[Bioperl-l] How to get the contents?
Information_details
karchana at ibab.ac.in
Fri Dec 14 03:56:14 UTC 2007
Hi,
I am new to bioperl.
I am using module Bio::SeqIO;
I have genbank file. http://www.nabble.com/file/p14329679/seq.gb seq.gb
In this file i have to match gene tag and get all its contents.
which function i have to use?
The gene portion look like this
gene 1..485
/gene="PRM1"
/note="Derived by automated computational analysis
using
gene prediction method: BestRefseq. Supporting evidence
includes similarity to: 1 mRNA"
/db_xref="GeneID:5619"
/db_xref="HGNC:9447"
i have to match gene tag and get its contents?
[CODE]
$seq=$seqobj->next_seq();
foreach $feat ($seq->get_all_SeqFeatures())
{
if($feat->primary_tag eq "mRNA")
{
foreach $tag ($feat->get_all_tags())
{
if($tag eq "gene")
{
#here i have to retrieve the information like
this.
1..485
/gene="PRM1"
}
}
}
[/CODE]
How do i do that?
with regards
Archana
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