view release on metacpan or  search on metacpan

lib/App/SimulateReads/Base.pm  view on Meta::CPAN

	};
}

binmode STDERR, ":encoding(utf8)";
our $LOG_VERBOSE = 1;

sub log_msg {
	my ($msg) = @_;
	return if not defined $msg;
	chomp $msg;
	say STDERR $msg if $LOG_VERBOSE;
}

sub import {
	my ($class, @opts) = @_;
	my $caller = caller;

	# Import as in Moder::Perl
	strict->import;
	feature->import(':5.10');
	utf8->import($caller);

lib/App/SimulateReads/Simulator.pm  view on Meta::CPAN

			my @fastq_entry;
			try {
				@fastq_entry = $self->sprint_fastq($tid, $i, $id,
					\$fasta->{$id}{seq}, $fasta->{$id}{size}, $strand->());
			} catch {
				die "Not defined entry for seqid '>$id' at job $tid: $_";
			} finally {
				unless (@_) {
					for my $fh_idx (0..$#fhs) {
						$counter{$id}++;
						$fhs[$fh_idx]->say(${$fastq_entry[$fh_idx]})
							or die "Cannot write to $files_t[$fh_idx]: $!\n";
					}
				}
			};
		}

		log_msg "  => Job $tid: Writing and closing file: @files_t";
		# Close temporary files
		for my $fh_idx (0..$#fhs) {
			$fhs[$fh_idx]->close

lib/App/SimulateReads/Simulator.pm  view on Meta::CPAN

		$fh[$fh_idx]->close
			or die "Cannot write file $files{$fastq_class}[$fh_idx]: $!\n";
	}

	# Save counts
	log_msg ":: Saving count file ...";
	my $count_fh = $self->my_open_w($count_file, 0);

	log_msg ":; Wrinting counts to $count_file ...";
	while (my ($id, $count) = each %counters) {
		$count_fh->say("$id\t$count");
	}

	# Just in case, calculate 'gene' like expression
	my $parent_count = $self->_calculate_parent_count(\%counters);

	if (defined $parent_count) {
		while (my ($id, $count) = each %$parent_count) {
			$count_fh->say("$id\t$count");
		}
	}

	# Close $count_file
	log_msg ":; Writing and closing $count_file ...";
	$count_fh->close
		or die "Cannot write file $count_file: $!\n";

	# Clean up the mess
	log_msg ":: Removing temporary files ...";