#!/usr/bin/perl # Author: Damien Mattei C.N.R.S / U.N.S.A - UMR 6549 # 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" ; 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 $feat->has_tag('new'); } exit; __END__ It will display something like that: [dmattei@pclgmch2 gmap]$ ./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