130 lines
2.5 KiB
Perl
130 lines
2.5 KiB
Perl
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#!/usr/bin/perl -w
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#
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# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
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#
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# This file is part of Bowtie 2.
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#
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# Bowtie 2 is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# Bowtie 2 is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
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#
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package DNA;
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use strict;
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use warnings;
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use Carp;
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my %revcompMap = (
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"A" => "T", "a" => "t",
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"T" => "A", "t" => "a",
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"C" => "G", "c" => "g",
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"G" => "C", "g" => "c",
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"R" => "Y", "r" => "y",
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"Y" => "R", "y" => "r",
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"M" => "K", "m" => "k",
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"K" => "M", "k" => "m",
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"S" => "S", "s" => "s",
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"W" => "W", "w" => "w",
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"B" => "V", "b" => "v",
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"V" => "B", "v" => "b",
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"H" => "D", "h" => "d",
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"D" => "H", "d" => "h",
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"N" => "N", "n" => "n"
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);
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my %compat = (
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"A" => "A",
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"T" => "T",
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"C" => "C",
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"G" => "G",
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"R" => "AG",
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"Y" => "CT",
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"M" => "AC",
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"K" => "GT",
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"S" => "CG",
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"W" => "AT",
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"B" => "CGT",
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"V" => "ACG",
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"H" => "ACT",
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"D" => "AGT",
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"N" => "N"
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);
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my %incompat = (
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"A" => "CGT",
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"T" => "ACG",
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"C" => "AGT",
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"G" => "ACT",
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"R" => "CT",
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"Y" => "AG",
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"M" => "GT",
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"K" => "AC",
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"S" => "AT",
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"W" => "CG",
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"B" => "A",
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"V" => "T",
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"H" => "G",
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"D" => "C",
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"N" => "N"
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);
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my %unambigSet = (
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"A" => 1, "a" => 1,
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"C" => 1, "c" => 1,
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"G" => 1, "g" => 1,
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"T" => 1, "t" => 1
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);
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##
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# Return the complement, incl. if it's IUPAC.
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#
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sub comp($) {
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my $ret = $revcompMap{$_[0]} || die "Can't reverse-complement '$_[0]'";
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return $ret;
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}
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##
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# Return the complement, incl. if it's IUPAC.
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#
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sub revcomp {
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my ($ret, $color) = @_;
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$ret = reverse $ret;
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unless($color) {
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for(my $i = 0; $i < length($ret); $i++) {
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substr($ret, $i, 1) = comp(substr($ret, $i, 1));
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}
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}
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return $ret;
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}
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##
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# Return true iff it's unambiguous.
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#
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sub unambig($) {
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return $unambigSet{$_[0]};
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}
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##
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# Manipulate DNA in an integer-indexed fashion.
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#
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sub plus($$) {
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my ($c, $amt) = @_;
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my %ctoi = ("A" => 0, "C" => 1, "G" => 2, "T" => 3);
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my %itoc = (0 => "A", 1 => "C", 2 => "G", 3 => "T");
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$c = uc $c;
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defined($ctoi{$c}) || die;
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return $itoc{($ctoi{$c}+$amt) % 4};
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}
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1;
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