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bioperl 格式化genebank的输出

时间:2017-07-05 16:31:04      阅读:333      评论:0      收藏:0      [点我收藏+]

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

 

bioperl 格式化genebank的输出

原文:http://www.cnblogs.com/xudongliang/p/7121970.html

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