[Bioperl-l] Accessing /gene and /note fields in a GenBank file
Brian Osborne
brian_osborne@cognia.com
Fri, 17 May 2002 09:22:14 -0400
Damien,
Would you mind if I add this to our examples/ collection of scripts. I don't
think we have any example code that shows does exactly this. I'd add it in
your name, of course!
Brian O.
-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Damien Mattei
Sent: Friday, May 17, 2002 4:23 AM
To: Adam Witney
Cc: bioperl-l@bioperl.org
Subject: Re: [Bioperl-l] Accessing /gene and /note fields in a GenBank file
here is an example that could help you:
#!/usr/bin/perl -w
#
# example: ./idfetch.pl AP001266
use Bio::DB::GenBank;
$gb = new Bio::DB::GenBank();
# this returns a Seq object :
$seq1 = $gb->get_Seq_by_acc($ARGV[0]);
print $seq1->display_id() . "\n" ;
#print $seq1->subseq(5,10) . "\n" ;
foreach $feat ($seq1->all_SeqFeatures()) {
#print $feat->primary_tag . " " . $feat->source_tag() . "\n" ;
print "Feature from ", $feat->start, " to ",
$feat->end, " Primary tag ", $feat->primary_tag,
", produced by ", $feat->source_tag(), "\n";
if( $feat->strand == 0 ) {
print "Feature applicable to either strand\n";
} else {
print "Feature on strand ", $feat->strand,"\n"; # -1,1
}
foreach $tag ( $feat->all_tags() ) {
print "Feature has tag ", $tag, " with values, ",
join(' ',$feat->each_tag_value($tag)), "\n";
}
print "new feature\n" if $feat->has_tag('new');
}
exit;
it will display something like that:
[dmattei@pclgmch2 gmap]$ ./idfetch.pl AP001266
AP001266
Feature from 1 to 168978 Primary tag source, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag chromosome with values, 11
Feature has tag map with values, 11q13
Feature has tag clone with values, RP11-770G2
Feature has tag organism with values, Homo sapiens
Feature has tag db_xref with values, taxon:9606
Feature from 1 to 31550 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 31651 to 48510 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 48611 to 64044 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 64145 to 78208 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 78309 to 89008 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 89109 to 99704 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 99805 to 107965 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 108066 to 116032 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 116133 to 124010 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 124111 to 130494 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 130595 to 136072 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 136173 to 139649 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 139750 to 144590 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 144691 to 148482 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 148583 to 152279 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 152380 to 153632 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment clone_end:T7
vector_side:left
Feature from 153733 to 155746 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 155847 to 156405 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment clone_end:SP6
vector_side:right
Feature from 156506 to 158398 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 158499 to 161333 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 161434 to 163304 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 163405 to 164604 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 164705 to 166693 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 166794 to 168978 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Damien
Adam Witney wrote:
> Hi, just been trying to write a GenBank parser for a GenBank file
containing
> a whole genome
>
> How do I get access to the /gene and /note fields of each gene? I have
this
> so far
>
> my $gbk_obj = Bio::SeqIO->new('-file' => "gbk_file",
> '-format' => 'GenBank');
>
> while (my $seq = $gbk_obj->next_seq())
> {
> my @features = $seq->all_SeqFeatures;
>
> foreach my $feat (@features)
> {
> print $feat->primary_tag."\n";
>
> print $feat->start.' - '.$feat->end."\t".$feat->strand."\n";
>
> my $seq_obj = $feat->seq;
>
> print $seq_obj->seq."\n";
>
> }
>
>
> Thanks
>
> adam
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
>
--------------------------------------
Damien Mattei
C.N.R.S / U.N.S.A - UMR 6549
Instabilite & Alterations des Genomes
Universite de Nice - Sophia Antipolis
Faculte de Medecine, Av. de Valombrose
06107 NICE Cedex 2 FRANCE
Phone: +33 (0)4 93 37 76 66
Fax: +33 (0)4 93 53 30 71
mailto:mattei@unice.fr
http://www-iag.unice.fr/
--------------------------------------
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