
>> Currently I have a problem with locations tags of sequences. I read in
>> seed alignments of Rfam (in stockholm format, but I think it is
>> similar to other formats).
>>
>> If the location is like:
>>
>> AB194432.1/908-846
>>
>> the start/end values are changed to
>>
>> $seq->start = 846
>> $seq->end = 908
>>
>> and therefore the new location (e.g.$seq->get_nse) is:
>>
>> AB194432.1/846-908
>>
>> The $seq->strand tag is correctly set to -1 in this case, but if the
>> alignment is written out again (clustal, stockholm,...) this strand
>> info is lost and the sequences have this "wrong" location. But this
>> information is important in respect to the sequence accession number.
>>
>> Is there a way to set the location back to the original one or is this
>> behavior desired? Any manually setting with $seq->start($val) failed
>> due to automatic checking.
>>
>> I'm using bioperl 1.6.1
>>
>> Thanks!
>>
>> steffen
>
> This is a definite bug. We recently discussed amending the NSE format
> due to this (the subject came up over the last few months or so); it's
> fallen through the cracks. Fortunaely it is very easy to fix (the
> relevant method is in LocatableSeq).
>
> Does anyone have a problem with me adding this in? It will change
> output for only those instances where the strand is -1, so
>
> AB194432.1/908-846
>
> would be start = 846, end = 908, strand = -1
>
> AB194432.1/846-908
>
> would be start = 846, end = 908, strand = 1
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
---
Steffen Heyne, Dipl.-Bioinf.
Lehrstuhl für Bioinformatik
Institut für Informatik
Albert-Ludwigs-Universität Freiburg
Georges-Köhler-Allee 106
79110 Freiburg, Germany

Tel: (+49) 761 203 7465
Fax: (+49) 761 203 7462
Mail: heyne@...

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Re: Merging separate sequence and quality files to FASTQ ?

2009-12-03T05:07:27Z

2009/12/3 Peter <biopython@...>:

> On Thu, Dec 3, 2009 at 11:44 AM, Dan Bolser <dan.bolser@...> wrote:
>> Hi, can someone test the script here on zero length fasta / qual files?
>>
>> http://www.bioperl.org/wiki/Merging_separate_sequence_and_quality_files_to_FASTQ
>>
>> It seems the output has an extra newline in the sequence part of the
>> output (which throws off scripts that rely on the 'four lines per
>> record' structure of the fastq (although I'm not sure if it's illegal
>> fastq).
>
> Hi Dan,
>
> The OBF consensus was FASTQ records with a zero length
> sequence might be useful, and should be output as exactly
> four lines (one blank sequence line, one blank quality line).
> However for parsing, any number of blank lines should be OK.
> http://lists.open-bio.org/pipermail/open-bio-l/2009-July/000522.html
>
> I can confirm the perl script currently outputs a FASTQ file
> with TWO blank lines for the sequence, giving five lines in
> total for the zero length record. That does suggest a bug.
> What version of BioPerl are you running?

Hi Peter,

Basically, I'm not running the 'latest' version of BP, which is why I
asked this question of the list rather than filing a bug report. What
version are you running? ;-)

Sounds like 5 lines instead of the expected 4 is a minor bug. (Thanks
for the info).

> Peter
>
> P.S. The script is throwing away any description after the
> identifier.

That's probably bad. Feel free to edit the script on the wiki. Sadly,
MediaWiki's diff features are less than optimal, so developing scripts
on the wiki isn't ideal. Anyone know how to plug git-hub into a script
apparently hosted on a wiki?

Or is git-hub basically designed to be 'wiki for code'?

I'm wondering, because with the FlaggedRevs extension you could
basically build a whole release in the wiki. Which would be fun if
nothing else!

--

JHP: Biology is bioinformatics and bioinformatics is biology.
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Re: Merging separate sequence and quality files to FASTQ ?

2009-12-03T04:12:15Z

On Thu, Dec 3, 2009 at 11:44 AM, Dan Bolser <dan.bolser@...> wrote:
> Hi, can someone test the script here on zero length fasta / qual files?
>
> http://www.bioperl.org/wiki/Merging_separate_sequence_and_quality_files_to_FASTQ
>
> It seems the output has an extra newline in the sequence part of the
> output (which throws off scripts that rely on the 'four lines per
> record' structure of the fastq (although I'm not sure if it's illegal
> fastq).

Hi Dan,

The OBF consensus was FASTQ records with a zero length
sequence might be useful, and should be output as exactly
four lines (one blank sequence line, one blank quality line).
However for parsing, any number of blank lines should be OK.
http://lists.open-bio.org/pipermail/open-bio-l/2009-July/000522.html

I can confirm the perl script currently outputs a FASTQ file
with TWO blank lines for the sequence, giving five lines in
total for the zero length record. That does suggest a bug.
What version of BioPerl are you running?

Peter

P.S. The script is throwing away any description after the
identifier.
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Merging separate sequence and quality files to FASTQ ?

2009-12-03T03:44:40Z

Hi, can someone test the script here on zero length fasta / qual files?

http://www.bioperl.org/wiki/Merging_separate_sequence_and_quality_files_to_FASTQ

It seems the output has an extra newline in the sequence part of the
output (which throws off scripts that rely on the 'four lines per
record' structure of the fastq (although I'm not sure if it's illegal
fastq).

Here is what I see

BEGIN
$ head one.fna
>FVF7ZWH02PFOVG length=0 xy=2116_2074 region=2
$ head one.qual
>FVF7ZWH02PFOVG length=0 xy=2116_2074 region=2
$ createFastq.plx one.fna one.qual
@FVF7ZWH02PFOVG

+FVF7ZWH02PFOVG

END

Currently I just put in a clause in the script to skip any zero length
sequences, but I think the Qual shouldn't output an extra newline like
this.

Cheers,
Dan.

--

JHB: Bioinformatics is Biology and Biology is Bioinformatics.
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modENCODE seeking data managers

2009-12-03T02:31:31Z

Hi All,

My apologies for spamming the list, but this announcement may be of
interest:

The modENCODE Data Coordinating Center (Model Organism Encylopedia of DNA
Elements; www.modencode.org) is seeking data managers to gather and curate
large scale functional genomics data sets in fly and worm. For details, see
http://blog.modencode.org/?p=350.

Lincoln

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>
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Re: Parsing Genbank

2009-12-02T13:07:58Z

One never knows, but I would be very surprised if this somehow snuck by the test suite we have, particularly since Gbrowse extensively uses SeqFeatures (any changes should have popped out along the way).

Not much we can do unless we have something to help confirm the problem. Also might help to know the source of the genbank file itself.

chris

On Dec 2, 2009, at 2:52 PM, Mark A. Jensen wrote:

> Yes, 1.006 is 1.6. There is a later update 1.6.1, but it sounds
> as if there is a bug. If you can provide data that can reproduce
> it, as Chris suggests, we can get onto it.
> thanks MAJ
> ----- Original Message -----
> From: Brandi Cantarel
> To: Mark A. Jensen
> Sent: Wednesday, December 02, 2009 3:38 PM
> Subject: Re: [Bioperl-l] Parsing Genbank
>
>
> How can I tell what version I am using?When I use the command from the website:
>
>
> perl -MBio::Root::Version -e 'printf "%vd\n", $Bio::Root::Version::VERSION'
>
>
> I get 1.006, but the bioperl lib was updated in July, so probably 1.6.0 version since that was the last stable release….
>
>
> Brandi
>
>
>
>
> On Dec 2, 2009, at 2:48 PM, Mark A. Jensen wrote:
>
>
> with fake seq data and that header, I don't get a problem:
>
> DB<2> x $cds->location
> 0 Bio::Location::Simple=HASH(0x37b1df4)
> '_end' => 974
> '_location_type' => 'EXACT'
> '_root_verbose' => 0
> '_seqid' => 'subjpool12_contig3'
> '_start' => 911
> '_strand' => '-1'
>
> Are you using the latest BioPerl (1.6.1 or the trunk) ?
> MAJ
> ----- Original Message ----- From: "Brandi Cantarel" <bcantarel@...>
> Cc: <bioperl-l@...>
> Sent: Wednesday, December 02, 2009 2:29 PM
> Subject: Re: [Bioperl-l] Parsing Genbank
>
>
> Here is some of my code, the real code actually enters the data into a database.
>
>
> $in = Bio::SeqIO->new(-file => $gbkfile,
> '-format' => 'genbank');
>
> W1:while (my $seq = $in->next_seq()) {
> my @feats = $seq->get_all_SeqFeatures();
> my $j = 0;
> F1:foreach $cds (@feats) {
> next F1 unless ($cds->primary_tag() eq 'CDS');
> ###>> debugger stops here for above output
>
> #do something with the cds start and cds end
> }
> }
>
>
> LOCUS subjpool12_contig3 974 bp DNA linear UNK 19-Nov-2009
> ACCESSION subjpool12_contig3
> KEYWORDS .
> SOURCE human metagenome
> ORGANISM human metagenome
> unclassified sequences; organismal metagenomes,metagenomes.
> FEATURES Location/Qualifiers
> source 1..974
> /mol_type="genomic DNA"
> /isolation_source="Homo sapiens"
> /organism="human metagenome"
> /collection_date="19-Nov-2009"
> CDS complement(911..974)
> /locus_tag="subjpool12_contig3|metagene|gene_2"
> /translation="IRIMTVELINPYIRHVEHST"
> /score="2.52804"
> /product="hypothetical protein"
> /note="score=2.52804"
> /note="score=2.52804"
> /note="frame=1"
> ORIGIN
> #some sequence….
>
>
>
>
>
> From this example, I would like to get the coordinates 911 and 974, rather than 1 and 64.
>
>
>
>
> ~~~~~~~~~~~~~~~~~~~~
> Brandi Cantarel, PhD
> Bioinformatics Analyst
> Institute for Genome Sciences
> School of Medicine
> University of Maryland, Baltimore
>
> On Dec 2, 2009, at 2:09 PM, Mark A. Jensen wrote:
>
>
> Hi Brandi-
>
> If $cds is a Bio::SeqFeature::Generic, that's weird (I believe); if its an ordinary Bio::Seq, that's normal.
>
> Can you elaborate by posting your code?
>
> cheers,
>
> MAJ
>
> ----- Original Message ----- From: "Brandi Cantarel" <bcantarel@...>
>
> To: <bioperl-l@...>
>
> Sent: Wednesday, December 02, 2009 1:36 PM
>
> Subject: [Bioperl-l] Parsing Genbank
>
>
>
>
>
> Hi all,
>
> I am not sure if this is normal, but when I use SEQIO to parse genbank files, it changes the coordinates of things on the minus strand.
>
>
>
>
>
> For example, I have a sequence that has a CDS on the minus strand at it is from 911 to 974. The sequence is 974 nt.
>
>
>
> x $cds->start
>
> 1
>
> x $cds->end
>
> 64
>
>
>
> How can I get the original coordinates? Is there a command for that or will I have to just do the math?
>
>
>
> Feature or Bug?
>
>
>
>
>
> ~~~~~~~~~~~~~~~~~~~~
>
> Brandi Cantarel, PhD
>
> Bioinformatics Analyst
>
> Institute for Genome Sciences
>
> School of Medicine
>
> University of Maryland, Baltimore
>
>
>
>
>
> _______________________________________________
>
> Bioperl-l mailing list
>
> Bioperl-l@...
>
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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Re: Parsing Genbank

