From 07dbf49d6d4d6ecda8a482e57dcde76abba1644f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 26 Aug 2003 16:36:21 +0000
Subject: [PATCH] Percent-identity-bug hopefully fixed.
---
.../protein_match/new_pmatch_wrapper.pl | 58 +++++++++++--------
1 file changed, 34 insertions(+), 24 deletions(-)
diff --git a/misc-scripts/protein_match/new_pmatch_wrapper.pl b/misc-scripts/protein_match/new_pmatch_wrapper.pl
index 174d933377..ff43613d56 100755
--- a/misc-scripts/protein_match/new_pmatch_wrapper.pl
+++ b/misc-scripts/protein_match/new_pmatch_wrapper.pl
@@ -127,10 +127,39 @@ while (defined(my $line = <PMATCH>)) {
QEND => $qend,
TSTART => $tstart,
TEND => $tend });
+
+ push(@{ $hits{$qid}{$tid}{QRANGES} },
+ new Bio::Range(-start => $qstart, -end => $qend));
+ push(@{ $hits{$qid}{$tid}{TRANGES} },
+ new Bio::Range(-start => $tstart, -end => $tend));
}
close(PMATCH);
+# Stitch Q and T ranges
+foreach my $query (values(%hits)) {
+ foreach my $target (values(%{ $query })) {
+ foreach my $c ('Q', 'T') {
+ my @stitched;
+ foreach my $range (@{ $target->{$c . 'RANGES'} }) {
+
+ my @new;
+ for (my $i = 0; $i < scalar @stitched; ++$i) {
+ if (defined ($stitched[$i]) && $range->overlaps($stitched[$i])) {
+ $range = $stitched[$i]->union($range);
+ } else {
+ push(@new, $stitched[$i]);
+ }
+ }
+ push(@new, $range);
+ @stitched = @new;
+
+ }
+ }
+ }
+}
+
+
if (!$opts{'k'}) {
unlink($pmatch_out); # Get rid of pmatch output file
} else {
@@ -146,36 +175,17 @@ foreach my $query (values(%hits)) {
foreach my $c ('Q', 'T') {
- my $overlap = 0; # Total query overlap length
my $totlen = 0; # Total hit length
- my @pair;
- foreach my $hit (
- sort { $a->{$c . 'START'} <=>
- $b->{$c . 'START'} }
- @{ $target->{HITS} }) {
-
- $totlen += $hit->{$c . 'END'} -
- $hit->{$c . 'START'} + 1;
-
- shift(@pair) if (scalar(@pair) == 2);
- push(@pair, $hit);
- next if (scalar(@pair) != 2);
-
- $r1->start($pair[0]{$c . 'START'});
- $r1->end($pair[0]{$c . 'END'});
-
- $r2->start($pair[1]{$c . 'START'});
- $r2->end($pair[1]{$c . 'END'});
-
- if ($r1->overlaps($r2)) {
- $overlap += $r1->intersection($r2)->length;
- }
+ foreach my $range (@{ $target->{$c . 'STITCH'} }) {
+ next unless defined $range;
+ $totlen += $range->length;
}
# Calculate the query and target identities
$target->{$c . 'IDENT'} =
- 100*($totlen - $overlap)/$target->{$c . 'LEN'};
+ 100 * $totlen / $target->{$c . 'LEN'};
+
}
}
}
--
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