File Coverage

blib/lib/App/RecordStream/Operation/fromfasta.pm

Criterion	Covered	Total	%
statement	37	41	90.2
branch	8	8	100.0
condition			n/a
subroutine	7	8	87.5
pod	0	5	0.0
total	52	62	83.8

package App::RecordStream::Operation::fromfasta;

use strict;
use warnings;

use base qw(App::RecordStream::Operation);

sub init {
    my $self = shift;
    my $args = shift;

    my $oneline = 0;
    my %options = (
        "oneline"   => \$oneline,
    );

    $self->parse_options($args, \%options);

    $self->{ONELINE} = $oneline;
}

sub accept_line {
    my $self = shift;
    my $line = shift;

    if ($line =~ /^>\s*(.*?)\s*$/) {
        my $name = $1;
        my ($id, $desc) = split /\h/, $name, 2;
        $self->push_accumulated_record;
        $self->{RECORD} = App::RecordStream::Record->new(
            name        => $name,
            id          => $id,
            description => $desc,
            _filename   => $self->get_current_filename,
        );
    } else {
        $self->{SEQUENCE} .= $line . ($self->{ONELINE} ? "" : "\n");
    }

    return 1;
}

sub push_accumulated_record {
    my $self = shift;
    if ( my $record = delete $self->{RECORD} ) {
        my $seq = delete $self->{SEQUENCE};
        chomp $seq if defined $seq;
        $record->set( sequence => $seq );

        my $filename = $self->get_current_filename;
        $self->update_current_filename( delete $record->{_filename} );
        $self->push_record( $record );
        $self->update_current_filename( $filename );
        return 1;
    } else {
        return 0;
    }
}

sub stream_done {
    my $self = shift;
    $self->push_accumulated_record;
}

sub usage {
  my $self = shift;

  my $options = [
    [ 'oneline', 'Strip any newlines from the sequence so it is one long line'],
  ];

  my $args_string = $self->options_string($options);

  return <
Usage: recs-fromfasta  []
   __FORMAT_TEXT__
   Each sequence from the FASTA input files (or stdin) produces an output
   record with the keys name and sequence.  Each sequence name is also split into
   id and description on the first whitespace, if any.
   __FORMAT_TEXT__

Arguments:
$args_string

Examples:
   Parse a FASTA file into records, stripping newlines in the sequence
      recs-fromfasta --oneline < example.fasta
USAGE
}

1;