Removed the last files and added the ones which are now going to be used for the mapping

misc-scripts/protein_match/get_Xmapping.pl

+use strict;
+use Getopt::Long;
+use Bio::SeqIO;
+
+
+
+BEGIN {
+    unshift (@INC,"/work1/mongin/src/ensembl-live/misc-scripts/protein_match");
+    require "mapping_conf.pl";
+}
+
+
+
+my %conf =  %::mapping_conf; # configuration options
+
+# global vars
+
+my $sptr_swiss = $conf{'sptr_swiss'};
+my $refseq_gnp = $conf{'refseq_gnp'};
+my $ens1       = $conf{'ens1'};
+my $ens4       = $conf{'ens4'};
+my $out        = $conf{'x_map'};
+
+my %refseq_map;
+my %sp_db;
+my %hugo_id;
+my %hugo_syn;
+
+open (OUT,">$out") || die "Can't open $out\n";;
+
+#First read the SPTR file in swiss format
+print STDERR "Reading SPTR file\n";
+
+my $in  = Bio::SeqIO->new(-file => $sptr_swiss, '-format' =>'swiss');
+
+while ( my $seq = $in->next_seq() ) {
+
+    #For each SP entry, store the information concerning the entry
+    my $db;
+    my $ac = $seq->accession;
+    my $id = $seq->display_id;
+    my ($displ_id,$tag) = split(/:/,$id);
+
+    if ($tag eq "STANDARD") {
+	$db = "SP";
+    }
+    elsif ($tag eq "PRELIMINARY") {
+	$db = "SPTREMBL";
+    }
+    else {
+	die "Try to load unknown SPTR database\n";
+    }
+    my $un_ac = "$ac:$db";
+    my @secs = $seq->get_secondary_accessions;
+    my $syns = join(';',@secs);
+    print OUT "$ac\tSPTR\t$ac\t$db\t$displ_id\t$syns\n";
+
+    $sp_db{$ac} = $db;
+
+    #Then get info about the Xref mapping
+    my @dblink = $seq->annotation->each_DBLink;
+    
+    foreach my $link(@dblink) {
+	if ($link->database eq "EMBL") {
+	    print OUT "$ac\tSPTR\t".$link->primary_id."\t".$link->database."\t\t\n";
+
+	    my ($protac) = $link->optional_id =~ /^(\w+).\S+/;
+	    print OUT "$ac\tSPTR\t".$protac."\tEMBL_PROT_AC\t\t\n";
+	}
+
+	if  ($link->database eq "MIM") {
+	    print OUT "$ac\tSPTR\t".$link->primary_id."\t".$link->database."\t\t\n";
+	}
+    }
+}
+
+
+#Read the refseq file in gnp format
+print STDERR "Reading REFSEQ File\n";
+
+open (REFSEQ,"$refseq_gnp") || die "Can't open $refseq_gnp\n";
+
+$/ = "\/\/\n";
+
+while (<REFSEQ>) {
+    my ($prot_ac) = $_ =~ /ACCESSION\s+(\S+)/;
+    my ($dna_ac) = $_ =~ /DBSOURCE    REFSEQ: accession\s+(\w+)/;
+
+    $refseq_map{$dna_ac} = $prot_ac; 
+    
+    print OUT "$dna_ac\tREFSEQ\t$prot_ac\tREFSEQ\t$prot_ac\t\n";
+       
+    my ($mim) = $_ =~ /\/db_xref=\"MIM:(\d+)/;
+    my ($locus) = $_ =~ /\/db_xref=\"LocusID:(\d*)/;
+
+    if ($mim) {
+	print OUT "$dna_ac\tREFSEQ\t$mim\tOMIM\t$mim\t\n";
+    }
+
+    if ($locus) {
+	print OUT "$dna_ac\tREFSEQ\t$locus\tLOCUS\t$locus\t\n";
+    }
+}
+close (REFSEQ);
+
+$/ = "\n";
+
+
+#Read the Hugo files
+print STDERR "Reading Hugo files\n";
+
+open (ENS4,"$ens4") || die "Can't open $ens4\n";;
+
+while (<ENS4>) {
+    chomp;
+    my @array = split(/\t/,$_);
+    my $hgnc = $array[0];
+    my $id = $array[1];
+    #my $syn1 = $array[2];
+    #my $syn2 = $array[3];
+    
+    my $syn1 = join (';',split (/,\s/,$array[2]));
+    my $syn2 = join (';',split (/,\s/,$array[3]));
+    
+    my $syn = "$syn1;$syn2";
+    
+    $hugo_id{$hgnc} = $id;
+    $hugo_syn{$hgnc} = $syn;
+    #print $hugo_syn{$hgnc};
+}
+close (ENS4);
+
+open (ENS1,"$ens1") || die "Can't open $ens1\n";
+
+while (<ENS1>) {
+    chomp;
+    my @array = split(/\t/,$_);
+    my $hgnc = $array[0];
+    
+    if ($array[1]) {
+	#my $db = $sp_db{$array[1]};
+	print OUT "$array[1]\tSPTR\t$hgnc\tHUGO\t$hugo_id{$hgnc}\t$hugo_syn{$hgnc}\n";
+    }
+    
+    if ($array[2]) {
+	#my $db = $sp_db{$array[1]};
+	print OUT "$array[2]\tREFSEQ\t$hgnc\tHUGO\t$hugo_id{$hgnc}\t$hugo_syn{$hgnc}\n";
+    }
+}
+close (ENS1);
+
+