2009-12-02T12:52:28Z

Yes, 1.006 is 1.6. There is a later update 1.6.1, but it sounds
as if there is a bug. If you can provide data that can reproduce
it, as Chris suggests, we can get onto it.
thanks MAJ
----- Original Message -----
From: Brandi Cantarel
To: Mark A. Jensen
Sent: Wednesday, December 02, 2009 3:38 PM
Subject: Re: [Bioperl-l] Parsing Genbank

How can I tell what version I am using?When I use the command from the website:

perl -MBio::Root::Version -e 'printf "%vd\n", $Bio::Root::Version::VERSION'

I get 1.006, but the bioperl lib was updated in July, so probably 1.6.0 version since that was the last stable release….

Brandi

On Dec 2, 2009, at 2:48 PM, Mark A. Jensen wrote:

with fake seq data and that header, I don't get a problem:

DB<2> x $cds->location
0 Bio::Location::Simple=HASH(0x37b1df4)
'_end' => 974
'_location_type' => 'EXACT'
'_root_verbose' => 0
'_seqid' => 'subjpool12_contig3'
'_start' => 911
'_strand' => '-1'

Are you using the latest BioPerl (1.6.1 or the trunk) ?
MAJ
----- Original Message ----- From: "Brandi Cantarel" <bcantarel@...>
Cc: <bioperl-l@...>
Sent: Wednesday, December 02, 2009 2:29 PM
Subject: Re: [Bioperl-l] Parsing Genbank

Here is some of my code, the real code actually enters the data into a database.

$in = Bio::SeqIO->new(-file => $gbkfile,
'-format' => 'genbank');

W1:while (my $seq = $in->next_seq()) {
my @feats = $seq->get_all_SeqFeatures();
my $j = 0;
F1:foreach $cds (@feats) {
next F1 unless ($cds->primary_tag() eq 'CDS');
###>> debugger stops here for above output

#do something with the cds start and cds end
}
}

LOCUS subjpool12_contig3 974 bp DNA linear UNK 19-Nov-2009
ACCESSION subjpool12_contig3
KEYWORDS .
SOURCE human metagenome
ORGANISM human metagenome
unclassified sequences; organismal metagenomes,metagenomes.
FEATURES Location/Qualifiers
source 1..974
/mol_type="genomic DNA"
/isolation_source="Homo sapiens"
/organism="human metagenome"
/collection_date="19-Nov-2009"
CDS complement(911..974)
/locus_tag="subjpool12_contig3|metagene|gene_2"
/translation="IRIMTVELINPYIRHVEHST"
/score="2.52804"
/product="hypothetical protein"
/note="score=2.52804"
/note="score=2.52804"
/note="frame=1"
ORIGIN
#some sequence….

From this example, I would like to get the coordinates 911 and 974, rather than 1 and 64.

~~~~~~~~~~~~~~~~~~~~
Brandi Cantarel, PhD
Bioinformatics Analyst
Institute for Genome Sciences
School of Medicine
University of Maryland, Baltimore

On Dec 2, 2009, at 2:09 PM, Mark A. Jensen wrote:

Hi Brandi-

If $cds is a Bio::SeqFeature::Generic, that's weird (I believe); if its an ordinary Bio::Seq, that's normal.

Can you elaborate by posting your code?

cheers,

MAJ

----- Original Message ----- From: "Brandi Cantarel" <bcantarel@...>

To: <bioperl-l@...>

Sent: Wednesday, December 02, 2009 1:36 PM

Subject: [Bioperl-l] Parsing Genbank

Hi all,

I am not sure if this is normal, but when I use SEQIO to parse genbank files, it changes the coordinates of things on the minus strand.

For example, I have a sequence that has a CDS on the minus strand at it is from 911 to 974. The sequence is 974 nt.

x $cds->start

1

x $cds->end

64

How can I get the original coordinates? Is there a command for that or will I have to just do the math?

Feature or Bug?

~~~~~~~~~~~~~~~~~~~~

Brandi Cantarel, PhD

Bioinformatics Analyst

Institute for Genome Sciences

School of Medicine

University of Maryland, Baltimore

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Re: Parsing Genbank

2009-12-02T11:48:44Z

with fake seq data and that header, I don't get a problem:

DB<2> x $cds->location
0 Bio::Location::Simple=HASH(0x37b1df4)
'_end' => 974
'_location_type' => 'EXACT'
'_root_verbose' => 0
'_seqid' => 'subjpool12_contig3'
'_start' => 911
'_strand' => '-1'

Are you using the latest BioPerl (1.6.1 or the trunk) ?
MAJ
----- Original Message -----
From: "Brandi Cantarel" <bcantarel@...>
Cc: <bioperl-l@...>
Sent: Wednesday, December 02, 2009 2:29 PM
Subject: Re: [Bioperl-l] Parsing Genbank

Here is some of my code, the real code actually enters the data into a database.

$in = Bio::SeqIO->new(-file => $gbkfile,
'-format' => 'genbank');

W1:while (my $seq = $in->next_seq()) {
my @feats = $seq->get_all_SeqFeatures();
my $j = 0;
F1:foreach $cds (@feats) {
next F1 unless ($cds->primary_tag() eq 'CDS');
###>> debugger stops here for above output

#do something with the cds start and cds end
}
}

LOCUS subjpool12_contig3 974 bp DNA linear UNK
19-Nov-2009
ACCESSION subjpool12_contig3
KEYWORDS .
SOURCE human metagenome
ORGANISM human metagenome
unclassified sequences; organismal metagenomes,metagenomes.
FEATURES Location/Qualifiers
source 1..974
/mol_type="genomic DNA"
/isolation_source="Homo sapiens"
/organism="human metagenome"
/collection_date="19-Nov-2009"
CDS complement(911..974)
/locus_tag="subjpool12_contig3|metagene|gene_2"
/translation="IRIMTVELINPYIRHVEHST"
/score="2.52804"
/product="hypothetical protein"
/note="score=2.52804"
/note="score=2.52804"
/note="frame=1"
ORIGIN
#some sequence….

