Beefy Boxes and Bandwidth Generously Provided by pair Networks
Your skill will accomplish
what the force of many cannot

Re: Extract subset of sequences from a FASTA file

by InfiniteSilence (Curate)
on Jan 14, 2012 at 18:26 UTC ( #947910=note: print w/replies, xml ) Need Help??

in reply to Extract subset of sequences from a FASTA file

We basically get questions like this from time to time here on Perlmonks regarding stuff that is probably already being done somewhere in BioPerl. It is not that we don't like answering Perl questions but you might be better served Googling 'bioperl forum.'

Celebrate Intellectual Diversity

  • Comment on Re: Extract subset of sequences from a FASTA file

Replies are listed 'Best First'.
Re^2: Extract subset of sequences from a FASTA file
by educated_foo (Vicar) on Jan 14, 2012 at 23:46 UTC
    BioPerl is usually an over-complicated mess. You want to generate a random set of indices from a range (with or without replacement?), then get the sequences at those indices. BioPerl won't help you do this.

      I was going to disagree with you but I figured that I should try to download the BioPerl core and try this out. Well, that was something like 1/2 hour ago. Apparently the 'core' is stored on github rather than CPAN and that may be the problem. If I just want a handful of packages to solve a particular problem I probably should not have to download this huge thing. If I had known this before I probably would not have made this suggestion.

      Celebrate Intellectual Diversity

Log In?

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://947910]
and all is quiet...

How do I use this? | Other CB clients
Other Users?
Others cooling their heels in the Monastery: (6)
As of 2018-05-23 07:51 GMT
Find Nodes?
    Voting Booth?