misc-scripts/protein_match/mapping_conf.pl

+=head1 mappping_conf.pl
+
+=head2 Description
+
+This script gives the basic configuration needed by the mapping. This configuration script will be used by each script of the mapping. Each field is described bellow.
+
+    + organism: The name of the organism which has to be mapped. eg: human, mouse, worm
+
+    + sptr:     Location of the SPTR file
+
+    + refseq:   Location of the Refseq file (only valide for the human organism)
+
+    + (ens1, ens2, ens5) : Various files produced by Hugo (http://www.gene.ucl.ac.uk/public-files/nomen/) which would be used to map SP to hugo and refseq to Hugo (only valide for the human organism)
+
+    
+
+=cut
+
+
+
+
+
+BEGIN {
+package main;
+
+%mapping_conf = ( 
+	     # Files location (Input/Output)
+
+             'query'        => '/work4/mongin/data/ensembl.pep',
+             #'query'       => '',   
+        
+	     'sptr_fa'      => '/work1/mongin/mapping/primary/refseq.fa',
+	     #'sptr_fa'      => '',
+	     
+	     'sptr_swiss'      => '/work1/mongin/mapping/primary/sptr.swiss',
+	     #'sptr_swiss'      => '',
+	     
+	     'refseq_fa'    => '/work1/mongin/mapping/primary/refseq.fa',
+	     #'refseq'    => '',
+	     
+	     'refseq_gnp'    => '/work1/mongin/mapping/primary/refseq.gnp',
+	     #'refseq_gnp'    => '',
+	    
+	     'ens1'      => '/work1/mongin/mapping/primary/ens1.txt',
+	     #'ens1'      => '',
+
+	     'ens4'      => '/work1/mongin/mapping/primary/ens4.txt',
+	     # 'ens4'      => '',
+
+             'refseq_map' => '/work1/mongin/mapping/tests/refseq_map.txt',
+             #'refseq_map' => '',
+
+             'sp_map' => '/work1/mongin/mapping/tests/refseq_map2.txt',
+             #'sp_map' => '',
+
+             'x_map'  => '/work1/mongin/mapping/tests/xmap_out1.txt',
+             #'x_map_out'  => '',
+
+             #Database handling
+             'db' => 'prot_pipeline_test',
+             #'db' => '',
+
+             'host' => 'ecs1b',
+             #'host' => '',
+
+             
+
+ );
+
+
+}
+
+1;

