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extracting CDS location from Genbank

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	extracting CDS location from Genbank by Captainrave :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Help. I'm very new to perl and bioperl. Basically I need to extract the location of each CDS in a genbank entry e.g.103...120 and export them to an output file as a list. How would I do this? Your help would be much appreciated!
	Re: extracting CDS location from Genbank by michael watson (IAH-C) :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message >From the SeqIO howto: #!/bin/perl use strict; use Bio::SeqIO; my $file = shift; # get the file name, somehow my $seqio_object = Bio::SeqIO->new(-file => $file); my $seq_object = $seqio_object->next_seq; >From the Feature HOWTO: for my $feat_object ($seq_object->get_SeqFeatures) { print "primary tag: ", $feat_object->primary_tag, "\n"; for my $tag ($feat_object->get_all_tags) { print " tag: ", $tag, "\n"; for my $value ($feat_object->get_tag_values($tag)) { print " value: ", $value, "\n"; } } } Surely you could have fouind that yourself? ;0 -----Original Message----- From: bioperl-l-bounces@... [mailto:bioperl-l-bounces@...] On Behalf Of Captainrave Sent: 04 December 2007 11:05 To: Bioperl-l@... Subject: [Bioperl-l] extracting CDS location from Genbank Help. I'm very new to perl and bioperl. Basically I need to extract the location of each CDS in a genbank entry e.g.103...120 and export them to an output file as a list. How would I do this? Your help would be much appreciated! -- View this message in context: http://www.nabble.com/extracting-CDS-location-from-Genbank-tf4942483.htm l#a14148723 Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. _______________________________________________ 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
	Re: extracting CDS location from Genbank by Captainrave :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Yes but actually implementing it is another story. I get an error: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: file argument provided, but with an undefined value STACK: Error::throw STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:359 STACK: Bio::SeqIO::new C:/Perl/site/lib/Bio/SeqIO.pm:359 STACK: test3.pl:7 ----------------------------------------------------------- Basically because I dont understand the code well enough. For example, how do I tell it which input file to read? I know this might sound stupid, but I dont understand the Biowiki very well!
	Re: extracting CDS location from Genbank by michael watson (IAH-C) :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Post the script that produces that error, and your file's location -----Original Message----- From: bioperl-l-bounces@... [mailto:bioperl-l-bounces@...] On Behalf Of Captainrave Sent: 04 December 2007 15:07 To: Bioperl-l@... Subject: Re: [Bioperl-l] extracting CDS location from Genbank Yes but actually implementing it is another story. I get an error: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: file argument provided, but with an undefined value STACK: Error::throw STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:359 STACK: Bio::SeqIO::new C:/Perl/site/lib/Bio/SeqIO.pm:359 STACK: test3.pl:7 ----------------------------------------------------------- Basically because I dont understand the code well enough. For example, how do I tell it which input file to read? I know this might sound stupid, but I dont understand the Biowiki very well! -- View this message in context: http://www.nabble.com/extracting-CDS-location-from-Genbank-tf4942483.htm l#a14152264 Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. _______________________________________________ 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
	Re: extracting CDS location from Genbank by Sendu Bala-2 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Captainrave wrote: > Yes but actually implementing it is another story. > > I get an error: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: file argument provided, but with an undefined value > STACK: Error::throw > STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:359 > STACK: Bio::SeqIO::new C:/Perl/site/lib/Bio/SeqIO.pm:359 > STACK: test3.pl:7 > ----------------------------------------------------------- The best way to get help is to give us your script and the error message, and the command you used to run your script. The less you know, the more you should give us (ie. don't edit anything out). _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l
	Re: extracting CDS location from Genbank by Captainrave :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message #!/bin/perl use strict; use Bio::SeqIO; my $file = shift; # get the file name, somehow my $seqio_object = Bio::SeqIO->new(-file => $file); my $seq_object = $seqio_object->next_seq; for my $feat_object ($seq_object->get_SeqFeatures) { print "primary tag: ", $feat_object->primary_tag, "\n"; for my $tag ($feat_object->get_all_tags) { print " tag: ", $tag, "\n"; for my $value ($feat_object->get_tag_values($tag)) { print " value: ", $value, "\n"; } } } exit; The file is on the same folder. But how do I tell it to use this file? michael watson (IAH-C) wrote: Post the script that produces that error, and your file's location -----Original Message----- From: bioperl-l-bounces@lists.open-bio.org [mailto:bioperl-l-bounces@lists.open-bio.org] On Behalf Of Captainrave Sent: 04 December 2007 15:07 To: Bioperl-l@lists.open-bio.org Subject: Re: [Bioperl-l] extracting CDS location from Genbank Yes but actually implementing it is another story. I get an error: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: file argument provided, but with an undefined value STACK: Error::throw STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:359 STACK: Bio::SeqIO::new C:/Perl/site/lib/Bio/SeqIO.pm:359 STACK: test3.pl:7 ----------------------------------------------------------- Basically because I dont understand the code well enough. For example, how do I tell it which input file to read? I know this might sound stupid, but I dont understand the Biowiki very well! -- View this message in context: http://www.nabble.com/extracting-CDS-location-from-Genbank-tf4942483.htm l#a14152264 Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. _______________________________________________ Bioperl-l mailing list Bioperl-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l
