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Commit 738b6b16 authored by Emmanuel Mongin's avatar Emmanuel Mongin
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Removed useless files which were used for the mapping. Should be more straithforward to run now.

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misc-scripts/protein_match/get_dbmap.pl deleted 100644 → 0
View file @ 25075c62
use strict;
=head1 get_all_external
=head2 Description
This script will set up a mapping of each primary database (SP, SPTREMBL, Refseq and PDB) to their respective name. This mapping will be then used to give a database name to each ACs.
=head2 Options
-sp
-sptrembl
-refseq
-pdb
=head2 Contact
mongin@ebi.ac.uk
birney@ebi.ac.uk
=cut
#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_dbmap.pl -sp ../primary/01_04_hum_sprot.txt -sptrembl ../primary/07_04_hum_sptrembl.txt -refseq ../primary/hs.gnp -scop ../primary/scop.fas
use Getopt::Long;
use Bio::SeqIO;
my ($sp, $sptrembl, $refseq, $scop, $out);
&GetOptions(
'sp:s'=>\$sp,
'sptrembl:s'=>\$sptrembl,
'refseq:s'=>\$refseq,
'scop:s'=>\$scop,
'out:s'=>\$out
);
open (OUT,">mapdb.map");
print STDERR "Getting SP mapping\n";
my $in = Bio::SeqIO->new(-file => $sp, '-format' =>'swiss');
while ( my $seq = $in->next_seq() ) {
print OUT $seq->accession."\tSP\n";
my @secs = $seq->get_secondary_accessions;
if (@secs) {
foreach my $sec (@secs) {
print OUT "$sec\tSP\n";
}
}
}
print STDERR "Getting SPTREMBL mapping\n";
my $in1 = Bio::SeqIO->new(-file => $sptrembl, '-format' =>'swiss');
while ( my $seq1 = $in1->next_seq() ) {
print OUT $seq1->accession."\tSPTREMBL\n";
my @secs = $seq1->get_secondary_accessions;
if (@secs) {
foreach my $sec (@secs) {
print OUT "$sec\tSPTREMBL\n";
}
}
}
print "Getting refseq mapping\n";
open (REFSEQ,"$refseq") || die "Can't open file\n";
$/ = "\/\/\n";
while (<REFSEQ>) {
my ($prot_ac) = $_ =~ /ACCESSION\s+(\S+)/;
my ($dna_ac) = $_ =~ /DBSOURCE REFSEQ: accession\s+(\w+)/;
if ($dna_ac) {
print OUT "$dna_ac\tREFSEQ\n";
}
}
close (REFSEQ);
$/ = "\n";
print "Getting Scop mapping\n";
open (SCOP,"$scop") || die "Can't open file\n";
while (<SCOP>) {
my ($scop_ac) = $_ =~ /^>(\S+)/;
if ($scop_ac) {
print OUT "$scop_ac\tSCOP\n";
}
}
close (SCOP);
close (OUT);
misc-scripts/protein_match/get_embl_mim_mapping.pl deleted 100644 → 0
View file @ 25075c62
use strict;
#Some doc will come ...
#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_embl_mim_mapping.pl -sp ../primary/hum_sp_sptrembl.pep -dbmap mapdb.map -output sp_embl_mim.map
use Getopt::Long;
use Bio::SeqIO;
my ($sp,$dbmap,$out);
my %map;
&GetOptions(
'sp:s'=>\$sp,
'output:s'=>\$out,
'dbmap:s'=>\$dbmap
);
open (DBMAP,"$dbmap") || die "Can't open file $dbmap\n";
open (OUT,">$out") || die "Can't open file\n";
print STDERR "Reading DBmap\n";
while (<DBMAP>) {
chomp;
my ($mapac,$mapdb) = split(/\t/,$_);
$map{$mapac} = $mapdb;
}
print STDERR "Reading SP\n";
my $in1 = Bio::SeqIO->new(-file => $sp, '-format' =>'swiss');
while ( my $seq1 = $in1->next_seq() ) {
my $ac = $seq1->accession;
my @dblink = $seq1->annotation->each_DBLink;
foreach my $link(@dblink) {
if ($link->database eq "EMBL") {
if (!defined $map{$ac}) {
die "Can't map $ac\n";
}
print OUT "$map{$ac}\t$ac\tEMBL_AC\t".$link->primary_id,"\n";
my ($protac) = $link->optional_id =~ /^(\w+).\S+/;
print OUT "$map{$ac}\t$ac\tEMBL_PROT_AC\t$protac\n";
}
if ($link->database eq "MIM") {
if (!defined $map{$ac}) {
die "Can't map $ac\n";
}
print OUT "$map{$ac}\t$ac\tOMIM\t".$link->primary_id,"\n";
}
}
}
misc-scripts/protein_match/get_ens2embl.pl deleted 100644 → 0
View file @ 25075c62
use strict;
=head1 Get_ens2ensembl.pl
=head1 Description
=head2 Aims
The aim of thi script is to get from the database the corresponding clones for each Ensembl peptides. This will be then used to postprocess pmatch and get a more sensible mapping.
