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package App::RecordStream::Bio;

use strict;
use 5.010;
our $VERSION = '0.24';

# For informational purposes only in the fatpacked file, so it's OK to fail.
# For now, classes are still under the App::RecordStream::Operation namespace
# instead of ::Bio::Operation.
eval {
    require App::RecordStream::Site;
    App::RecordStream::Site->register_site(
        name => __PACKAGE__,
        path => __PACKAGE__,
    );
};

1;
__END__

=encoding utf-8

=head1 NAME

App::RecordStream::Bio - A collection of record-handling tools related to biology

=head1 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

=head1 DESCRIPTION

App::RecordStream::Bio is a collection of record-handling tools related to
biology built upon the excellent L<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.

=head1 TOOLS

L<recs-fromfasta>

L<recs-fromgff3>

L<recs-fromsam>

L<recs-tofasta>

L<recs-togff3>

Looking for C<fromfastq> or C<tofastq>?  Install the
L<recs-fastq|https://github.com/MullinsLab/recs-fastq> package.