>From this example, I would like to get the coordinates 911 and 974, rather than
>1 and 64.

~~~~~~~~~~~~~~~~~~~~
Brandi Cantarel, PhD
Bioinformatics Analyst
Institute for Genome Sciences
School of Medicine
University of Maryland, Baltimore

On Dec 2, 2009, at 2:09 PM, Mark A. Jensen wrote:

> Hi Brandi-
> If $cds is a Bio::SeqFeature::Generic, that's weird (I believe); if its an
> ordinary Bio::Seq, that's normal.
> Can you elaborate by posting your code?
> cheers,
> MAJ
> ----- Original Message ----- From: "Brandi Cantarel"
> <bcantarel@...>
> To: <bioperl-l@...>
> Sent: Wednesday, December 02, 2009 1:36 PM
> Subject: [Bioperl-l] Parsing Genbank
>
>
>> Hi all,
>> I am not sure if this is normal, but when I use SEQIO to parse genbank files,
>> it changes the coordinates of things on the minus strand.
>>
>>
>> For example, I have a sequence that has a CDS on the minus strand at it is
>> from 911 to 974. The sequence is 974 nt.
>>
>> x $cds->start
>> 1
>> x $cds->end
>> 64
>>
>> How can I get the original coordinates? Is there a command for that or will
>> I have to just do the math?
>>
>> Feature or Bug?
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~
>> Brandi Cantarel, PhD
>> Bioinformatics Analyst
>> Institute for Genome Sciences
>> School of Medicine
>> University of Maryland, Baltimore
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@...
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>

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Re: Parsing Genbank

2009-12-02T11:39:40Z

That one's odd; the coordinates should relate back to the original sequence. Any chance you could pass on the sequence file so we can confirm it? you can do this off-list if the information is sensitive, or you can create a faux sequence that has the same problem).

chris

On Dec 2, 2009, at 1:29 PM, Brandi Cantarel wrote:

> Here is some of my code, the real code actually enters the data into a database.
>
>
> $in = Bio::SeqIO->new(-file => $gbkfile,
> '-format' => 'genbank');
>
> W1:while (my $seq = $in->next_seq()) {
> my @feats = $seq->get_all_SeqFeatures();
> my $j = 0;
> F1:foreach $cds (@feats) {
> next F1 unless ($cds->primary_tag() eq 'CDS');
> #do something with the cds start and cds end
> }
> }
>
>
> LOCUS subjpool12_contig3 974 bp DNA linear UNK 19-Nov-2009
> ACCESSION subjpool12_contig3
> KEYWORDS .
> SOURCE human metagenome
> ORGANISM human metagenome
> unclassified sequences; organismal metagenomes,metagenomes.
> FEATURES Location/Qualifiers
> source 1..974
> /mol_type="genomic DNA"
> /isolation_source="Homo sapiens"
> /organism="human metagenome"
> /collection_date="19-Nov-2009"
> CDS complement(911..974)
> /locus_tag="subjpool12_contig3|metagene|gene_2"
> /translation="IRIMTVELINPYIRHVEHST"
> /score="2.52804"
> /product="hypothetical protein"
> /note="score=2.52804"
> /note="score=2.52804"
> /note="frame=1"
> ORIGIN
> #some sequence….
>
>
>
>
>> From this example, I would like to get the coordinates 911 and 974, rather than 1 and 64.
>
>
>
> ~~~~~~~~~~~~~~~~~~~~
> Brandi Cantarel, PhD
> Bioinformatics Analyst
> Institute for Genome Sciences
> School of Medicine
> University of Maryland, Baltimore
>
> On Dec 2, 2009, at 2:09 PM, Mark A. Jensen wrote:
>
>> Hi Brandi-
>> If $cds is a Bio::SeqFeature::Generic, that's weird (I believe); if its an ordinary Bio::Seq, that's normal.
>> Can you elaborate by posting your code?
>> cheers,
>> MAJ
>> ----- Original Message ----- From: "Brandi Cantarel" <bcantarel@...>
>> To: <bioperl-l@...>
>> Sent: Wednesday, December 02, 2009 1:36 PM
>> Subject: [Bioperl-l] Parsing Genbank
>>
>>
>>> Hi all,
>>> I am not sure if this is normal, but when I use SEQIO to parse genbank files, it changes the coordinates of things on the minus strand.
>>>
>>>
>>> For example, I have a sequence that has a CDS on the minus strand at it is from 911 to 974. The sequence is 974 nt.
>>>
>>> x $cds->start
>>> 1
>>> x $cds->end
>>> 64
>>>
>>> How can I get the original coordinates? Is there a command for that or will I have to just do the math?
>>>
>>> Feature or Bug?
>>>
>>>
>>> ~~~~~~~~~~~~~~~~~~~~
>>> Brandi Cantarel, PhD
>>> Bioinformatics Analyst
>>> Institute for Genome Sciences
>>> School of Medicine
>>> University of Maryland, Baltimore
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l@...
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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Re: Parsing Genbank

2009-12-02T11:29:56Z

Here is some of my code, the real code actually enters the data into a database.

$in = Bio::SeqIO->new(-file => $gbkfile,
'-format' => 'genbank');

W1:while (my $seq = $in->next_seq()) {
my @feats = $seq->get_all_SeqFeatures();
my $j = 0;
F1:foreach $cds (@feats) {
next F1 unless ($cds->primary_tag() eq 'CDS');
#do something with the cds start and cds end
}
}

LOCUS subjpool12_contig3 974 bp DNA linear UNK 19-Nov-2009
ACCESSION subjpool12_contig3
KEYWORDS .
SOURCE human metagenome
ORGANISM human metagenome
unclassified sequences; organismal metagenomes,metagenomes.
FEATURES Location/Qualifiers
source 1..974
/mol_type="genomic DNA"
/isolation_source="Homo sapiens"
/organism="human metagenome"
/collection_date="19-Nov-2009"
CDS complement(911..974)
/locus_tag="subjpool12_contig3|metagene|gene_2"
/translation="IRIMTVELINPYIRHVEHST"
/score="2.52804"
/product="hypothetical protein"
/note="score=2.52804"
/note="score=2.52804"
/note="frame=1"
ORIGIN
#some sequence….

>From this example, I would like to get the coordinates 911 and 974, rather than 1 and 64.

~~~~~~~~~~~~~~~~~~~~
Brandi Cantarel, PhD
Bioinformatics Analyst
Institute for Genome Sciences
School of Medicine
University of Maryland, Baltimore

On Dec 2, 2009, at 2:09 PM, Mark A. Jensen wrote:

> Hi Brandi-
> If $cds is a Bio::SeqFeature::Generic, that's weird (I believe); if its an ordinary Bio::Seq, that's normal.
> Can you elaborate by posting your code?
> cheers,
> MAJ
> ----- Original Message ----- From: "Brandi Cantarel" <bcantarel@...>
> To: <bioperl-l@...>
> Sent: Wednesday, December 02, 2009 1:36 PM
> Subject: [Bioperl-l] Parsing Genbank
>
>
>> Hi all,
>> I am not sure if this is normal, but when I use SEQIO to parse genbank files, it changes the coordinates of things on the minus strand.
>>
>>
>> For example, I have a sequence that has a CDS on the minus strand at it is from 911 to 974. The sequence is 974 nt.
>>
>> x $cds->start
>> 1
>> x $cds->end
>> 64
>>
>> How can I get the original coordinates? Is there a command for that or will I have to just do the math?
>>
>> Feature or Bug?
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~
>> Brandi Cantarel, PhD
>> Bioinformatics Analyst
>> Institute for Genome Sciences
>> School of Medicine
>> University of Maryland, Baltimore
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@...
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>

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Re: Parsing Genbank

2009-12-02T11:09:11Z

Hi Brandi-
If $cds is a Bio::SeqFeature::Generic, that's weird (I believe); if its an
ordinary Bio::Seq, that's normal.
Can you elaborate by posting your code?
cheers,
MAJ
----- Original Message -----
From: "Brandi Cantarel" <bcantarel@...>
To: <bioperl-l@...>
Sent: Wednesday, December 02, 2009 1:36 PM
Subject: [Bioperl-l] Parsing Genbank

> Hi all,
> I am not sure if this is normal, but when I use SEQIO to parse genbank files,
> it changes the coordinates of things on the minus strand.
>
>
> For example, I have a sequence that has a CDS on the minus strand at it is
> from 911 to 974. The sequence is 974 nt.
>
> x $cds->start
> 1
> x $cds->end
> 64
>
> How can I get the original coordinates? Is there a command for that or will I
> have to just do the math?
>
> Feature or Bug?
>
>
> ~~~~~~~~~~~~~~~~~~~~
> Brandi Cantarel, PhD
> Bioinformatics Analyst
> Institute for Genome Sciences
> School of Medicine
> University of Maryland, Baltimore
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

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Parsing Genbank

2009-12-02T10:36:27Z

Hi all,
I am not sure if this is normal, but when I use SEQIO to parse genbank files, it changes the coordinates of things on the minus strand.

For example, I have a sequence that has a CDS on the minus strand at it is from 911 to 974. The sequence is 974 nt.

x $cds->start
1
x $cds->end
64

How can I get the original coordinates? Is there a command for that or will I have to just do the math?

