App::RecordStream::Bio - A collection of record-handling tools related to biology
# 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
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.
recs-fromfasta
recs-tofasta
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.
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
Thomas Sibley <trsibley@uw.edu>
Copyright 2014- Mullins Lab, Department of Microbiology, University of Washington
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
App::RecordStream
To install App::RecordStream::Bio, copy and paste the appropriate command in to your terminal.
cpanm
CPAN shell
perl -MCPAN -e shell install App::RecordStream::Bio
For more information on module installation, please visit the detailed CPAN module installation guide.