fastapl and fastqpl

What?

fastapl: FASTA Perl Loop, a tool for processing multifasta data. Pronounced as "fast apple". and its companion program fastqpl, pronounced "fast Q-ple", for fastq format data.

First Glimpse

fastapl -pe '$seq = reverse $seq; $seq =~ tr/acgtACGT/tgcaTGCA/' in.fasta > out.fasta
Reverse complements DNA sequences.

fastapl -ge '$seq !~ /^M/'
Print records of sequences not starting with 'M'.

fastapl one-liners ← Start here!
fastqpl one-liners
fastapl Program (to download, right click mouse)
fastqpl Program (to download, right click mouse)
fastapl Man page style manual
fastqpl Man page style manual

Required Modules

IO::File, Getopt::Long, Pod::Usage, Text::Balanced. All are available via apt-get or directly from CPAN.

Recommended Modules

fastaplAmino
More::Util -- available via apt-get or directly from CPAN.

Related Resources

fastapl and fasqpl are small, self-contained tools; mostly designed for ad hoc tasks. For a more structured approach, several software libraries and tool packages exist. Here I list a few obviously relevant ones.

EMBOSS suite -- Software package for molecular biology, including handling fasta and fastq format data
BioPerl -- Perl libraries for molecular biology, including handling fasta and fastaq format data