Feature or Bug?

~~~~~~~~~~~~~~~~~~~~
Brandi Cantarel, PhD
Bioinformatics Analyst
Institute for Genome Sciences
School of Medicine
University of Maryland, Baltimore

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Re: Problems with installation

2009-12-02T06:18:37Z

Hello Vipin,

"do not seem to work" doesn't give us much to go on; can you tell us
what happened?

Scott

On Wed, Dec 2, 2009 at 12:24 AM, Vipin Singh <ashvip@...> wrote:

> Dear Sir/Madam,
> I have not been able to install bioperl on my Windows 32 machine despite
> repeated attempts. I have tried both Active Perl and Strwaberry perl but
> both do not seem to work.
> I have followed the instruction given at
> -- http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>
> Please guide.
> Thanks,
> Vipin.
> Vipin Singh,
> Senior Research Fellow,
> Centre for Cellular and Molecular Biology,
> Hyderabad - 500007
> India.
> contact - 91-040-27192778
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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Re: Problems with installation

2009-12-02T06:18:31Z

Hi Vipin--
We need some more information; your commands, error messages you received.
Thanks,
Mark
----- Original Message -----
From: "Vipin Singh" <ashvip@...>
To: <bioperl-l@...>
Sent: Wednesday, December 02, 2009 12:24 AM
Subject: [Bioperl-l] Problems with installation

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Remote blast

2009-12-02T04:07:08Z

Hello everyone,

I have a problem. I am new to Bioperl. I am working on RNAi tool wherein a
cgi script was written which connects to NCBI blast using remote blast
program,i.e.,

The input sequence given in the html page is taken as input and Remote blast
is performed on this based on the code for Remote blast.But,I have a problem
in the Remote blast code.

My code goes like this

@compseqs=blastcode($in{'Inputseq'});

sub blastcode
{
$input1= $_[0];

open(NUC,'>',$nuc);
print NUC $input1;
close(NUC);

my $prog = 'blastn';
my $db = 'refseq_rna';
my $e_val= '1e-10';
my $organism= 'Trypanosoma Brucei';

$gb = new Bio::DB::GenBank;

my @params = ( '-prog' => $prog,
'-data' => $db,
'-expect' => $e_val,
'-readmethod' => 'SearchIO',
'-Organism' => $organism );

my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

#change a paramter
$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Trypanosoma
brucei[ORGN]';

my $v = 1;
#$v is just to turn on and off the messages

my $str = Bio::SeqIO->new(-file => $nuc , '-format' => 'fasta' ,
'-organism' => 'Trypanosoma Brucei' );

while (my $input = $str->next_seq())

{
#Blast a sequence against a database:
#Alternatively, you could pass in a file with many
#sequences rather than loop through sequence one at a time
#Remove the loop starting 'while (my $input = $str->next_seq())'
#and swap the two lines below for an example of that.

my $r = $factory->submit_blast($input);

print STDERR "waiting...." if($v>0);

while ( my @rids = $factory->each_rid ) {

foreach my $rid ( @rids ) {

my $rc = $factory->retrieve_blast($rid);

if( !ref($rc) )
{
if( $rc < 0 )
{
$factory->remove_rid($rid);
}
print STDERR "." if ( $v > 0 );
sleep 5;
}
else {
my $result = $rc->next_result();
#save the output
my $filename = $result->query_name()."\.out";
$factory->save_output($filename);
$factory->remove_rid($rid);
# open(BLASTDEBUGFILE,'>',$blastdebugfile);
# print BLASTDEBUGFILE "Test1 $result";
# close(BLASTDEBUGFILE);

open(OUTFILE,'>',$outfile);
print OUTFILE "Test2 $result->database_name()";
close(OUTFILE);

while ( my $hit = $result->next_hit ) {
next unless ( $v > 0);

# open(OUTFILE,'>',$outfile);
# print OUTFILE "in while hits";
#close(OUTFILE);

my $sequ = $gb->get_Seq_by_version($hit->name);
my $dna = $sequ->seq(); # get the sequence as a string
push(@seqs,$dna);
}
}
}
}
}
# open(OUTFILE,'>',$outfile);
#print OUTFILE $seqs[0];
# close(OUTFILE);

return(@seqs);
}

Here in the above code,my program is able to go till the 'else' part and
writing the output file i.e.,this step.
my $filename = $result->query_name()."\.out";

But when I tried to enter in to the next while loop where I can get the
hits,the program is not entering into the while loop i.e.,

Not entering into this
while ( my $hit = $result->next_hit ) {
next unless ( $v > 0);

Hence I am unable to get any hits for my query.
Ex:-If the query's accession number is Tb11.02.2210, I could just get a file
Tb11.02.2210.out file,it is just displaying the file name on the browser.

Please help me in solving this problem and mail me regarding any confusions.

Regards,
Roopa.
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Problems with installation

2009-12-01T21:24:09Z

Dear Sir/Madam,
I have not been able to install bioperl on my Windows 32 machine despite
repeated attempts. I have tried both Active Perl and Strwaberry perl but
both do not seem to work.
I have followed the instruction given at
-- http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows

Please guide.
Thanks,
Vipin.
Vipin Singh,
Senior Research Fellow,
Centre for Cellular and Molecular Biology,
Hyderabad - 500007
India.
contact - 91-040-27192778
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Re: test test test

2009-12-01T19:08:23Z

I love when people are paying attention!
----- Original Message -----
From: Ocar Campos
To: Mark A. Jensen ; Bioperl Mailing List.
Sent: Tuesday, December 01, 2009 9:59 PM
Subject: Re: [Bioperl-l] test test test

test test test test back

O'car Campos C.
Bioinformatics Engineering Student.
University of Talca.
Chile.

2009/12/1 Mark A. Jensen <maj@...>

MAJ
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Re: test test test

2009-12-01T18:59:48Z

test test test test back

O'car Campos C.
Bioinformatics Engineering Student.
University of Talca.
Chile.

2009/12/1 Mark A. Jensen <maj@...>

> MAJ
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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test test test

2009-12-01T18:27:06Z

MAJ
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Fwd: [Utilities-announce] NCBI E-Utility Policy Change

2009-12-01T11:25:03Z

I'll be adjusting the requisite parameters as indicated below. I'm reluctant to include a time-based limit on submissions (NCBI wants a max of 100 requests at peak hours), but it may become necessary if they request it.

chris

Begin forwarded message:

> From: <utilities-announce@...>
> Date: December 1, 2009 12:59:34 PM CST
> To: <utilities-announce@...>
> Subject: [Utilities-announce] NCBI E-Utility Policy Change
> Reply-To: utilities-announce@...
>
> As part of an ongoing effort to ensure efficient access to the Entrez Utilities (E-utilities) by all users, NCBI has decided to change the usage policy for the E-utilities effective June 1, 2010. Effective on June 1, 2010, all E-utility requests, either using standard URLs or SOAP, must contain non-null values for both the &tool and &email parameters. Any E-utility request made after June 1, 2010 that does not contain values for both parameters will return an error explaining that these parameters must be included in E-utility requests.
>
> The value of the &tool parameter should be a URI-safe string that is the name of the software package, script or web page producing the E-utility request.
>
> The value of the &email parameter should be a valid e-mail address for the appropriate contact person or group responsible for maintaining the tool producing the E-utility request.
>
> NCBI uses these parameters to contact users whose use of the E-utilities violates the standard usage policies described athttp://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements. These usage policies are designed to prevent excessive requests from a small group of users from reducing or eliminating the wider community's access to the E-utilities. NCBI will attempt to contact a user at the e-mail address provided in the &email parameter prior to blocking access to the E-utilities.
>
> NCBI realizes that this policy change will require many of our users to change their code. Based on past experience, we anticipate that most of our users should be able to make the necessary changes before the June 1, 2010 deadline. If you have any concerns about making these changes by that date, or if you have any questions about these policies, please contact eutilities@....
>
> Thank you for your understanding and cooperation in helping us continue to deliver a reliable and efficient web service.
>
> _______________________________________________
> Utilities-announce mailing list
