From 0e9faebb62141354377b254a10c53c41ab4e8fb3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 10 Jul 2003 11:50:01 +0000
Subject: [PATCH] The number of gaps is not interesting.
---
.../protein_match/new_pmatch_wrapper.pl | 18 ++++++------------
1 file changed, 6 insertions(+), 12 deletions(-)
diff --git a/misc-scripts/protein_match/new_pmatch_wrapper.pl b/misc-scripts/protein_match/new_pmatch_wrapper.pl
index 0ed5e55962..b09f8a6dfd 100755
--- a/misc-scripts/protein_match/new_pmatch_wrapper.pl
+++ b/misc-scripts/protein_match/new_pmatch_wrapper.pl
@@ -123,9 +123,6 @@ foreach my $query (values(%hits)) {
my $overlap = 0; # Total query overlap length
my $totlen = 0; # Total hit length
- my $gaps = 0; # Number of gaps in the query
- # Are these interesting?
-
my @pair;
foreach my $hit (
sort { $a->{$c . 'START'} <=>
@@ -144,31 +141,28 @@ foreach my $query (values(%hits)) {
[$pair[1]{$c . 'START'},
$pair[1]{$c . 'END'}]);
$overlap += $o;
-
- ++$gaps if ($o == 0); # ($o <= 1 ???)
}
# Calculate the query and target identities
$target->{$c . 'IDENT'} =
100*($totlen - $overlap)/$target->{$c . 'LEN'};
- $target->{$c . 'GAPS'} = $gaps;
}
}
}
if ($opts{'b'}) {
- printf("%8s%8s%8s%8s%8s%8s%8s%8s\n",
- 'QID', 'QLEN', 'QIDENT', 'QGAPS',
- 'TID', 'TLEN', 'TIDENT', 'TGAPS');
+ printf("%8s%8s%8s%8s%8s%8s\n",
+ 'QID', 'QLEN', 'QIDENT',
+ 'TID', 'TLEN', 'TIDENT');
}
while (my ($qid, $query) = each %hits) {
while (my ($tid, $target) = each %{ $query }) {
- printf("%8s%8d%8.3f%8d%8s%8d%8.3f%8d\n",
+ printf("%8s%8d%8.3f%8s%8d%8.3f\n",
$qid, $target->{QLEN},
- $target->{QIDENT}, $target->{QGAPS},
+ $target->{QIDENT},
$tid, $target->{TLEN},
- $target->{TIDENT}, $target->{TGAPS});
+ $target->{TIDENT});
}
}
--
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