[Bioperl-l] Two 'host' tags?

Jeremy Hayward haywardjeremya at gmail.com
Fri Jul 6 13:56:12 EDT 2012


Hi--  Clueless newbie here, for which apologies.

I've posted a description of my problem, inputs and outputs, at Gist
2816510; https://gist.github.com/2816510

Briefly, I'm trying to take a genbank file (.gb), and create a FASTA
file with a specific identifier line for each sequence. Specifically,
I want the "host" tag as the identifier. With the help of the Bioperl
beginner readme and the HOWTO's (which are great!) I've worked out how
to loop through my sequences and get the 'host' tag for each one. For
some reason, I get two identifier lines for each sequence. I guess the
problem is in the 'for' loop--it's running the stuff below it twice,
once with the actual 'host' tag data and once with...nothing? Not
sure.

I think I can work out how to use s/ and a regex just to delete the
second identifier line, but that feels like I'm avoiding the problem
instead of fixing it. Any help appreciated!


Many thanks,

--Jeremy Hayward


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