From b98650e07536987fb25a6e171b9a1518cbd4ffed Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Sun, 13 Mar 2005 14:38:58 +0000
Subject: [PATCH] create submit script for those mappings that produced
problems
---
.../xref_mapping/test_mapping_files.pl | 43 +++++++++++++++++--
1 file changed, 39 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/xref_mapping/test_mapping_files.pl b/misc-scripts/xref_mapping/test_mapping_files.pl
index e3e4e039b6..d8dbfe6665 100644
--- a/misc-scripts/xref_mapping/test_mapping_files.pl
+++ b/misc-scripts/xref_mapping/test_mapping_files.pl
@@ -2,6 +2,7 @@ use strict;
use warnings;
my $dir = shift;
+my $submit = shift;
opendir(DIR, $dir);
my @allfiles = readdir DIR;
@@ -13,6 +14,11 @@ closedir DIR;
my %hash;
my %max;
+my %fasta;
+my $method;
+
+$max{'pep'} = 0;
+$max{'dna'} = 0;
foreach my $file(@allfiles){
if($file eq '.' || $file eq '..'){
@@ -21,18 +27,29 @@ foreach my $file(@allfiles){
next;
}else{
my $type;
- if($file =~ /dna/){
+ if($file =~ /dna.fasta/){
+ $fasta{'dna'} = $file;
+ next;
+ }
+ elsif($file =~ /protein.fasta/){
+ $fasta{'pep'} = $file;
+ next;
+ }
+ elsif($file =~ /dna/){
$type = 'dna';
+ if(!defined($method)){
+ if($file =~ /(.*)_dna_\d+.map/){
+ $method= $1;
+ }
+ }
}
elsif($file =~ /pep/){
$type = 'pep';
}
- elsif($file =~ /fasta/){
- next;
- }
else{
next;
}
+
if($file =~ /_(\d+).map/){
$hash{$type}{'map'}{$1} = $1;
}
@@ -48,13 +65,29 @@ foreach my $file(@allfiles){
}
}
+print "Method $method\n";
+
+if(defined($submit)){
+ open(OUT,">SUBMIT")|| die "could not open SUBMIT output file\n";
+}
+
foreach my $type ('pep', 'dna'){
print "max ".$type."-->".$max{$type}."\n";
for (my $i=1; $i <= $max{$type}; $i++){
+
if(!defined($hash{$type}{'map'}{$i})){
print $i,".map\n";
+ if(defined($submit)){
+ print OUT "/usr/local/ensembl/bin/exonerate-0.9.0 xref/xref_0_dna.fasta ";
+ print OUT $dir."/homo_sapiens_dna.fasta --querychunkid ".$i." --querychunktotal ";
+ print OUT $max{$type}." --showvulgar false --showalignment FALSE --ryo ";
+ print OUT '"xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\n"';
+ print OUT ' --model affine:local --subopt no --bestn 1 | grep "^xref" > ';
+ print OUT $dir."/".$method."_".$type."_".$i.".map\n";
+ }
}
+
if(!defined($hash{$type}{'err'}{$i})){
print $i,".err\n";
}
@@ -63,3 +96,5 @@ foreach my $type ('pep', 'dna'){
}
}
}
+
+
--
GitLab