Commit 7671f083 authored by Emmanuel Mongin's avatar Emmanuel Mongin
Browse files

Mapping getting bigger and bigger, added a script which

prepare the data for scop mapping.

E.
parent 123a2a50
...@@ -2,6 +2,8 @@ use strict; ...@@ -2,6 +2,8 @@ use strict;
#Some doc will come ... #Some doc will come ...
#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_embl_mim_mapping.pl -sp ../primary/hum_sp_sptrembl.pep -dbmap mapdb.map -output sp_embl_mim.map
use Getopt::Long; use Getopt::Long;
use Bio::SeqIO; use Bio::SeqIO;
......
use strict;
#Some doc will come
#The scop mapping which should be used here can be found at:
#http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.dom.scop.txt_1.53 (for the 1.53 release)
#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_scops.pl -scop ../secondary/dir.dom.scop.txt_1.53 -dbmap mapdb.map -out scops.map
use Getopt::Long;
my ($scop,$dbmap,$out);
my %map;
&GetOptions(
'scop:s'=>\$scop,
'out:s'=>\$out,
'dbmap:s'=>\$dbmap
);
open (DBMAP,"$dbmap") || die "Can't open file $dbmap\n";
open (SCOP,"$scop") || die "Can't open file $scop\n";
open (OUT,">$out") || die "Can't open file $out\n";
open (ERROR, ">scop.err") || die "Can't open file scop.err\n";
print STDERR "Reading dbmap\n";
while (<DBMAP>) {
chomp;
my ($mapac,$mapdb) = split(/\t/,$_);
$map{$mapac} = $mapdb;
}
print STDERR "Reading Scop file\n";
while (<SCOP>) {
chomp;
my ($scopac, $pdb, $chain, $scopnb) = split(/\t/,$_);
if (!defined $map{$scopac}) {
print ERROR "can't map $scopac\n";
}
print OUT "$map{$scopac}\t$scopac\tSCOP1\t$pdb\|\|$chain\n";
print OUT "$map{$scopac}\t$scopac\tSCOP1\t$scopnb\n";
}
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