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,mapqDESCRIPTION
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
Looking for fromfastq or tofastq? Install the 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 recsThen grab these bio tools and put them in place for recs:
mkdir -p ~/.recs/site/
curl -fsSL https://recs.pl/bio > ~/.recs/site/bio.pmCongrats, you should now be able to run:
./recs fromfasta --help
./recs tofasta --help
./recs fromsam --helprecs 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::BioOther 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::cpanminusAUTHOR
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.