[Bioperl-l] Bio::BroodComb - RFC

Jay Hannah jay at jays.net
Mon Jan 18 19:22:48 EST 2010

I formalized a little framework so I could stop re-writing little programs that do some things people frequently ask me to do.


It stores everything in SQLite so users can write custom reports if they want to. It uses BioPerl and some shiny CPAN beads (DBIx::Class, Moose::Role). Tests included. 

The first two functions I stuck in the framework:

Find subsequences (Bio::BroodComb::SubSeq):

   use Bio::BroodComb;
   my $bc = Bio::BroodComb->new();
   $bc->load_large_seq(file => "large_seq.fasta");
   $bc->load_small_seq(file => "small_seq.fasta");
   print $bc->subseq_report1;

In-silico PCR (Bio::BroodComb::PCR):

  use Bio::BroodComb;
  my $bc = Bio::BroodComb->new();
  $bc->load_large_seq(file => "large_seq.fasta");
     description    => "U5/R",   # however you want it reported
     forward_primer => 'GCGGGCAGCAATACTGCTTTGTAA',
     reverse_primer => 'ACCAGCGTTCAGCATATGGAGGAT',
  print $bc->pcr_report1;

I find this rather handy, so will probably be adding all my applicable future work to it instead of writing stand-alone programs. Not sure if it should be renamed for eventual CPAN / wherever.

Suggestions, contributions welcome.   :)


Jay Hannah

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