Bio

In my work as a Computational Biologist I often find myself reimplementing the same or similar set of functionality across several places and script. I can't count the number of times I've implemented simple reverse-complement, parse-csv, or efficient string searching algorithms. This module serves to tackle this problem by putting this functionality in one convenient place.

Functionality

• Bio::IO implements common parsers and pretty-printers for many of the file formats I deal with daily. Current sub-modules include:
  • Bio::IO::CSV for manipulating CSV files.
  • Bio::IO::Fasta for manipulating FASTA files.
  • Bio::IO::BAM for manipulating BAM/SAM files
  • Bio::IO::FastQ for manipulating FastQ sequence read files.
• Bio::Seq implements common sequence manipulation functionality.

Examples

my $bam   = "test.bam";

my $af = AlignmentFile.new(:bam-file($bam), :flags("r"));
my @results = $af.query('NC_000001.11:2-300');

for @results {
    say $_.rname;
    say $_.name;
    say $_.seq;
    say $_.strand;
};