From 3043d3eb46e0e333efbd29ea71bc4ef4e4ab75cb Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Wed, 20 Jun 2012 09:22:05 +0000
Subject: [PATCH] corrected file names - fix for Exonerate method override
change
---
.../xref_mapping/XrefMapper/Methods/ExonerateBasic.pm | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
index b671688b31..02e763b880 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
@@ -189,7 +189,7 @@ sub submit_exonerate {
my $prefix = $root_dir . "/" . basename($query);
$prefix =~ s/\.\w+$//;
- my ($jid, $ensembl_type) = $prefix =~ /.*(\d+)_(dna|peptide)$/; # dna or prot
+ my ($ensembl_type) = $prefix =~ /.*_(dna|peptide)$/; # dna or prot
my $options_str = join(" ", @options);
my $unique_name = $self->get_class_name() . "_" . time();
@@ -207,7 +207,7 @@ sub submit_exonerate {
if(defined($mapper->nofarm)){
- my $output = $self->get_class_name() . "_" . $ensembl_type ."_".$jid. "_1.map";
+ my $output = $self->get_class_name() . "_" . $ensembl_type. "_1.map";
my $cmd = <<EON;
$exe $query $target --showvulgar false --showalignment FALSE --ryo "xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\n" $options_str | grep '^xref' > $root_dir/$output
EON
@@ -237,7 +237,7 @@ EON
$sth = $mapper->xref->dbc->prepare("insert into mapping_jobs (root_dir, map_file, status, out_file, err_file, array_number, job_id) values (?,?,?,?,?,?,?)");
- my $map_file = $self->get_class_name()."_".$ensembl_type."_".$jid."_".$i.".map";
+ my $map_file = $self->get_class_name()."_".$ensembl_type."_".$i.".map";
my $out_file = "xref_0_".$ensembl_type.".".$jobid."-".$i.".out";
my $err_file = "xref_0_".$ensembl_type.".".$jobid."-".$i.".err";
$sth->execute($root_dir, $map_file, 'SUBMITTED', $out_file, $err_file, $i, $jobid);
@@ -260,7 +260,7 @@ EON
- my $output = $self->get_class_name() . "_" . $ensembl_type . "_".$jid."_" . "\$LSB_JOBINDEX.map";
+ my $output = $self->get_class_name() . "_" . $ensembl_type . "_" . "\$LSB_JOBINDEX.map";
my $queue = $self->mapper->farm_queue || 'long';
@@ -319,7 +319,7 @@ EON
$sth = $mapper->xref->dbc->prepare("insert into mapping_jobs (root_dir, map_file, status, out_file, err_file, array_number, job_id) values (?,?,?,?,?,?,?)");
for( my $i=1; $i<=$num_jobs; $i++){
- my $map_file = $self->get_class_name()."_".$ensembl_type."_".$jid."_".$i.".map";
+ my $map_file = $self->get_class_name()."_".$ensembl_type."_".$i.".map";
my $out_file = "xref_0_".$ensembl_type.".".$jobid."-".$i.".out";
my $err_file = "xref_0_".$ensembl_type.".".$jobid."-".$i.".err";
$sth->execute($root_dir, $map_file, 'SUBMITTED', $out_file, $err_file, $i, $jobid);
--
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