bioperl 格式化genebank的输出

代码如下：

use Bio::SeqIO; use Bio::DB::GenBank; use Bio::DB::Query::GenBank;
my $db_obj = Bio::DB::GenBank->new; my $seq_obj = $db_obj->get_Seq_by_acc('JN093905'); my $id = $seq_obj->display_id(); my $organ; foreach my $feat_object ($seq_obj->get_SeqFeatures) {if ($feat_object->primary_tag eq "source") {($organ) = $feat_object->get_tag_values('organism');}if ($feat_object->primary_tag eq "CDS") {my ($gene_name) = $feat_object->get_tag_values('gene');next if $gene_name ne 'nifH';my ($seq) = $feat_object->get_tag_values('translation');my ($pro) = $feat_object->get_tag_values('product');$seq = lc($seq);my $len = (length($seq) + 1) * 3;print qq{>$id coded_by=<1..>$len,organism=$organ,definition=$pro\n$seq\n};} }

运行结果如下：

>JN093905 coded_by=<1..>330,organism=uncultured Trichodesmium sp.,definition=dinitrogenase reductase rlilnakaqttvlhvaaergavedveldevlkpgfggikcvesggpepgvgcagrgiitainfleeegaytdldfvsydvlgdvvcggfampirenkaqeiyivcsgem

 

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