++ed by:

1 non-PAUSE user(s).

Thomas Sibley

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.fasta

DESCRIPTION

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

recs-fromfasta

recs-tofasta

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.

SEE ALSO

App::RecordStream