=cut
use Bio::SeqIO;
use Bio::EnsEMBL::DBSQL::Obj;
use Bio::EnsEMBL::DBLoader;
use Getopt::Long;
use Bio::SeqIO;
my $dbpass = undef;
my $dbuser = 'ensro';
my $ensdbname = 'ensembl080';
my $host = 'ecs1c.sanger.ac.uk';
my $output;
&GetOptions(
'db:s' => \$ensdbname,
'host:s'=> \$host,
'dbuser:s'=> \$dbuser,
'output:s' => \$output
);
my $enslocator = "Bio::EnsEMBL::DBSQL::Obj/host=$host;dbname=$ensdbname;user=$dbuser;pass=$dbpass;perlonlyfeatures=1";
my $ensdb = Bio::EnsEMBL::DBLoader->new($enslocator);
my $sth = $ensdb->prepare ("select t.id,cl.embl_id from transcript as t, exon_transcript as et, clone as cl, contig as c, exon as e where t.id=et.transcript and et.exon = e.id and e.contig = c.internal_id and c.clone = cl.internal_id");
$sth->execute;
my %hash;
my %seen;
print STDERR "Getting data\n";
while (my @row = $sth->fetchrow) {
if (! defined $seen{$row[1]}) {
push(@{$hash{$row[0]}},$row[1]);
$seen{$row[1]} = 1;
}
}
print STDERR "Writing out\n";
open (OUT,">$output");
foreach my $keys (keys %hash) {
my @array = @{$hash{$keys}};
foreach my $arr (@array) {
print OUT "ENSEMBL\t$keys\tEMBL\t$arr\n";
}
}
misc-scripts/protein_match/get_hugo_mapping.pl deleted 100644 → 0
View file @ 25075c62
use strict;
=head1 get_hugo_mapping
=head2 Description
This script reads a set of files produced by HUGO and built a file which will be used to get the DBlink table.The format of the file is the following
SP P27348 HUGO YWHAQ
(known database\t known ac\t hugo or alias\t hugo ac)
=head2 Options
The different options only deal with file names
-nomeid: Hugo file (http://www.gene.ucl.ac.uk/public-files/nomen/nomeids.txt)
-ens1: Hugo file (http://www.gene.ucl.ac.uk/public-files/nomen/ens1.txt)
-ens2: Hugo file (http://www.gene.ucl.ac.uk/public-files/nomen/ens2.txt)
-output: Filename were the output should be written
-dbmap: File which give the corresponding database for each known protein
=cut
use Getopt::Long;
#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_hugo_mapping.pl -ens1 ../secondary/ens1.txt -ens2 ../secondary/ens2.txt -ens4 ../secondary/ens4.txt -ens5 ../secondary/ens5.txt -out hugo.map -dbmap mapdb.map
my ($ens1,$ens2,$ens4,$ens5,$out,$dbmap);
my %map;
my %hugo_sp;
my %hugo_refseq;
my %en2;
my %hugohash;
&GetOptions(
'ens1:s'=>\$ens1,
'ens2:s'=>\$ens2,
'ens4:s'=>\$ens4,
'ens5:s'=>\$ens5,
'dbmap:s'=>\$dbmap,
'output:s'=>\$out
);
open (ENS1,"$ens1") || die "Can't open file $ens1\n";
open (ENS2,"$ens2") || die "Can't open file $ens2\n";
open (ENS4,"$ens4") || die "Can't open file $ens4\n";
open (ENS5,"$ens5") || die "Can't open file $ens5\n";
open (DBMAP,"$dbmap") || die "Can't open file $dbmap\n";
open (OUT,">$out") || die "Can't open output file $out\n";
open (ERROR,">hugo.err") || die "Can't open output file hugo.err\n";
while (<DBMAP>) {
chomp;
my ($mapac,$mapdb) = split(/\t/,$_);
$map{$mapac} = $mapdb;
}
while (<ENS1>) {
chomp;
#Get hugo id
#Get rid of the annoying carriage return!