> http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce

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Statistics: how to obtain the p value of a T test

2009-12-01T10:05:48Z

Hello everyone,
I'm trying to get the p value of a statistic made with Statistics::TTest
I cannot find this function: I can find if the null hypothesis is rejected
at a certain confidence level, but I cannot make the script show me the
actual p value.
Do you know other scripts that can do that?

Thanks
Emanuele
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Re: [Bug 2937] Strand in fasta35 output does not seem to be parsed

2009-12-01T02:14:40Z

Hi Mick,

Did you try running the test case that you had originally attached to the bug report? Or is the below from different code and a diffrent fasta output file?

In any case, I'll need to look at the fasta35 output file and the parse2.pl you ran in order to reproduce and fix this -- could you please open a new bug report and attach them to it?

Thanks,
Dave

On Nov 30, 2009, at 17:49, michael watson (IAH-C) wrote:

> Hi Dave
>
> Just got round to looking at this.
>
> In bioperl-1.6.0, the strand didn't get parsed, but the module only warned about something:
>
> --------------------- WARNING ---------------------
> MSG: Unrecognized alignment line (1) ' /usr/local/fasta3/bin/fasta35 -n -U -Q -H -A -E 2.0 -C 19 -m 0 -m 9i -O iltv_pre.fasta35 iltv_pre.fasta clusters.fasta'
> ---------------------------------------------------
>
> However, in the bioperl-live I just downloaded, this had turned into a full-on stack trace:
>
> ------------- EXCEPTION -------------
> MSG: Unrecognized alignment line (1) ' /usr/local/fasta3/bin/fasta35 -n -U -Q -H -A -E 2.0 -C 19 -m 0 -m 9i -O iltv_pre.fasta35 iltv_pre.fasta clusters.fasta'
> STACK Bio::SearchIO::fasta::next_result /usr/local/bioperl-live_301109//Bio/SearchIO/fasta.pm:1347
> STACK toplevel parse2.pl:20
> -------------------------------------
>
> I'm not sure if this is even related to the strand issue (I suspect not, but you never know) but something changed between bioperl-1.6.0 and the live trunk I downloaded today to ensure I still can't use the module.
>
> Is this another bug report?
>
> Thanks again for all your help
>
> Mick
>
> -----Original Message-----
> From: Dave Messina [mailto:David.Messina@...]
> Sent: 23 November 2009 17:46
> To: michael watson (IAH-C)
> Subject: Re: [Bug 2937] Strand in fasta35 output does not seem to be parsed
>
> Hi Mick,
>
> Sure thing -- the current build from subversion is packaged up every
> night and available here:
> http://www.bioperl.org/DIST/nightly_builds/
>
> Just grab bioperl-live.tar.gz from there and you'll get the changes.
>
>
> Dave
>
>
>
>
> On Nov 23, 2009, at 6:34 PM, michael watson (IAH-C) wrote:
>
>> Hi Dave
>>
>> Thanks for the hard work.
>>
>> Trying to get the latest updates so I can use this... don't have svn
>> on my server, tried to install it and I don't have python either,
>> which is needed to install it.
>>
>> I face about 3 weeks whilst my IT department sort this out, unless I
>> can access the changes any other way?
>>
>> Thanks
>> Mick
>>
>> -----Original Message-----
>> From: bugzilla-daemon@... [mailto:bugzilla-
>> daemon@...]
>> Sent: 20 November 2009 15:12
>> To: michael watson (IAH-C)
>> Subject: [Bug 2937] Strand in fasta35 output does not seem to be
>> parsed
>>
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2937
>>
>>
>> online@... changed:
>>
>> What |Removed |Added
>> ----------------------------------------------------------------------------
>> Status|NEW |RESOLVED
>> Resolution| |FIXED
>>
>>
>>
>>
>> ------- Comment #7 from online@... 2009-11-20 10:12 EST
>> -------
>> Fixed in r16394.
>>
>> Michael, thanks for the report. Your test cases pass, but please
>> reopen the bug
>> if needed.
>>
>>
>> --
>> Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?
>> tab=email
>> ------- You are receiving this mail because: -------
>> You reported the bug, or are watching the reporter.
>

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Re: How to parse BLAST output - all hits of each queryinnew file

2009-11-30T09:41:44Z

thanks Tim! corrected (I hope) in r16432...
MAJ
----- Original Message -----
From: Tim Koehler
To: Smithies, Russell
Cc: Mark A. Jensen ; bioperl-l@...
Sent: Monday, November 30, 2009 12:23 PM
Subject: Re: [Bioperl-l] How to parse BLAST output - all hits of each queryinnew file

Hello everybody,

thanks a lot for the overwhelming answers! All these codes are different flavors and worked all.

For me the added code works the best. But I think I found a bug in ...Bio/SearchIO/blast.pm.
There the DEFAULT_BLAST_... variable is set to Bio::Search::Writer::HitTableWriter instead of Bio::SearchIO::Writer::HitTableWriter. This variable I changed also to HTMLResultWriter and others.

So again: THANKS for the support!

Cheers,
Tim

#!/usr/bin/perl -w

use strict;

use Bio::Tools::Run::StandAloneBlast;

use Bio::SeqIO;

use Bio::SearchIO;

### add here the writer you want
use Bio::SearchIO::Writer::HitTableWriter;

use Bio::Search::Result::BlastResult;

use Data::Dumper;

my $Seq_in = Bio::SeqIO->new( -file => "/home/koehler/Programs/for_BLAST/1_to_BLAST_two_seq.fasta",

-format => "fasta" );

while ( my $query = $Seq_in->next_seq() ) {

warn "Processing ",$query->id, "\n";

my $factory =

Bio::Tools::Run::StandAloneBlast->new(

program => "blastn",

database => "/home/koehler/Programs/for_BLAST/BLAST_Pipeline/3_BLAST_db",

_READMETHOD => "Blast"

);

my $blast_report = $factory->blastall($query);

sleep 5;

# just write the result we got for this query into a

#new blast-formatted file...named after the id of the query seq...

my $result = $blast_report->next_result;

my $blio = Bio::SearchIO->new( -file => ">".$query->id.".bls", -format => "blast" ) or die $!;

$blio->write_result($result);

# below, just looking at the current blast result

###this does not appear in the output files

while ( my $result = $blast_report->next_result ) {

## $result is a Bio::Search::Result::ResultI compliant object

while ( my $hit = $result->next_hit ) {

## $hit is a Bio::Search::Hit::HitI compliant object

while ( my $hsp = $hit->next_hsp ) {

## $hsp is a Bio::Search::HSP::HSPI compliant object

if ( $hsp->length('total') > 50 ) {

if ( $hsp->percent_identity >= 75 ) {

print "Query= ", $result->query_name,

"Hit= ", $hit->name,

"Length= ", $hsp->length('total'),

"Percent_id= ", $hsp->percent_identity,

"Subject=", $hsp->hit_string, "\n";

}

}

}

}

}

}

On Sun, Nov 29, 2009 at 11:29 PM, Smithies, Russell <Russell.Smithies@...> wrote:

Changed it to a generic result and added a writer and it seems tio work:

foreach my $qid ( keys %hits_by_query ) {

warn "qid = $qid\n";

my $res = Bio::Search::Result::GenericResult->new(-algorithm => "blastn") or die $!;

# print Dumper $res;

foreach my $h ( @{ $hits_by_query{$qid} } ){

warn "adding hit ", $h->name, "\n";

$res->add_hit($h) if defined($h);

}

my $writerhtml = Bio::SearchIO::Writer::HTMLResultWriter->new();

my $blio = Bio::SearchIO->new(-writer => $writerhtml, -file => ">$qid\.bls\.html", -format => "blast" ) or die $!;

$blio->write_result($res);

}

From: Mark A. Jensen [mailto:maj@...]
Sent: Monday, 30 November 2009 10:19 a.m.
To: Smithies, Russell; 'Tim Koehler'

Subject: Re: [Bioperl-l] How to parse BLAST output - all hits of each queryinnew file

My thought here was that since Tim's already going one at a time thru

his queries, my scrap was not really necessary:

use strict;

use Bio::Tools::Run::StandAloneBlast;

use Bio::SeqIO;

use Bio::SearchIO;

use Bio::Search::Result::BlastResult;

use Data::Dumper;

my $Seq_in = Bio::SeqIO->new( -file => "sequences.fasta",

-format => "fasta" );

while ( my $query = $Seq_in->next_seq() ) {

warn "Processing ",$query->id, "\n";

my $factory =

Bio::Tools::Run::StandAloneBlast->new(

program => "blastn",

database => "/data/databases/flatfile/illuminati_blastdata/nt",

_READMETHOD => "Blast"

);

my $blast_report = $factory->blastall($query);

sleep 5;

# just write the result we got for this query into a

#new blast-formatted file...named after the id of the query seq...

my $result = $blast_report->next_result;

my $blio = Bio::SearchIO->new( -file => ">".$query->id.".bls", -format => "blast" ) or die $!;

$blio->write_result($result);

# below, just looking at the current blast result

while ( my $result = $blast_report->next_result ) {

## $result is a Bio::Search::Result::ResultI compliant object

while ( my $hit = $result->next_hit ) {

