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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.'

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

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