[Bioperl-l] how to prevent forced exit?

Ross KK Leung ross at cuhk.edu.hk
Tue Mar 15 20:55:42 EDT 2011


-----Original Message-----
From: Chris Fields [mailto:cjfields at illinois.edu] 
Sent: 2011年3月15日 22:44
To: Ross KK Leung
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to prevent forced exit?

Frankly, there are much better/faster ways to do this, not least of which is to just download a GenBank section and parse it directly, or use a BLAST-formatted database and fastacmd to get the seqs of interest in FASTA format.  Any reason why you are not doing this?

chris


Dear Chris,

Thanks for your suggestion. The problem we encounter is that we don't know what database/genbank files we have to retrieve in order to accomplish the job. It seems that the nr database does not include all the records, and we don't know whether we have to concatenate all the genbank files into a very big one so to parse one by one. Any advice?

Gratefully, Ross




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