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package App::SimulateReads::Read::PairedEnd; |
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# ABSTRACT: App::SimulateReads::Read subclass for simulate paired-end reads. |
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use App::SimulateReads::Base 'class'; |
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2647
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use Math::Random 'random_normal'; |
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26200
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extends 'App::SimulateReads::Read'; |
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our $VERSION = '0.06'; # VERSION |
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use constant { |
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NUM_TRIES => 1000 |
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}; |
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has 'fragment_mean' => ( |
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is => 'ro', |
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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 => 'ro', |
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isa => 'My:IntGe0', |
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required => 1 |
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); |
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sub BUILD { |
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0
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my $self = shift; |
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unless (($self->fragment_mean - $self->fragment_stdd) >= $self->read_size) { |
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croak sprintf "fragment_mean (%d) minus fragment_stdd (%d) must be greater or equal to read_size (%d)\n" |
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=> $self->fragment_mean, $self->fragment_stdd, $self->read_size; |
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} |
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} |
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sub gen_read { |
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my ($self, $seq_ref, $seq_size, $is_leader) = @_; |
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if ($seq_size < $self->fragment_mean) { |
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1
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croak sprintf "seq_size (%d) must be greater or equal to fragment_mean (%d)\n" |
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=> $seq_size, $self->fragment_mean; |
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} |
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700
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my $fragment_size = 0; |
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700
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my $random_tries = 0; |
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700
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until (($fragment_size <= $seq_size) && ($fragment_size >= $self->read_size)) { |
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# seq_size must be greater or equal to fragment_size and |
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# fragment_size must be greater or equal to read_size |
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# As fragment_size is randomly calculated, try out NUM_TRIES times |
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700
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if (++$random_tries > NUM_TRIES) { |
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0
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croak sprintf |
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"So many tries to calculate a fragment. the constraints were not met:\n" . |
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"fragment_size <= seq_size (%d) and fragment_size >= read_size (%d)\n" |
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=> $seq_size, $self->read_size; |
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} |
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700
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$fragment_size = $self->_random_half_normal; |
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} |
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700
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my ($fragment_ref, $fragment_pos) = $self->subseq_rand($seq_ref, $seq_size, $fragment_size); |
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700
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16552
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my $read1_ref = $self->subseq($fragment_ref, $fragment_size, $self->read_size, 0); |
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700
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15832
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$self->update_count_base($self->read_size); |
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700
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$self->insert_sequencing_error($read1_ref); |
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700
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my $read2_ref = $self->subseq($fragment_ref, $fragment_size, $self->read_size, $fragment_size - $self->read_size); |
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700
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$self->reverse_complement($read2_ref); |
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700
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$self->update_count_base($self->read_size); |
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700
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$self->insert_sequencing_error($read2_ref); |
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700
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100
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return $is_leader ? |
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($read1_ref, $read2_ref, $fragment_pos, $fragment_size) : |
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($read2_ref, $read1_ref, $fragment_pos, $fragment_size); |
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} |
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sub _random_half_normal { |
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700
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700
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1030
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my $self = shift; |
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700
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return abs(int(random_normal(1, $self->fragment_mean, $self->fragment_stdd))); |
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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::Read::PairedEnd - App::SimulateReads::Read subclass for simulate paired-end reads. |
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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 |