## $hit is a Bio::Search::Hit::HitI compliant object

while ( my $hsp = $hit->next_hsp ) {

## $hsp is a Bio::Search::HSP::HSPI compliant object

if ( $hsp->length('total') > 50 ) {

if ( $hsp->percent_identity >= 75 ) {

print "Query= ", $result->query_name,

"Hit= ", $hit->name,

"Length= ", $hsp->length('total'),

"Percent_id= ", $hsp->percent_identity,

"Subject=", $hsp->hit_string, "\n";

}

}

}

}

}

}

----- Original Message -----

From: Smithies, Russell

To: 'Tim Koehler' ; 'maj@...'

Sent: Sunday, November 29, 2009 3:58 PM

Subject: RE: [Bioperl-l] How to parse BLAST output - all hits of each queryinnew file

Hi Tim

With various people writing the “howtos” and other docs, the examples are bound to have differing names for the variables used but as long as you’re consistent, it should all fit together.

I think I’ve almost got your code working, just getting errors from Bio::Search::Result::BlastResult which I’m not entirely sure how to use. Perhaps Mark can get this bit going?

--Russell

===============================

use strict;

use Bio::Tools::Run::StandAloneBlast;

use Bio::SeqIO;

use Bio::SearchIO;

use Bio::Search::Result::BlastResult;

use Data::Dumper;

my $Seq_in = Bio::SeqIO->new( -file => "sequences.fasta",

-format => "fasta" );

while ( my $query = $Seq_in->next_seq() ) {

warn "Processing ",$query->id, "\n";

my $factory =

Bio::Tools::Run::StandAloneBlast->new(

program => "blastn",

database => "/data/databases/flatfile/illuminati_blastdata/nt",

_READMETHOD => "Blast"

);

my $blast_report = $factory->blastall($query);

sleep 5;

my %hits_by_query;

while ( my $result = $blast_report->next_result ) {

foreach my $hit ( $result->hits ) {

warn "Pushed a hit for ",$hit->name, "\n";

push( @{ $hits_by_query{ $hit->name } }, $hit );

}

}

foreach my $qid ( keys %hits_by_query ) {

warn "qid = $qid\n";

my $res = Bio::Search::Result::BlastResult->new() or die $!;

print Dumper $res;

foreach my $h ( @{ $hits_by_query{$qid} } ){

warn "adding hit ", $h->name, "\n";

$res->add_hit($h) if defined($h);

}

my $blio = Bio::SearchIO->new( -file => ">$qid\.bls", -format => "blast" ) or die $!;

$blio->write_result($res);

}

while ( my $result = $blast_report->next_result ) {

## $result is a Bio::Search::Result::ResultI compliant object

while ( my $hit = $result->next_hit ) {

## $hit is a Bio::Search::Hit::HitI compliant object

while ( my $hsp = $hit->next_hsp ) {

## $hsp is a Bio::Search::HSP::HSPI compliant object

if ( $hsp->length('total') > 50 ) {

if ( $hsp->percent_identity >= 75 ) {

print "Query= ", $result->query_name,

"Hit= ", $hit->name,

"Length= ", $hsp->length('total'),

"Percent_id= ", $hsp->percent_identity,

"Subject=", $hsp->hit_string, "\n";

}

}

}

}

}

}

===============================

From: Tim Koehler [mailto:timbourine81@...]
Sent: Friday, 27 November 2009 10:24 p.m.
To: Smithies, Russell; maj@...
Subject: Re: [Bioperl-l] How to parse BLAST output - all hits of each queryinnew file

Hey guys,

please, do not get me wrong that I wanted to put the workload on you. So far I only found the HowTo's but in there in some way the language changed with time (e.g. $in to $Seq_in) or some things I simply could not find.
Now I got a tip where else to search: the scrapbook and deobfuscator.

I immediately will have a look at that.

This is the first time for me touching linux / perl commands; that's why I thought after several days of trial and many errors ;) asking the mailinglist.

I was very happy about your fast answers!

Cheers and a nice weekend,

Tim

On Thu, Nov 26, 2009 at 5:02 PM, Tim Koehler <timbourine81@...> wrote:

ups, sent too early...

Hey Mark,

thanks for the answer. But I am still struggling, especially where to put in your code.

Here ist the code I have, so far:

#!/usr/bin/perl -w

### should I put your code here as push is a perl command?

my %hits_by_query;
for ($result->hits) {

### I inserted a comma after name}}; if there is no comma, there was the error: Scalar found where operator expected at 12_BLAST_two_sequence_each_query_one_file.PL line7, near "} $hit"
### (Missing operator before $hit?)
###Useless use of push with no values at 12_BLAST_two_sequence_each_query_one_file.PL line 7.
###syntax error at 12_BLAST_two_sequence_each_query_one_file.PL line 7, near "} $hit"
###BEGIN not safe after errors--compilation aborted at 12_BLAST_two_sequence_each_query_one_file.PL line 13.

push @{$hits_by_query{$hit->name}}, $hit;

###here, every time this terror appears: Name "main::result" used only once: possible typo at 12_BLAST_two_sequence_each_query_one_file.PL line 5.
###error: Can't call method "hits" on an undefined value at 12_BLAST_two_sequence_each_query_one_file.PL line 5.

}

use strict;
use Bio::Tools::Run::StandAloneBlast;
use Bio::SeqIO;
use Bio::SearchIO;

use Bio::Search::Result::BlastResult;

my $Seq_in = Bio::SeqIO->new (
-file => "/home/koehler/Programs/for_BLAST/BLAST_Pipeline/1_to_BLAST_two_seq.fasta",
-format => 'fasta'
);
while (my $query = $Seq_in->next_seq()) {

my $factory = Bio::Tools::Run::StandAloneBlast->new(

'program' => 'blastn',
'database' => '/home/koehler/Programs/for_BLAST/BLAST_Pipeline/3_BLAST_db',
_READMETHOD => "Blast"
);

my $blast_report = $factory->blastall($query);

### Should I need to use a module? are the commands here at the right position? errors, e.g., Global symbol "$hit" requires explicit package name
#my %hits_by_query;
#for ($result->hits) {
### inserted comma after name}}
# push @{$hits_by_query{$hit->name}}, $hit;
#}

foreach my $qid ( keys %hits_by_query ) {
my $result = Bio::Search::Result::BlastResult->new();
$result->add_hit($_) for ( @{$hits_by_query{$qid}} );
my $blio = Bio::SearchIO->new( -file => ">$qid\.bls", -format=>'blast' );
$blio->write_result($result);
}

###where are the files stored? what is their name. Sorry, but I cannot get behind that :(

while( my $result = $blast_report->next_result ) {
## $result is a Bio::Search::Result::ResultI compliant object

while( my $hit = $result->next_hit ) {

## $hit is a Bio::Search::Hit::HitI compliant object

while( my $hsp = $hit->next_hsp ) {

## $hsp is a Bio::Search::HSP::HSPI compliant object
if( $hsp->length('total') > 50 ) {
if ( $hsp->percent_identity >= 75 ) {
print "Query= ", $result->query_name,
"Hit= ", $hit->name,
"Length= ", $hsp->length('total'),
"Percent_id= ", $hsp->percent_identity,
"Subject=", $hsp->hit_string,"\n";
}
}
}
}
}
}

Again, a big thanks in advance :)

All the best,

Tim

On Thu, Nov 26, 2009 at 4:52 PM, Tim <timbourine81@...> wrote:

Hey Mark,

thanks for the answer

On 25.11.2009 20:21, Mark A. Jensen wrote:
> whoops: change the following line:
> my $blio = Bio::SearchIO->new( -file => $qid.".bls", -format=>'blast' );
>
> to
>
> my $blio = Bio::SearchIO->new( -file => ">$qid\.bls", -format=>'blast' );
>
> (I always forget that...)
> MAJ
>
> ----- Original Message ----- From: "Mark A. Jensen" <maj@...>
> To: "Tim" <timbourine81@...>; <bioperl-l@...>
> Sent: Wednesday, November 25, 2009 1:20 PM
> Subject: Re: [Bioperl-l] How to parse BLAST output - all hits of each
> queryinnew file
>
>
>> hey Tim--
>>
>> Sound like you need to go about collecting your queries inside out:
>>
>> my %hits_by_query;
>> for ($result->hits) {
>> push @{$hits_by_query{$hit->name}} $hit;
>> }
>>
>> I believe now each hash element, keyed by the query name, will contain
>> an arrayref to the set of hits assoc with that query.
>>> From here, I believe
>>
>> use Bio::Search::Result::BlastResult;
>> use Bio::SearchIO;
>>
>> foreach my $qid ( keys %hits_by_query ) {
>> my $result = Bio::Search::Result::BlastResult->new();
>> $result->add_hit($_) for ( @{$hits_by_query{$qid}} );
>> my $blio = Bio::SearchIO->new( -file => $qid.".bls", -format=>'blast' );
>> $blio->write_result($result);
>> }
>>
>> will do what you want.
>>
>> hope this helps -
>> Mark
>>
>> ----- Original Message ----- From: "Tim" <timbourine81@...>
>> To: <bioperl-l@...>
>> Sent: Wednesday, November 25, 2009 12:40 PM
>> Subject: [Bioperl-l] How to parse BLAST output - all hits of each
>> query innew file
>>
>>
>>> Dear bioperl users,
>>>
>>> I am a real newbie and have - maybe a very trivial - question.
>>>
>>> I searched the mailing list archive and many howtos but I have not found
>>> a concrete answer to my problem. So hopefully you can help me :)
>>>
>>> Background: I use the latest Bioperl version (installed it two weeks
>>> before).
>>> When I use Bio::Tools::Run::StandAloneBlast to BLAST one fasta file
>>> including different sequences, I get a BLAST output with many queries
