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 <[email protected]>

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