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#!/usr/bin/perl -w
#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Bowtie 2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
#
package Read;
use strict;
use Carp;
use FindBin qw($Bin);
use lib $Bin;
use DNA;
use Test;
sub new {
my ($class, $name, $seq, $qual, $color, $fw, $orig) = @_;
$name = "noname" unless defined($name);
return bless {
_name => $name,
_seq => $seq || croak("No sequence"),
_qual => $qual || croak("No qualities"),
_color => $color || 0,
_fw => $fw || croak("No orientation"),
_orig => $orig || croak("No original read string")
}, $class;
}
sub name { return $_[0]->{_name} }
sub seq { return $_[0]->{_seq} }
sub qual { return $_[0]->{_qual} }
sub color { return $_[0]->{_color} }
sub fw { return $_[0]->{_fw} }
sub orig { return $_[0]->{_orig} }
sub len { return length($_[0]->seq()) }
##
# Obtain a character from the read.
#
sub at {
my ($self, $off, $ori) = @_;
my ($c, $q) = "";
if($ori eq "RtL") {
$c = uc substr($self->seq(), -$off-1, 1);
$q = substr($self->qual(), -$off-1, 1);
} else {
$c = uc substr($self->seq(), $off, 1);
$q = substr($self->qual(), $off, 1);
}
length($c) == 1 || die;
return ($c, $q);
}
##
# Load a set of FASTQ reads into the given reads array.
#
sub fromFastq {
my ($fh, $color, $reads) = @_;
$reads = [] unless defined($reads);
while(<$fh>) {
my $l1 = $_;
my $l2 = <$fh>; defined($l2) || croak("Name line followed by EOF");
my $l3 = <$fh>; defined($l3) || croak("Sequence line followed by EOF");
my $l4 = <$fh>; defined($l4) || croak("Name2 line followed by EOF");
my $orig = "$l1$l2$l3$l4";
chomp($l1); chomp($l2); chomp($l3); chomp($l4);
push @{$reads}, Read->new(substr($l1, 1), $l2, $l4, $color, "FW", $orig);
}
return $reads;
}
##
# Load a set of FASTQ reads into the given reads array.
#
sub fromFastqs {
my ($fqs, $color, $reads) = @_;
$reads = [] unless defined($reads);
for my $f (@$fqs) {
my $fqfh;
open($fqfh, $f =~ /\.gz$/ ? "gzip -dc $f |" : "$f") || croak("Could not open $f for reading");
fromFastq($fqfh, $color, $reads);
close($fqfh);
}
return $reads;
}
##
# Load a set of FASTA reads into the given reads array.
#
sub fromFasta {
my ($fh, $color, $reads) = @_;
$reads = [] unless defined($reads);
while(<$fh>) {
my $l1 = $_;
my $l2 = <$fh>; defined($l2) || croak("Name line followed by EOF");
my $orig = "$l1$l2";
chomp($l1); chomp($l2);
my $qual = "I" x length($l2);
push @{$reads}, Read->new(substr($l1, 1), $l2, $qual, $color, "FW", $orig);
}
return $reads;
}
##
# Load a set of FASTA reads into the given reads array.
#
sub fromFastas {
my ($fas, $color, $reads) = @_;
$reads = [] unless defined($reads);
for my $f (@$fas) {
my $fafh;
open($fafh, $f =~ /\.gz$/ ? "gzip -dc $f |" : "$f") || croak("Could not open $f for reading");
fromFasta($fafh, $color, $reads);
close($fafh);
}
return $reads;
}
##
# Load a set of FASTA reads into the given reads array.
#
sub fromStrings {
my ($strs, $color, $reads) = @_;
$reads = [] unless defined($reads);
my $idx = 0;
for my $str (@$strs) {
my $qual = "I" x length($str);
push @{$reads}, new Read($idx, $str, $qual, $color, "FW", $str);
$idx++;
}
return $reads;
}
sub test1 {
my $r = new Read("blah", "TTACGAACCACAACGTATCG", "I"x20, 0, "FW", "?");
my ($c, $q) = $r->at(0, "LtR");
($c eq "T" && $q eq "I") || croak("Expected (T, I), got ($c, $q)\n");
($c, $q) = $r->at(0, "RtL");
($c eq "G" && $q eq "I") || croak("Expected (G, I), got ($c, $q)\n");
($c, $q) = $r->at(1, "LtR");
($c eq "T" && $q eq "I") || croak("Expected (T, I), got ($c, $q)\n");
($c, $q) = $r->at(1, "RtL");
($c eq "C" && $q eq "I") || croak("Expected (C, I), got ($c, $q)\n");
return 1;
}
sub test2 {
my $rs = fromStrings(["ACGATGCTACG", "TGACGATGCTAG"], 0);
$rs->[0]->seq() eq "ACGATGCTACG" || croak($rs->[0]->seq());
$rs->[0]->qual() eq "IIIIIIIIIII" || croak($rs->[0]->qual());
$rs->[0]->name() eq "0" || croak($rs->[0]->name());
$rs->[1]->seq() eq "TGACGATGCTAG" || croak($rs->[1]->seq());
$rs->[1]->qual() eq "IIIIIIIIIIII" || croak($rs->[1]->qual());
$rs->[1]->name() eq "1" || croak($rs->[1]->name());
return 1;
}
if($0 =~ /Read\.pm$/) {
print "Running unit tests\n";
# Run unit tests
print "Test \"test1\"..."; test1(); print "PASSED\n";
print "Test \"test2\"..."; test2(); print "PASSED\n";
}
1;
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