>>> each having several hits / sbjcts.
>>>
>>> My problem is how to parse *all* hits of *one* query into a single new
>>> file. And this for all the queries I have in my BLAST output file.
>>>
>>> Or is it better the other way round; first to make fasta files with only
>>> single sequences inside and BLAST each file? But how can I automize that
>>> using Bioperl?
>>>
>>> I tried Bio::SearchIO but can only parse all queries and their
>>> respective hits in only one file...
>>> I think iteration is also necessary here, but I do not really know how
>>> to include that into Bio::SearchIO.
>>> Or do I have to use Module:Bio::Index::Blast?
>>>
>>> I can index a file (see below), but I have no idea what comes next...
>>>
>>> ###How I index a file...
>>>
>>> #!/usr/bin/perl -w
>>>
>>> $ENV{BIOPERL_INDEX_TYPE} = "SDBM_File";
>>>
>>> use Bio::Index::Fasta;
>>>
>>>
>>> $file_name = "8_to_BLAST_two_seq_index.fasta";
>>> $id = "48882";
>>> $inx = Bio::Index::Fasta->new (-filename => $file_name . ".idx",
>>> -write_flag => 1);
>>> $inx->make_index($file_name);
>>>
>>>
>>> Hopefully, you can give me at least hints what to look for.
>>>
>>> A big THANKS in advance!
>>>
>>> Cheers,
>>>
>>> Tim
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l@...
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@...
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>

Tim Köhler
MPI for Terrestrial Microbiology
Karl-von-Frisch-Straße
D-35043 Marburg / Germany

Email: koehlerd@...
Phone: +49 6421 178-740
Fax: +49 6421 178-999

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Re: How to parse BLAST output - all hits of each queryinnew file

2009-11-30T09:23:58Z

Hello everybody,

thanks a lot for the overwhelming answers! All these codes are different
flavors and worked all.

For me the added code works the best. But I think I found a bug in
...Bio/SearchIO/blast.pm.
There the DEFAULT_BLAST_... variable is set to
Bio::Search::Writer::HitTableWriter instead of
Bio::SearchIO::Writer::HitTableWriter. This variable I changed also to
HTMLResultWriter
and others.

So again: THANKS for the support!

Cheers,
Tim

#!/usr/bin/perl -w

use strict;

use Bio::Tools::Run::StandAloneBlast;

use Bio::SeqIO;

use Bio::SearchIO;

### add here the writer you want
use Bio::SearchIO::Writer::HitTableWriter;

use Bio::Search::Result::BlastResult;

use Data::Dumper;

my $Seq_in = Bio::SeqIO->new( -file =>
"/home/koehler/Programs/for_BLAST/1_to_BLAST_two_seq.fasta",

-format => "fasta" );

while ( my $query = $Seq_in->next_seq() ) {

warn "Processing ",$query->id, "\n";

my $factory =

Bio::Tools::Run::StandAloneBlast->new(

program => "blastn",

database =>
"/home/koehler/Programs/for_BLAST/BLAST_Pipeline/3_BLAST_db",

_READMETHOD => "Blast"

);

my $blast_report = $factory->blastall($query);

sleep 5;

# just write the result we got for this query into a

#new blast-formatted file...named after the id of the query seq...

my $result = $blast_report->next_result;

my $blio = Bio::SearchIO->new( -file => ">".$query->id.".bls", -format =>
"blast" ) or die $!;

$blio->write_result($result);

# below, just looking at the current blast result

###this does not appear in the output files

while ( my $result = $blast_report->next_result ) {

## $result is a Bio::Search::Result::ResultI compliant object

while ( my $hit = $result->next_hit ) {

## $hit is a Bio::Search::Hit::HitI compliant object

while ( my $hsp = $hit->next_hsp ) {

## $hsp is a Bio::Search::HSP::HSPI compliant object

if ( $hsp->length('total') > 50 ) {

if ( $hsp->percent_identity >= 75 ) {

print "Query= ", $result->query_name,

"Hit= ", $hit->name,

"Length= ", $hsp->length('total'),

"Percent_id= ", $hsp->percent_identity,

"Subject=", $hsp->hit_string, "\n";

}

}

}

}

}

}

On Sun, Nov 29, 2009 at 11:29 PM, Smithies, Russell <
Russell.Smithies@...> wrote:

> Changed it to a generic result and added a writer and it seems tio work:
>
>
>
> foreach my $qid ( keys %hits_by_query ) {
>
> warn "qid = $qid\n";
>
> my $res = Bio::Search::Result::GenericResult->new(-algorithm =>
> "blastn") or die $!;
>
> # print Dumper $res;
>
> foreach my $h ( @{ $hits_by_query{$qid} } ){
>
> warn "adding hit ", $h->name, "\n";
>
> $res->add_hit($h) if defined($h);
>
> }
>
> my $writerhtml = Bio::SearchIO::Writer::HTMLResultWriter->new();
>
> my $blio = Bio::SearchIO->new(-writer => $writerhtml, -file =>
> ">$qid\.bls\.html", -format => "blast" ) or die $!;
>
> $blio->write_result($res);
>
> }
>
>
>
>
>
> *From:* Mark A. Jensen [mailto:maj@...]
> *Sent:* Monday, 30 November 2009 10:19 a.m.
> *To:* Smithies, Russell; 'Tim Koehler'
>
> *Subject:* Re: [Bioperl-l] How to parse BLAST output - all hits of each
> queryinnew file
>
>
>
> My thought here was that since Tim's already going one at a time thru
>
> his queries, my scrap was not really necessary:
>
>
>
> use strict;
>
> use Bio::Tools::Run::StandAloneBlast;
>
> use Bio::SeqIO;
>
> use Bio::SearchIO;
>
> use Bio::Search::Result::BlastResult;
>
>
>
> use Data::Dumper;
>
>
>
> my $Seq_in = Bio::SeqIO->new( -file => "sequences.fasta",
>
> -format => "fasta" );
>
>
>
> while ( my $query = $Seq_in->next_seq() ) {
>
> warn "Processing ",$query->id, "\n";
>
> my $factory =
>
> Bio::Tools::Run::StandAloneBlast->new(
>
> program => "blastn",
>
> database =>
> "/data/databases/flatfile/illuminati_blastdata/nt",
>
> _READMETHOD => "Blast"
>
> );
>
>
>
> my $blast_report = $factory->blastall($query);
>
> sleep 5;
>
>
>
> # just write the result we got for this query into a
>
> #new blast-formatted file...named after the id of the query seq...
>
> my $result = $blast_report->next_result;
>
> my $blio = Bio::SearchIO->new( -file => ">".$query->id.".bls", -format =>
> "blast" ) or die $!;
>
> $blio->write_result($result);
>
>
>
> # below, just looking at the current blast result
>
> while ( my $result = $blast_report->next_result ) {
>
> ## $result is a Bio::Search::Result::ResultI compliant object
>
> while ( my $hit = $result->next_hit ) {
>
> ## $hit is a Bio::Search::Hit::HitI compliant object
>
> while ( my $hsp = $hit->next_hsp ) {
>
> ## $hsp is a Bio::Search::HSP::HSPI compliant object
>
> if ( $hsp->length('total') > 50 ) {
>
> if ( $hsp->percent_identity >= 75 ) {
>
> print "Query= ", $result->query_name,
>
> "Hit= ", $hit->name,
>
> "Length= ", $hsp->length('total'),
>
> "Percent_id= ", $hsp->percent_identity,
>
> "Subject=", $hsp->hit_string, "\n";
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> ----- Original Message -----
>
> *From:* Smithies, Russell <Russell.Smithies@...>
>
> *To:* 'Tim Koehler' <timbourine81@...> ; 'maj@...'<%27maj@...%27>
>
> *Sent:* Sunday, November 29, 2009 3:58 PM
>
> *Subject:* RE: [Bioperl-l] How to parse BLAST output - all hits of each
> queryinnew file
>
>
>
> Hi Tim
>
> With various people writing the “howtos” and other docs, the examples are
> bound to have differing names for the variables used but as long as you’re
> consistent, it should all fit together.
>
>
>
> I think I’ve almost got your code working, just getting errors from
> Bio::Search::Result::BlastResult which I’m not entirely sure how to use.
> Perhaps Mark can get this bit going?
>
>
>
> --Russell
>
> ===============================
>
>
>
> use strict;
>
> use Bio::Tools::Run::StandAloneBlast;
>
> use Bio::SeqIO;
>
> use Bio::SearchIO;
>
> use Bio::Search::Result::BlastResult;
>
>
>
> use Data::Dumper;
>
>
>
> my $Seq_in = Bio::SeqIO->new( -file => "sequences.fasta",
>
> -format => "fasta" );
>
>
>
> while ( my $query = $Seq_in->next_seq() ) {
>
> warn "Processing ",$query->id, "\n";
>
> my $factory =
>
> Bio::Tools::Run::StandAloneBlast->new(
>
> program => "blastn",
>
> database =>
> "/data/databases/flatfile/illuminati_blastdata/nt",
>
> _READMETHOD => "Blast"
>
> );
>
>
>
> my $blast_report = $factory->blastall($query);
>
> sleep 5;
>
>
>
>
>
> my %hits_by_query;
>
>
>
> while ( my $result = $blast_report->next_result ) {
>
> foreach my $hit ( $result->hits ) {
>
> warn "Pushed a hit for ",$hit->name, "\n";
>
> push( @{ $hits_by_query{ $hit->name } }, $hit );
>
> }
>
> }
>
>
>
> foreach my $qid ( keys %hits_by_query ) {
>
> warn "qid = $qid\n";
>
> my $res = Bio::Search::Result::BlastResult->new() or die $!;
>
> print Dumper $res;
>
> foreach my $h ( @{ $hits_by_query{$qid} } ){
>
> warn "adding hit ", $h->name, "\n";
>
> $res->add_hit($h) if defined($h);
>
> }
>
> my $blio = Bio::SearchIO->new( -file => ">$qid\.bls", -format =>
> "blast" ) or die $!;
>
> $blio->write_result($res);
>
> }
>
>
>
