[Bioperl-l] Accessing /gene and /note fields in a GenBank file
Damien Mattei
Damien.Mattei@unice.fr
Fri, 17 May 2002 15:53:02 +0200
Of course , you can do it!!!
bio-perl is free software and i'm a free software developer!!
Damien
Brian Osborne wrote:
> 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/
> --------------------------------------
>