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package App::SimulateReads::Fastq::PairedEnd; |
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# ABSTRACT: App::SimulateReads::Fastq subclass for simulate paired-end fastq entries. |
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use App::SimulateReads::Base 'class'; |
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use App::SimulateReads::Read::PairedEnd; |
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2215
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2038
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extends 'App::SimulateReads::Fastq'; |
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our $VERSION = '0.06'; # VERSION |
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has 'fragment_mean' => ( |
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is => 'rw', |
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isa => 'My:IntGt0', |
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required => 1 |
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); |
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has 'fragment_stdd' => ( |
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is => 'rw', |
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isa => 'My:IntGe0', |
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required => 1 |
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); |
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has 'sequencing_error' => ( |
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is => 'ro', |
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isa => 'My:NumHS', |
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required => 1 |
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); |
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has '_read' => ( |
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is => 'ro', |
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isa => 'App::SimulateReads::Read::PairedEnd', |
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builder => '_build_read', |
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lazy_build => 1, |
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handles => [qw{ gen_read }] |
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); |
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sub BUILD { |
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my $self = shift; |
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## Just to ensure that the lazy attributes are built before &new returns |
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$self->_read; |
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} |
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sub _build_read { |
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my $self = shift; |
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App::SimulateReads::Read::PairedEnd->new( |
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sequencing_error => $self->sequencing_error, |
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read_size => $self->read_size, |
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fragment_mean => $self->fragment_mean, |
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fragment_stdd => $self->fragment_stdd |
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); |
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} |
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sub sprint_fastq { |
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my ($self, $id, $seq_name, $seq_ref, $seq_size, $is_leader) = @_; |
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my ($read1_ref, $read2_ref, $fragment_pos, $fragment_size) = $self->gen_read($seq_ref, $seq_size, $is_leader); |
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my ($seq_pos1, $seq_pos2) = ( |
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"$seq_name:" . ($fragment_pos + 1) . "-" . ($fragment_pos + $self->read_size), |
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"$seq_name:" . ($fragment_pos + $fragment_size) . "-" . ($fragment_pos + $fragment_size - $self->read_size + 1) |
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); |
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unless ($is_leader) { |
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($seq_pos1, $seq_pos2) = ($seq_pos2, $seq_pos1); |
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} |
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my $header1 = "$id simulation_read length=" . $self->read_size . " position=$seq_pos1"; |
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my $header2 = "$id simulation_read length=" . $self->read_size . " position=$seq_pos2"; |
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my $fastq1_ref = $self->fastq_template(\$header1, $read1_ref); |
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my $fastq2_ref = $self->fastq_template(\$header2, $read2_ref); |
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return ($fastq1_ref, $fastq2_ref); |
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} |
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__END__ |
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=pod |
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=encoding UTF-8 |
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=head1 NAME |
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App::SimulateReads::Fastq::PairedEnd - App::SimulateReads::Fastq subclass for simulate paired-end fastq entries. |
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=head1 VERSION |
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version 0.06 |
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=head1 AUTHOR |
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Thiago L. A. Miller <tmiller@mochsl.org.br> |
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=head1 COPYRIGHT AND LICENSE |
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This software is Copyright (c) 2017 by Teaching and Research Institute from SÃrio-Libanês Hospital. |
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This is free software, licensed under: |
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The GNU General Public License, Version 3, June 2007 |
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=cut |