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
    
        # Calculate average mapping quality from SAM reads
        recs fromsam input.sam \
            | recs collate -a avg,mapq

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-fromgff3

    recs-fromsam

    recs-tofasta

    Looking for fromfastq or tofastq? Install the recs-fastq
    <https://github.com/MullinsLab/recs-fastq> package.

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 fromsam --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 2014-2017 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

