[Bioperl-l] Bio::BroodComb - RFC
Jay Hannah
jay at jays.net
Tue Jan 19 00:22:48 UTC 2010
I formalized a little framework so I could stop re-writing little programs that do some things people frequently ask me to do.
http://github.com/jhannah/bio-broodcomb
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");
$bc->find_subseqs();
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");
$bc->add_primerset(
description => "U5/R", # however you want it reported
forward_primer => 'GCGGGCAGCAATACTGCTTTGTAA',
reverse_primer => 'ACCAGCGTTCAGCATATGGAGGAT',
);
$bc->find_pcr_hits();
$bc->find_pcr_products();
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. :)
http://github.com/jhannah/bio-broodcomb
Jay Hannah
http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah
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