Re^2: Extract subset of sequences from a FASTA file

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.

Comment on Re^2: Extract subset of sequences from a FASTA file

Replies are listed 'Best First'.
Re^3: Extract subset of sequences from a FASTA file by InfiniteSilence (Curate) on Jan 19, 2012 at 03:34 UTC
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	[reply]

Replies are listed 'Best First'.

Re^3: Extract subset of sequences from a FASTA file
by InfiniteSilence (Curate) on Jan 19, 2012 at 03:34 UTC

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

[reply]