misc-scripts/protein_match/maps2db.pl

+use strict;
+use DBI;
+use Getopt::Long;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::DBLoader;
+use Bio::EnsEMBL::DBSQL::DBEntryAdaptor;
+use Bio::EnsEMBL::DBEntry;
+use Bio::SeqIO;
+
+BEGIN {
+    unshift (@INC,"/work1/mongin/src/ensembl-live/misc-scripts/protein_match");
+    require "mapping_conf.pl";
+}
+
+
+
+my %conf =  %::mapping_conf; # configuration options
+
+# global vars
+
+my $refseq_gnp = $conf{'refseq_gnp'};
+my $xmap       = $conf{'x_map'};
+my $map        = $conf{'sp_map'};
+my $dbname     = $conf{'db'};
+my $host       = $conf{'host'};
+
+my %map;
+my %ref_map;
+
+print STDERR "Connecting to the database...\n";
+my $enslocator = "Bio::EnsEMBL::DBSQL::DBAdaptor/host=$host;dbname=$dbname;user=ensadmin;perlonlyfeatures=1";
+print STDERR "Bio::EnsEMBL::DBSQL::DBAdaptor/host=$host;dbname=$dbname;user=ensadmin;perlonlyfeatures=1\n";
+my $db =  Bio::EnsEMBL::DBLoader->new($enslocator);
+
+my $adaptor = Bio::EnsEMBL::DBSQL::DBEntryAdaptor->new($db);
+
+open (REFSEQ,"$refseq_gnp") || die "Can't open $refseq_gnp\n";
+#Read the file by genbank entries (separated by //) 
+$/ = "\/\/\n";
+while (<REFSEQ>) {
+#This subroutine store for each NP (refseq protein accession number) its corresponding NM (DNA accession number)
+    my ($prot_ac) = $_ =~ /ACCESSION\s+(\S+)/;
+    my ($dna_ac) = $_ =~ /DBSOURCE    REFSEQ: accession\s+(\w+)/;
+
+    #print STDERR "$prot_ac\n";
+    $ref_map{$prot_ac} = $dna_ac;
+}
+#Put back the default (new line) for reading file
+$/ = "\n"; 
+
+open (XMAP,"$xmap") || die "Can't open $xmap\n";
+
+while (<XMAP>) {
+    chomp;
+    my ($targetid,$targetdb,$xac,$xdb,$xid,$xsyn) = split (/\t/,$_);
+    
+    #print STDERR "$targetid,$targetdb,$xac,$xdb,$xid,$xsyn\n";
+
+    my $p= Desc->new;
+    $p->targetDB($targetdb);
+    $p->xAC($xac);
+    $p->xDB($xdb);
+    $p->xID($xid);
+    $p->xSYN($xsyn);
+
+    push(@{$map{$targetid}},$p);
+}
+
+close (XMAP);
+
+open (MAP,"$map") || die "Can't open $map\n";
+
+while (<MAP>) {
+    #print STDERR "Loading data in the database\n";
+    chomp;
+    my ($queryid,$tid,$tag,$queryperc,$targetperc) = split (/\t/,$_);
+    #print STDERR "$queryid,$tid,$tag,$queryperc,$targetperc\n";
+
+    if ($tid ne "orphan") {
+	if ($tid =~ /^NP_\d+/) {
+	
+	    #($tid) = $tid =~ /^(NP_\d+)/;
+	#print STDERR "$tid\n";
+	    $tid = $ref_map{$tid};
+	}
+	
+	#print STDERR "$tid\n";
+	
+	my @array = @{$map{$tid}};
+
+	foreach my $a(@array) {
+	    #print STDERR $a->xDB."\n"; 
+	    
+	    my $dbentry = Bio::EnsEMBL::DBEntry->new
+		( -adaptor => $adaptor,
+		  -primary_id => $a->xAC,
+		  -display_id => $a->xID,
+		  -version => 1,
+		  -release => 1,
+		  -dbname => $a->xDB );
+    
+	    
+	    
+	    my @synonyms = split (/;/,$a->xSYN);
+		
+
+	    foreach my $syn (@synonyms) {
+		if ($syn =~ /\S+/) {
+		    $dbentry->add_synonym($syn);
+		}
+	    }
+	    $adaptor->store($dbentry,$queryid,"Translation");
+	}
+    
+    }
+}
+
+
+
+package Desc;
+
+=head2 new
+
+ Title   : new
+ Usage   : $obj->new($newval)
+ Function: 
+ Returns : value of new
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub new{
+ my $class= shift;
+    my $self = {};
+    bless $self,$class;
+    return $self;
+}
+
+=head2 targetDB
+
+ Title   : targetDB
+ Usage   : $obj->targetDB($newval)
+ Function: 
+ Returns : value of targetDB
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub targetDB{
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'targetDB'} = $value;
+    }
+    return $obj->{'targetDB'};
+
+}
+
+
+=head2 xAC
+
+ Title   : xAC
+ Usage   : $obj->xAC($newval)
+ Function: 
+ Returns : value of xAC
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub xAC{
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'xAC'} = $value;
+    }
+    return $obj->{'xAC'};
+
+}
+
+=head2 xDB
+
+ Title   : xDB
+ Usage   : $obj->xDB($newval)
+ Function: 
+ Returns : value of xDB
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub xDB{
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'xDB'} = $value;
+    }
+    return $obj->{'xDB'};
+
+}
+
+=head2 xID
+
+ Title   : xID
+ Usage   : $obj->xID($newval)
+ Function: 
+ Returns : value of xID
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub xID{
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'xID'} = $value;
+    }
+    return $obj->{'xID'};
+
+}
+
+=head2 xSYN
+
+ Title   : xSYN
+ Usage   : $obj->xSYN($newval)
+ Function: 
+ Returns : value of xSYN
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub xSYN{
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'xSYN'} = $value;
+    }
+    return $obj->{'xSYN'};
+
+}
+
+