	Re: extracting CDS location from Genbank by michael watson (IAH-C) :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Same script as below, but try: my $file = 'C:\path\to\my\filename.gbk'; -----Original Message----- From: bioperl-l-bounces@... [mailto:bioperl-l-bounces@...] On Behalf Of Captainrave Sent: 04 December 2007 15:42 To: Bioperl-l@... Subject: Re: [Bioperl-l] extracting CDS location from Genbank #!/bin/perl use strict; use Bio::SeqIO; my $file = shift; # get the file name, somehow my $seqio_object = Bio::SeqIO->new(-file => $file); my $seq_object = $seqio_object->next_seq; for my $feat_object ($seq_object->get_SeqFeatures) { print "primary tag: ", $feat_object->primary_tag, "\n"; for my $tag ($feat_object->get_all_tags) { print " tag: ", $tag, "\n"; for my $value ($feat_object->get_tag_values($tag)) { print " value: ", $value, "\n"; } } } exit; The file is on the same folder. But how do I tell it to use this file? michael watson (IAH-C) wrote: > > Post the script that produces that error, and your file's location > > -----Original Message----- > From: bioperl-l-bounces@... > [mailto:bioperl-l-bounces@...] On Behalf Of Captainrave > Sent: 04 December 2007 15:07 > To: Bioperl-l@... > Subject: Re: [Bioperl-l] extracting CDS location from Genbank > > > Yes but actually implementing it is another story. > > I get an error: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: file argument provided, but with an undefined value > STACK: Error::throw > STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:359 > STACK: Bio::SeqIO::new C:/Perl/site/lib/Bio/SeqIO.pm:359 > STACK: test3.pl:7 > ----------------------------------------------------------- > > Basically because I dont understand the code well enough. For example, > how > do I tell it which input file to read? I know this might sound stupid, > but I > dont understand the Biowiki very well! > > -- > View this message in context: > http://www.nabble.com/extracting-CDS-location-from-Genbank-tf4942483.htm > l#a14152264 > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > 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 > > -- View this message in context: http://www.nabble.com/extracting-CDS-location-from-Genbank-tf4942483.htm l#a14152907 Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. _______________________________________________ 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
	Re: extracting CDS location from Genbank by Chris Fields :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message The 'my $file = shift;' is a perl idiom. The built-in 'shift' used implicitly in this way uses @ARGV (from command line); the file would the be passed as the first arg when running the script: get_features.pl myfile.gb This should work for any OS. Personally, I use something like the following to indicate how the script is used in case a file is never entered: my $USAGE = <<END_USE; USAGE: get_features.pl <file> Perl script to grab features from a GenBank file and print to a table END_USE my $file = shift \|\| die $USAGE; chris On Dec 4, 2007, at 9:41 AM, Captainrave wrote: > > #!/bin/perl > > use strict; > use Bio::SeqIO; > my $file = shift; # get the file name, somehow > my $seqio_object = Bio::SeqIO->new(-file => $file); > my $seq_object = $seqio_object->next_seq; > > for my $feat_object ($seq_object->get_SeqFeatures) { > print "primary tag: ", $feat_object->primary_tag, "\n"; > for my $tag ($feat_object->get_all_tags) { > print " tag: ", $tag, "\n"; > for my $value ($feat_object->get_tag_values($tag)) { > > print " value: ", $value, "\n"; > } > } > } > > exit; > > The file is on the same folder. But how do I tell it to use this > file? > > > > michael watson (IAH-C) wrote: >> >> Post the script that produces that error, and your file's location >> >> -----Original Message----- >> From: bioperl-l-bounces@... >> [mailto:bioperl-l-bounces@...] On Behalf Of >> Captainrave >> Sent: 04 December 2007 15:07 >> To: Bioperl-l@... >> Subject: Re: [Bioperl-l] extracting CDS location from Genbank >> >> >> Yes but actually implementing it is another story. >> >> I get an error: >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: file argument provided, but with an undefined value >> STACK: Error::throw >> STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:359 >> STACK: Bio::SeqIO::new C:/Perl/site/lib/Bio/SeqIO.pm:359 >> STACK: test3.pl:7 >> ----------------------------------------------------------- >> >> Basically because I dont understand the code well enough. For >> example, >> how >> do I tell it which input file to read? I know this might sound >> stupid, >> but I >> dont understand the Biowiki very well! >> >> -- >> View this message in context: >> http://www.nabble.com/extracting-CDS-location-from-Genbank-tf4942483.htm >> l#a14152264 >> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. >> >> _______________________________________________ >> 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 >> >> > > -- > View this message in context: http://www.nabble.com/extracting-CDS-location-from-Genbank-tf4942483.html#a14152907 > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l
	Re: extracting CDS location from Genbank by Sendu Bala-2 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Captainrave wrote: > #!/bin/perl > my $file = shift; # get the file name, somehow > > The file is on the same folder. But how do I tell it to use this file? http://stein.cshl.org/genome_informatics/perl_intro/command_line.html Basically, when you run your script add the name of the file to your command line. me% perl myscript.pl myfile By saying 'my $file = shift' inside myscript.pl, the variable $file now contains the filename 'myfile'. You could also have hardcoded the filename: my $file = 'myfile'; Anyway, you're going to run into lots of these issues, and they're beyond the scope of this mailing list. For basic perl problems seek help via www.perl.org. When you have a BioPerl-specific question, don't hesitate to post here. _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l
	Re: extracting CDS location from Genbank by Captainrave :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Thanks, it works great now. Do any of you know if there is a tag to pull out CDS location. i.e. the values such as 132...145 etc? Those are all I need. Also, is there anyway to stop it reporting tag and value and literally JUST output the value? Thanks!!!