NAME
App::RecordStream::Bio - A collection of record-handling tools related to biology
SYNOPSIS
# Turn a FASTA into a CSV after filtering for sequence names containing the
# words POL or GAG.
recs-fromfasta --oneline < seqs.fasta \
| recs-grep '{{id}} =~ /\b(POL|GAG)\b/i' \
| recs-tocsv -k id,sequence
# Filter gaps from sequences
recs-fromfasta seqs.fasta \
| recs-xform '{{seq}} =~ s/-//g' \
| recs-tofasta > seqs-nogaps.fastaDESCRIPTION
App::RecordStream::Bio is a collection of record-handling tools related to biology built upon the excellent App::RecordStream.
The operations themselves are written as classes, but you'll almost always use them via their command line wrappers within a larger record stream pipeline.
TOOLS
AUTHOR
Thomas Sibley <trsibley@uw.edu>
COPYRIGHT
Copyright 2014- Mullins Lab, Department of Microbiology, University of Washington
LICENSE
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.