misc-scripts/protein_match/pmatch.pl

+#!/usr/local/bin/perl
+
+# Author: Marc Sohrmann (ms2@sanger.ac.uk)
+# Copyright (c) Marc Sohrmann, 2001
+# You may distribute this code under the same terms as perl itself
+
+# wrapper around Richard Durbin's pmatch code (fast protein matcher).
+
+# 06/01 Adapted for Ensembl (mongin@ebi.ac.uk)
+
+
+
+use strict;
+use Getopt::Std;
+use vars qw($opt_q $opt_t $opt_l $opt_o $opt_p $opt_w $opt_s $opt_c $opt_d);
+
+BEGIN {
+    unshift (@INC,"/work1/mongin/src/ensembl-live/misc-scripts/protein_match");
+    require "mapping_conf.pl";
+}
+
+
+
+my %conf =  %::mapping_conf;
+
+my $sptr_fa = $conf{'sptr_fa'};
+my $refseq_fa = $conf{'refseq_fa'};
+
+$opt_p = 66;
+
+$opt_q = $conf{'query'};
+$opt_t = $conf{'sptr_fa'};
+$opt_o = $conf{'sp_map'};
+
+getopts ("q:t:l:o:p:wsc:d");
+
+my $usage = "pmatch.pl\n";
+$usage .= "-q [query fasta db]\n";
+$usage .= "-t [target fasta db] OR -l [file listing target fasta db's] OR -w to create tmp file of all worm pep's from SWALL\n";
+$usage .= "-o [out file]\n";
+$usage .= "-s to calculate the best path of non-overlapping pmatch matches for each query-target pair  OPTIONAL\n";
+$usage .= "-c to classify the matches (relative to the query sequence)   OPTIONAL\n";
+$usage .= "-d to keep the intermediate tmp files   OPTIONAL\n";
+$usage .= "-p minimum percentage off identity accepted OPTIONAL (default value 66%)\n";
+
+#unless ($opt_q && ($opt_t || $opt_l || $opt_w) && $opt_o) {
+#    die "$usage";
+#}
+
+
+
+#################################
+
+my $query = $opt_q;
+my $target = $opt_t;
+
+#################################
+# make worm-specific protein set from SWALL if ($opt_w)
+
+if ($opt_w) {
+    print STDERR "extract worm sequences from SWALL...\n";
+    my $getz = "getz -f seq -sf fasta \'[swall-org:Caenorhabditis elegans]\' > $$.swall";
+    system "$getz";
+    $target = "$$.swall";
+}
+
+#################################
+# run pmatch (Richard Durbin's fast protein matcher, rd@sanger.ac.uk)
+
+print STDERR "run pmatch...\n";
+if ($opt_l) {
+    my @files;
+    open (DB , "$opt_l") || die "cannot read $opt_l\n";
+    while (<DB>) {
+        chomp;
+        my @a = split /\s+/;
+        push (@files , @a);
+    }
+    close DB;        
+    foreach my $file (@files) {
+        my $pmatch = "/nfs/disk65/ms2/bin/pmatch -T 14 $file $query >> $$.pmatch";
+        system "$pmatch";
+    }
+}
+else {
+    my $pmatch = "/nfs/disk65/ms2/bin/pmatch -T 14 $target $query > $$.pmatch";
+    system "$pmatch";
+}
+
+if ($opt_w && !$opt_d) {
+    unlink "$$.swall";
+}
+
+#################################
+# sort the pmatch output file, based on query and target name
+# (necessary since not all the matches relating to a query-target pair cluster)
+
+print STDERR "sort the pmatch output file...\n";
+my (@a , @q , @t);
+open (TMP , ">$$.sort") || die "cannot create $$.sort\n";
+open (PMATCH , "$$.pmatch") || die "cannot read $$.pmatch\n";
+while (<PMATCH>) {
+    my @f = split /\t/;
+    push @a, $_;
+    push @q, $f[1];
+    push @t, $f[6];
+}
+foreach my $i (sort { $q[$a] cmp $q[$b] or $t[$a] cmp $t[$b] } 0..$#a) { print TMP $a[$i] }
+close PMATCH;
+close TMP;
+rename ("$$.sort" , "$$.pmatch");
+
+#################################
+# determine the best path of non-overlapping matching substrings (if $opt_s)
+
+if ($opt_s) {
+    print STDERR "stitch pmatch substrings...\n";
+    open (STITCH , ">$$.stitch") || die "cannot create $$.stitch\n";
+    my @match_list = ();
+    my $old_query;
+    my $old_target;
+    my $old_qlen;
+    my $old_tlen;
+    my $previous_line;
+    open (PMATCH , "$$.pmatch") || die "cannot read $$.pmatch\n";
+    while (<PMATCH>) {
+        chomp;
+        my @a = split /\t/;
+        my $query = $a[1];
+        my $qstart = $a[2];
+        my $qend = $a[3];
+        my $qlen = $a[5];
+        my $target = $a[6];
+        my $tstart = $a[7];
+        my $tend = $a[8];
+        my $tlen = $a[10];
+
+        # new set of query/target 
+