> while ( my $result = $blast_report->next_result ) {
>
> ## $result is a Bio::Search::Result::ResultI compliant object
>
> while ( my $hit = $result->next_hit ) {
>
> ## $hit is a Bio::Search::Hit::HitI compliant object
>
> while ( my $hsp = $hit->next_hsp ) {
>
> ## $hsp is a Bio::Search::HSP::HSPI compliant object
>
> if ( $hsp->length('total') > 50 ) {
>
> if ( $hsp->percent_identity >= 75 ) {
>
> print "Query= ", $result->query_name,
>
> "Hit= ", $hit->name,
>
> "Length= ", $hsp->length('total'),
>
> "Percent_id= ", $hsp->percent_identity,
>
> "Subject=", $hsp->hit_string, "\n";
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> ===============================
>
>
>
> *From:* Tim Koehler [mailto:timbourine81@...]
> *Sent:* Friday, 27 November 2009 10:24 p.m.
> *To:* Smithies, Russell; maj@...
> *Subject:* Re: [Bioperl-l] How to parse BLAST output - all hits of each
> queryinnew file
>
>
>
> Hey guys,
>
> please, do not get me wrong that I wanted to put the workload on you. So
> far I only found the HowTo's but in there in some way the language changed
> with time (e.g. $in to $Seq_in) or some things I simply could not find.
> Now I got a tip where else to search: the scrapbook and deobfuscator.
>
> I immediately will have a look at that.
>
> This is the first time for me touching linux / perl commands; that's why I
> thought after several days of trial and many errors ;) asking the
> mailinglist.
>
> I was very happy about your fast answers!
>
> Cheers and a nice weekend,
>
> Tim
>
> On Thu, Nov 26, 2009 at 5:02 PM, Tim Koehler <timbourine81@...>
> wrote:
>
> ups, sent too early...
>
> Hey Mark,
>
> thanks for the answer. But I am still struggling, especially where to put
> in your code.
>
> Here ist the code I have, so far:
>
> #!/usr/bin/perl -w
>
> ### should I put your code here as push is a perl command?
>
>
> my %hits_by_query;
> for ($result->hits) {
>
> ### I inserted a comma after name}}; if there is no comma, there was the
> error: Scalar found where operator expected at
> 12_BLAST_two_sequence_each_query_one_file.PL line7, near "} $hit"
> ### (Missing operator before $hit?)
> ###Useless use of push with no values at
> 12_BLAST_two_sequence_each_query_one_file.PL line 7.
> ###syntax error at 12_BLAST_two_sequence_each_query_one_file.PL line 7,
> near "} $hit"
> ###BEGIN not safe after errors--compilation aborted at
> 12_BLAST_two_sequence_each_query_one_file.PL line 13.
>
>
> push @{$hits_by_query{$hit->name}}, $hit;
>
> ###here, every time this terror appears: Name "main::result" used only
> once: possible typo at 12_BLAST_two_sequence_each_query_one_file.PL line 5.
> ###error: Can't call method "hits" on an undefined value at
> 12_BLAST_two_sequence_each_query_one_file.PL line 5.
>
>
> }
>
>
> use strict;
> use Bio::Tools::Run::StandAloneBlast;
> use Bio::SeqIO;
> use Bio::SearchIO;
>
> use Bio::Search::Result::BlastResult;
>
> my $Seq_in = Bio::SeqIO->new (
> -file =>
> "/home/koehler/Programs/for_BLAST/BLAST_Pipeline/1_to_BLAST_two_seq.fasta",
> -format => 'fasta'
> );
> while (my $query = $Seq_in->next_seq()) {
>
>
> my $factory = Bio::Tools::Run::StandAloneBlast->new(
>
> 'program' => 'blastn',
> 'database' => '/home/koehler/Programs/for_BLAST/BLAST_Pipeline/3_BLAST_db',
> _READMETHOD => "Blast"
> );
>
> my $blast_report = $factory->blastall($query);
>
> ### Should I need to use a module? are the commands here at the right
> position? errors, e.g., Global symbol "$hit" requires explicit package name
> #my %hits_by_query;
> #for ($result->hits) {
> ### inserted comma after name}}
> # push @{$hits_by_query{$hit->name}}, $hit;
> #}
>
>
>
> foreach my $qid ( keys %hits_by_query ) {
> my $result = Bio::Search::Result::BlastResult->new();
> $result->add_hit($_) for ( @{$hits_by_query{$qid}} );
> my $blio = Bio::SearchIO->new( -file => ">$qid\.bls", -format=>'blast' );
> $blio->write_result($result);
> }
>
> ###where are the files stored? what is their name. Sorry, but I cannot get
> behind that :(
>
> while( my $result = $blast_report->next_result ) {
> ## $result is a Bio::Search::Result::ResultI compliant object
>
>
> while( my $hit = $result->next_hit ) {
>
> ## $hit is a Bio::Search::Hit::HitI compliant object
>
>
> while( my $hsp = $hit->next_hsp ) {
>
> ## $hsp is a Bio::Search::HSP::HSPI compliant object
> if( $hsp->length('total') > 50 ) {
> if ( $hsp->percent_identity >= 75 ) {
> print "Query= ", $result->query_name,
> "Hit= ", $hit->name,
> "Length= ", $hsp->length('total'),
> "Percent_id= ", $hsp->percent_identity,
> "Subject=", $hsp->hit_string,"\n";
> }
> }
> }
> }
> }
> }
>
> Again, a big thanks in advance :)
>
> All the best,
>
> Tim
>
> On Thu, Nov 26, 2009 at 4:52 PM, Tim <timbourine81@...> wrote:
>
> Hey Mark,
>
> thanks for the answer
>
>
>
>
> On 25.11.2009 20:21, Mark A. Jensen wrote:
> > whoops: change the following line:
> > my $blio = Bio::SearchIO->new( -file => $qid.".bls", -format=>'blast' );
> >
> > to
> >
> > my $blio = Bio::SearchIO->new( -file => ">$qid\.bls", -format=>'blast' );
> >
> > (I always forget that...)
> > MAJ
> >
> > ----- Original Message ----- From: "Mark A. Jensen" <maj@...>
> > To: "Tim" <timbourine81@...>; <bioperl-l@...>
> > Sent: Wednesday, November 25, 2009 1:20 PM
> > Subject: Re: [Bioperl-l] How to parse BLAST output - all hits of each
> > queryinnew file
> >
> >
> >> hey Tim--
> >>
> >> Sound like you need to go about collecting your queries inside out:
> >>
> >> my %hits_by_query;
> >> for ($result->hits) {
> >> push @{$hits_by_query{$hit->name}} $hit;
> >> }
> >>
> >> I believe now each hash element, keyed by the query name, will contain
> >> an arrayref to the set of hits assoc with that query.
> >>> From here, I believe
> >>
> >> use Bio::Search::Result::BlastResult;
> >> use Bio::SearchIO;
> >>
> >> foreach my $qid ( keys %hits_by_query ) {
> >> my $result = Bio::Search::Result::BlastResult->new();
> >> $result->add_hit($_) for ( @{$hits_by_query{$qid}} );
> >> my $blio = Bio::SearchIO->new( -file => $qid.".bls", -format=>'blast'
> );
> >> $blio->write_result($result);
> >> }
> >>
> >> will do what you want.
> >>
> >> hope this helps -
> >> Mark
> >>
> >> ----- Original Message ----- From: "Tim" <timbourine81@...>
> >> To: <bioperl-l@...>
> >> Sent: Wednesday, November 25, 2009 12:40 PM
> >> Subject: [Bioperl-l] How to parse BLAST output - all hits of each
> >> query innew file
> >>
> >>
> >>> Dear bioperl users,
> >>>
> >>> I am a real newbie and have - maybe a very trivial - question.
> >>>
> >>> I searched the mailing list archive and many howtos but I have not
> found
> >>> a concrete answer to my problem. So hopefully you can help me :)
> >>>
> >>> Background: I use the latest Bioperl version (installed it two weeks
> >>> before).
> >>> When I use Bio::Tools::Run::StandAloneBlast to BLAST one fasta file
> >>> including different sequences, I get a BLAST output with many queries
> >>> each having several hits / sbjcts.
> >>>
> >>> My problem is how to parse *all* hits of *one* query into a single new
> >>> file. And this for all the queries I have in my BLAST output file.
> >>>
> >>> Or is it better the other way round; first to make fasta files with
> only
> >>> single sequences inside and BLAST each file? But how can I automize
> that
> >>> using Bioperl?
> >>>
> >>> I tried Bio::SearchIO but can only parse all queries and their
> >>> respective hits in only one file...
> >>> I think iteration is also necessary here, but I do not really know how
> >>> to include that into Bio::SearchIO.
> >>> Or do I have to use Module:Bio::Index::Blast?
> >>>
> >>> I can index a file (see below), but I have no idea what comes next...
> >>>
> >>> ###How I index a file...
> >>>
> >>> #!/usr/bin/perl -w
> >>>
> >>> $ENV{BIOPERL_INDEX_TYPE} = "SDBM_File";
> >>>
> >>> use Bio::Index::Fasta;
> >>>
> >>>
> >>> $file_name = "8_to_BLAST_two_seq_index.fasta";
> >>> $id = "48882";
> >>> $inx = Bio::Index::Fasta->new (-filename => $file_name . ".idx",
> >>> -write_flag => 1);
> >>> $inx->make_index($file_name);
> >>>
> >>>
> >>> Hopefully, you can give me at least hints what to look for.
> >>>
> >>> A big THANKS in advance!
> >>>
> >>> Cheers,
> >>>
> >>> Tim
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l@...
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l@...
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >
>
> Tim Köhler
> MPI for Terrestrial Microbiology
> Karl-von-Frisch-Straße
> D-35043 Marburg / Germany
>
> Email: koehlerd@...
> Phone: +49 6421 178-740
> Fax: +49 6421 178-999
>
>
>
>
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