$_ =~ s/\r//g;
my ($hgnc,$sp,$refseq) = split(/\t/,$_);
if ($sp) {
print OUT "$map{$sp}\t$sp\tHUGOID\t$hgnc\n";
}
if ($refseq) {
print OUT "$map{refseq}\t$refseq\tHUGOID\t$hgnc\n";
}
if ($sp) {
$hugo_sp{$hgnc} = $sp;
}
if ($refseq) {
$hugo_refseq{$hgnc} = $refseq;
}
}
while (<ENS2>) {
chomp;
#Get hugo symbol
$_ =~ s/\r//g;
my ($hgnc1,$hugo) = split(/\t/,$_);
if ($hugo_sp{$hgnc1}) {
print OUT "$map{$hugo_sp{$hgnc1}}\t$hugo_sp{$hgnc1}\tHUGOSYMBOL\t$hugo\n";
}
if ($hugo_refseq{$hgnc1}) {
print OUT "$map{$hugo_refseq{$hgnc1}}\t$hugo_refseq{$hgnc1}\tHUGOSYMBOL\t$hugo\n";
}
if (!defined $en2{$hgnc1}) {
$en2{$hgnc1} = [];
}
$en2{$hgnc1} = $hugo;
}
while (<ENS4>) {
#Get hugo aliases given a hugo primary accession number. For each primary accession number, the aliases are put in a hash of array
chomp;
my ($hgnc2, $symbol, $alias, $withdrawn) = split (/\t/,$_);
if ((defined $hugo_sp{$hgnc2}) && (defined $alias)) {
my @aliases1 = split (/, /,$alias);
foreach my $aliase1 (@aliases1) {
print OUT "$map{$hugo_sp{$hgnc2}}\t$hugo_sp{$hgnc2}\tHUGOALIAS\t$aliase1\n";
}
}
if ((defined $hugo_sp{$hgnc2}) && ($withdrawn =~ /\S+/)) {
my @withdrawns1 = split (/, /,$withdrawn);
foreach my $withdrawn1 (@withdrawns1) {
print OUT "$map{$hugo_sp{$hgnc2}}\t$hugo_sp{$hgnc2}\tHUGOWITHDRAWN\t$withdrawn1\n";
}
}
if ((defined $hugo_refseq{$hgnc2}) && (defined $alias)) {
my @aliases2 = split (/, /,$alias);
foreach my $aliase2 (@aliases2) {
print OUT "$map{$hugo_sp{$hgnc2}}\t$hugo_sp{$hgnc2}\tHUGOALIAS\t$aliase2\n";
}
}
if ((defined $hugo_refseq{$hgnc2}) && ($withdrawn =~ /\S+/)) {
my @withdrawns2 = split (/, /,$withdrawn);
foreach my $withdrawn2 (@withdrawns2) {
print OUT "$map{$hugo_sp{$hgnc2}}\t$hugo_sp{$hgnc2}\tHUGOWITHDRAWN\t$withdrawn2\n";
}
}
}
while (<ENS5>) {
#Use Hugo mapping to get EC numbers
chomp;
my ($hgnc3, $symbol1, $name, $ec, $sp) = split (/\t/,$_);
if ((defined $hugo_sp{$hgnc3}) && (defined $ec)) {
print OUT "$map{$hugo_sp{$hgnc3}}\t$hugo_sp{$hgnc3}\tEC\t$ec\n";
}
if ((defined $hugo_refseq{$hgnc3}) && (defined $ec)) {
print OUT "$map{$hugo_sp{$hgnc3}}\t$hugo_sp{$hgnc3}\tEC\t$ec\n";
}
}
misc-scripts/protein_match/get_mim_locus.pl deleted 100644 → 0
View file @ 25075c62
use strict;
#Some doc will come
use Getopt::Long;
my ($refseq,$dbmap,$out);
my %map;
&GetOptions(
'refseq:s'=>\$refseq,
'out:s'=>\$out,
'dbmap:s'=>\$dbmap
);
open (DBMAP,"$dbmap") || die "Can't open file $dbmap\n";
open (REFSEQ,"$refseq") || die "Can't open file $refseq\n";
open (OUT,">$out") || die "Can't open file $out";
print STDERR "Reading dbmap\n";
while (<DBMAP>) {
chomp;
my ($mapac,$mapdb) = split(/\t/,$_);
$map{$mapac} = $mapdb;
}
#Separate by entry (each entry goes into $_)
$/ = "\/\/\n";
print STDERR "Reading Refseq file\n";
while (<REFSEQ>) {
my ($prot_ac) = $_ =~ /ACCESSION\s+(\S+)/;
