[Bioperl-l] Extracting gi no from refseq record

Siddhartha Basu basu at pharm.sunysb.edu
Thu Apr 3 10:07:13 EST 2003


Hi,
I am trying to extract the gi no from the refseq flat files that is in 
genbank format. This is what i have done so far...

*** Indexed the files with Bio::Index::GenBank module
*** Then try to fetch a particular entry by get_Seq_by_acc/id call.
*** It returns a Bio::Seq::RichSeq object.
*** Now i have tried to get the gi no by
*** $Seq->primary_id(), $Seq->display_id() calls but both of them return
the locus name. Since $Seq is a RichSeq object i have also tried with 
$Seq->pid() call but nothing happens.


So, how is it possible to extract that number for a particular NP or NM 
refseq number specially from flat files.


siddhartha



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