/ 
App-RecordStream-Bio-0.16
River stage zero No dependents
/ App::RecordStream::Bio

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 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