my ($dna_ac) = $_ =~ /DBSOURCE REFSEQ: accession\s+(\w+)/;
my ($mim) = $_ =~ /\/db_xref=\"MIM:(\d+)/;
my ($locus) = $_ =~ /\/db_xref=\"LocusID:(\d*)/;
if ($mim) {
if (!defined $map{$dna_ac}) {
die "can't map $dna_ac\n";
}
print OUT "$map{$dna_ac}\t$dna_ac\tOMIM\t$mim\n";
}
if ($locus) {
if (!defined $map{$dna_ac}) {
die "can't map $dna_ac\n";
}
print OUT "$map{$dna_ac}\t$dna_ac\tLOCUS\t$locus\n";
}
}
misc-scripts/protein_match/get_scops.pl deleted 100644 → 0
View file @ 25075c62
use strict;
#Some doc will come
#The scop mapping which should be used here can be found at:
#http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.dom.scop.txt_1.53 (for the 1.53 release)
#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_scops.pl -scop ../secondary/dir.dom.scop.txt_1.53 -dbmap mapdb.map -out scops.map
use Getopt::Long;
my ($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$scopac\tSCOP2\t$scopnb\n";
}
misc-scripts/protein_match/get_xrefs.pl deleted 100644 → 0
View file @ 25075c62
use strict;
=head1 get_xrefs
=head2 Description
This script take the post processed pmatch output (see process_pmatch.pl) and a file which contains the links of each known gene to other databases (eg: SP to hugo or EMBL) and put them back together in a format suitable for the DBlink tables.
=head2 Options
-mapping: Name of the file corresponding to postprocessed pmatch
-xrefs: Name of the file linking known genes to other DB
-dbmap: File giving for each known gene its DB
-refseq: If refseq ac is used, file which store for each NP its corresponding NM
-output: Name of the output file
=head2 Contact
mongin@ebi.ac.uk
birney@ebi.ac.uk
=cut
use Getopt::Long;
my ($mapping,$xrefs,$dbmap,$refseq,$out);
my %map;
my %hash;
my %ref_map;
my %ens2embl;
my %sp2embl;
my %embl_clone;
&GetOptions(
'mapping:s'=>\$mapping,
'xrefs:s'=>\$xrefs,
'dbmap:s'=>\$dbmap,
'refseq:s'=>\$refseq,
'output:s'=>\$out
);
#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_xrefs.pl -mapping ../map_outputs/map.total -xrefs ../sec_outputs/xref.total -dbmap ../sec_outputs/mapdb.map -refseq ../primary/hs.gnp -output final.map
open (DBMAP,"$dbmap") || die "Can't open file $dbmap\n";
open (XREF,"$xrefs") || die "Can't open file $xrefs\n";
open (MAP,"$mapping") || die "Can't open file $mapping\n";
if ($refseq) {
open (REFSEQ,"$refseq") || die "Can't open file $refseq\n";
}
open (OUT,">$out") || die "Can't open file $out\n";
#open (CLONE,"clones.txt") || die "Can't open file\n";
#Put in a hash all of the embl clones used by Ensembl
#while (<CLONE>) {
# chomp;
# my ($embl_ac,$id) = split(/\t/,$_);
# print "$embl_ac\n";
# $embl_clone{$embl_ac}=1;
#}
while (<DBMAP>) {
chomp;
#Get put in a hash the corresponding database for an external accession number.Get the infos from a file already processed following this format:
#P31946 SP