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

INSTALLATION
  Quick, standalone bundle
    The quickest way to start using these tools is via the minimal,
    standalone bundle (also known as the "fatpacked" version). First, grab
    recs if you don't already have it:

      curl -fsSL https://recs.pl > recs
      chmod +x recs

    Then grab these bio tools and put them in place for recs:

      mkdir -p ~/.recs/site/
      curl -fsSL https://recs.pl/bio > ~/.recs/site/bio.pm

    Congrats, you should now be able to run:

      ./recs fromfasta --help
      ./recs tofasta --help

    recs version 4.0.14 or newer is required to support site loading from
    ~/.recs/site.

  From CPAN
    You can also install from CPAN <http://cpan.org> as
    App::RecordStream::Bio:

      cpanm App::RecordStream::Bio

    Other CPAN clients such as cpan and cpanp also work just great.

    If you don't have cpanm itself, you can install it easily with:

      curl -fsSL https://cpanmin.us | perl - App::cpanminus

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

