/usr/lib/ChimeraSlayer/PerlLib/AlignCompare.pm is in chimeraslayer 20101212+dfsg1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 | package AlignCompare;
use strict;
use warnings;
use Carp qw (cluck confess);
use List::Util qw (min max);
## In all methods below, non-GATC characters do not count as valid bases ##
sub compute_per_ID {
my ($seqA, $seqB) = @_;
if (length($seqA) != length($seqB)) {
confess "Error, cannot compute perID for nonidentical sequence lengths";
}
my @charsA = split(//, uc $seqA);
my @charsB = split(//, uc $seqB);
my ($lendBoundA, $rendBoundA) = &find_ends_of_alignment(@charsA);
my ($lendBoundB, $rendBoundB) = &find_ends_of_alignment(@charsB);
my $lend_bound = max($lendBoundA, $lendBoundB);
my $rend_bound = min($rendBoundA, $rendBoundB);
my $same_chars = 0;
my $chars_in_A = 0;
my $chars_in_B = 0;
for (my $i = $lend_bound; $i <= $rend_bound; $i++) {
my $charA = $charsA[$i];
my $charB = $charsB[$i];
## If character is not recognized, it's completely ignored.
if ($charA !~ /[GATC\.\-]/i || $charB !~ /[GATC\.\-]/i ) { next; }
my $charA_GATC = ($charA =~ /[GATC]/) ? 1:0;
my $charB_GATC = ($charB =~ /[GATC]/) ? 1:0;
if ($charA_GATC || $charB_GATC) {
if ($charA_GATC) {
$chars_in_A++;
}
if ($charB_GATC) {
$chars_in_B++;
}
if ($charA eq $charB) {
$same_chars++;
}
}
}
## total number of chars in alignment is taken as the average of the two sequence lengths.
my $num_chars = ($chars_in_A + $chars_in_B) / 2;
if ($num_chars == 0) {
cluck "Warning, no base characters in either A or B sequences";
return(0);
}
return($same_chars/$num_chars * 100);
}
####
sub find_lend_match {
my ($charsA_aref, $charsB_aref) = @_;
for (my $i = 0; $i <= $#$charsA_aref; $i++) {
if ($charsA_aref->[$i] =~ /[GATC]/i && $charsB_aref->[$i] =~ /[GATC]/i) {
return($i);
}
}
return(0); # default is start at beginning
}
####
sub find_rend_match {
my ($charsA_aref, $charsB_aref) = @_;
for (my $i = $#$charsA_aref; $i >= 0; $i--) {
if ($charsA_aref->[$i] =~ /[GATC]/i && $charsB_aref->[$i] =~ /[GATC]/i) {
return($i);
}
}
return($#$charsA_aref); # default is stop at end
}
####
sub define_left_clip {
my ($chars_aref, $start, $length) = @_;
my $count = 0;
for (my $i = $start; $i >= 0; $i--) {
my $char = $chars_aref->[$i];
if ($char =~ /\w/) {
$count++;
if ($count >= $length) {
return($i);
}
}
}
confess "Error, couldn't define a left clip position";
}
####
sub define_right_clip {
my ($chars_aref, $start, $length) = @_;
my $count = 0;
for (my $j = $start; $j <= $#$chars_aref; $j++) {
my $char = $chars_aref->[$j];
if ($char =~ /\w/i) {
$count++;
if ($count >= $length) {
return($j);
}
}
}
confess ("Error, cannot define a right clip position");
}
####
sub find_ends_of_alignment {
my @align_array = @_;
my $index_left;
my $index_right;
for (my $i = 0; $i <= $#align_array; $i++) {
if ($align_array[$i] =~ /[GATC]/i) {
$index_left = $i;
last;
}
}
for (my $i = $#align_array; $i >= 0; $i--) {
if ($align_array[$i] =~ /[GATC]/i) {
$index_right = $i;
last;
}
}
return($index_left, $index_right);
}
1; #EOM
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