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Re: please help me!!by robsv (Curate) |
on Apr 11, 2002 at 18:15 UTC ( [id://158379]=note: print w/replies, xml ) | Need Help?? |
Have you looked into Bioperl? It will simplify parsing for you (especially for the sequence itself). Here's a program that gets the sequence and some other basic information:
In your program, you're putting all of the non-sequence lines into @annotation. I'm not sure specifically which information you need (i.e. descriprtion, accession number, etc.), but those are all accessible through the "$seqobj" object. There's some examples in the code above; you'll find many more in the documentation. This method also has the advantage of being able to handle multiple GenBank records per file. This is just a tiny portion of the functions available with BioPerl - it will also parse BLAST files, perform alignments, etc. If you're interested, you can grab the latest release from CPAN or from BioPerl here. Hope this helps! - robsv
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