examples/db/gb2features.pl

   1 #!/usr/bin/perl
   2 # Author: Damien Mattei C.N.R.S / U.N.S.A - UMR 6549
   3 # example: ./idfetch.pl AP001266
   4
   5 use Bio::DB::GenBank;
   6
   7 $gb = new Bio::DB::GenBank();
   8
   9 # this returns a Seq object :
  10 $seq1 = $gb->get_Seq_by_acc($ARGV[0]);
  11 print $seq1->display_id() . "\n" ;
  12
  13
  14 foreach $feat ($seq1->all_SeqFeatures()) {
  15
  16   #print $feat->primary_tag . " " . $feat->source_tag() . "\n" ;
  17
  18   print "Feature from ", $feat->start, " to ",
  19    $feat->end, " Primary tag  ", $feat->primary_tag,
  20    ", produced by ", $feat->source_tag(), "\n";
  21
  22   if( $feat->strand == 0 ) {
  23     print "Feature applicable to either strand\n";
  24   } else {
  25     print "Feature on strand ", $feat->strand,"\n"; # -1,1
  26   }
  27
  28   foreach $tag ( $feat->all_tags() ) {
  29     print "Feature has tag ", $tag, " with values, ",
  30     join(' ',$feat->each_tag_value($tag)), "\n";
  31   }
  32
  33   print "new feature\n" if $feat->has_tag('new');
  34
  35 }
  36
  37
  38 exit;
  39
  40 __END__
  41
  42 It will display something like that:
  43
  44 [dmattei@pclgmch2 gmap]$ ./idfetch.pl AP001266
  45 AP001266
  46 Feature from 1 to 168978 Primary tag  source, produced by
  47 EMBL/GenBank/SwissProt
  48 Feature on strand 1
  49 Feature has tag chromosome with values, 11
  50 Feature has tag map with values, 11q13
  51 Feature has tag clone with values, RP11-770G2
  52 Feature has tag organism with values, Homo sapiens
  53 Feature has tag db_xref with values, taxon:9606
  54 Feature from 1 to 31550 Primary tag  misc_feature, produced by
  55 EMBL/GenBank/SwissProt
  56 Feature on strand 1
  57 Feature has tag note with values, assembly_fragment
  58 Feature from 31651 to 48510 Primary tag  misc_feature, produced by
  59 EMBL/GenBank/SwissProt
  60 Feature on strand 1
  61 Feature has tag note with values, assembly_fragment
  62 Feature from 48611 to 64044 Primary tag  misc_feature, produced by
  63 EMBL/GenBank/SwissProt
  64 Feature on strand 1
  65 Feature has tag note with values, assembly_fragment
  66 Feature from 64145 to 78208 Primary tag  misc_feature, produced by
  67 EMBL/GenBank/SwissProt
  68 Feature on strand 1
  69 Feature has tag note with values, assembly_fragment
  70 Feature from 78309 to 89008 Primary tag  misc_feature, produced by
  71 EMBL/GenBank/SwissProt
  72 Feature on strand 1
  73 Feature has tag note with values, assembly_fragment
  74 Feature from 89109 to 99704 Primary tag  misc_feature, produced by
  75 EMBL/GenBank/SwissProt
  76 Feature on strand 1
  77 Feature has tag note with values, assembly_fragment
  78 Feature from 99805 to 107965 Primary tag  misc_feature, produced by
  79 EMBL/GenBank/SwissProt
  80 Feature on strand 1
  81 Feature has tag note with values, assembly_fragment
  82 Feature from 108066 to 116032 Primary tag  misc_feature, produced by
  83 EMBL/GenBank/SwissProt
  84 Feature on strand 1
  85 Feature has tag note with values, assembly_fragment
  86 Feature from 116133 to 124010 Primary tag  misc_feature, produced by
  87 EMBL/GenBank/SwissProt
  88 Feature on strand 1
  89 Feature has tag note with values, assembly_fragment
  90 Feature from 124111 to 130494 Primary tag  misc_feature, produced by
  91 EMBL/GenBank/SwissProt
  92 Feature on strand 1
  93 Feature has tag note with values, assembly_fragment
  94 Feature from 130595 to 136072 Primary tag  misc_feature, produced by
  95 EMBL/GenBank/SwissProt
  96 Feature on strand 1
  97 Feature has tag note with values, assembly_fragment
  98 Feature from 136173 to 139649 Primary tag  misc_feature, produced by
  99 EMBL/GenBank/SwissProt
 100 Feature on strand 1
 101 Feature has tag note with values, assembly_fragment
 102 Feature from 139750 to 144590 Primary tag  misc_feature, produced by
 103 EMBL/GenBank/SwissProt
 104 Feature on strand 1
 105 Feature has tag note with values, assembly_fragment
 106 Feature from 144691 to 148482 Primary tag  misc_feature, produced by
 107 EMBL/GenBank/SwissProt
 108 Feature on strand 1
 109 Feature has tag note with values, assembly_fragment
 110 Feature from 148583 to 152279 Primary tag  misc_feature, produced by
 111 EMBL/GenBank/SwissProt
 112 Feature on strand 1
 113 Feature has tag note with values, assembly_fragment
 114 Feature from 152380 to 153632 Primary tag  misc_feature, produced by
 115 EMBL/GenBank/SwissProt
 116 Feature on strand 1
 117 Feature has tag note with values, assembly_fragment clone_end:T7
 118 vector_side:left
 119 Feature from 153733 to 155746 Primary tag  misc_feature, produced by
 120 EMBL/GenBank/SwissProt
 121 Feature on strand 1
 122 Feature has tag note with values, assembly_fragment
 123 Feature from 155847 to 156405 Primary tag  misc_feature, produced by
 124 EMBL/GenBank/SwissProt
 125 Feature on strand 1
 126 Feature has tag note with values, assembly_fragment clone_end:SP6
 127 vector_side:right
 128 Feature from 156506 to 158398 Primary tag  misc_feature, produced by
 129 EMBL/GenBank/SwissProt
 130 Feature on strand 1
 131 Feature has tag note with values, assembly_fragment
 132 Feature from 158499 to 161333 Primary tag  misc_feature, produced by
 133 EMBL/GenBank/SwissProt
 134 Feature on strand 1
 135 Feature has tag note with values, assembly_fragment
 136 Feature from 161434 to 163304 Primary tag  misc_feature, produced by
 137 EMBL/GenBank/SwissProt
 138 Feature on strand 1
 139 Feature has tag note with values, assembly_fragment
 140 Feature from 163405 to 164604 Primary tag  misc_feature, produced by
 141 EMBL/GenBank/SwissProt
 142 Feature on strand 1
 143 Feature has tag note with values, assembly_fragment
 144 Feature from 164705 to 166693 Primary tag  misc_feature, produced by
 145 EMBL/GenBank/SwissProt
 146 Feature on strand 1
 147 Feature has tag note with values, assembly_fragment
 148 Feature from 166794 to 168978 Primary tag  misc_feature, produced by
 149 EMBL/GenBank/SwissProt
 150 Feature on strand 1
 151 Feature has tag note with values, assembly_fragment
 152