[Bioperl-l] How to get the contents?
mike.thon at gmail.com
Fri Dec 14 12:41:44 EST 2007
Hi Information_details, a.k.a. Archana :)
"1", and "485" can be retrieved with something like:
if you want start and end of each exon then you need:
my $location = $feat->location();
which returns a Bio::LocationI object.
I think the 'gene' tag is a tag-value pair that can be retrieved with:
my @values = $feat->get_tag_values("gene");
On Dec 14, 2007, at 4:56 AM, Information_details wrote:
> I am new to bioperl.
> I am using module Bio::SeqIO;
> I have genbank file. http://www.nabble.com/file/p14329679/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
> /note="Derived by automated computational analysis
> gene prediction method: BestRefseq. Supporting
> includes similarity to: 1 mRNA"
> i have to match gene tag and get its contents?
> 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
> How do i do that?
> with regards
> View this message in context: http://www.nabble.com/How-to-get-the-contents--tp14329679p14329679.html
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