Skip to content

GitLab

Commit f4359138 authored by Emmanuel Mongin's avatar Emmanuel Mongin
Browse files

Set of script with the changes I've used for the mapping

parent 054348b2
Hide whitespace changes
Inline Side-by-side
Showing with 89 additions and 51 deletions
misc-scripts/protein_match/get_embl_mim_mapping.pl
View file @ f4359138
......@@ -45,7 +45,9 @@ while ( my $seq1 = $in1->next_seq() ) {
}
print OUT "$map{$ac}\t$ac\tEMBL_AC\t".$link->primary_id,"\n";
print OUT "$map{$ac}\t$ac\tEMBL_PROT_AC\t".$link->optional_id,"\n";
my ($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}) {
......@@ -57,6 +59,8 @@ while ( my $seq1 = $in1->next_seq() ) {
}
}
......
misc-scripts/protein_match/get_xrefs.pl
View file @ f4359138
......@@ -39,7 +39,7 @@ my %embl_clone;
'output:s'=>\$out
);
#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_xrefs.pl -mapping ../map_outputs/totalmap.final -xrefs ../sec_outputs/xrefs.map -dbmap ../sec_outputs/mapdb.map -refseq ../primary/hs.gnp -output final.map
#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_xrefs.pl -mapping ../map_outputs/map.total -xrefs ../sec_outputs/xref.total -dbmap ../sec_outputs/mapdb.map -refseq ../primary/hs.gnp -output final.map
open (DBMAP,"$dbmap") || die "Can't open file $dbmap\n";
open (XREF,"$xrefs") || die "Can't open file $xrefs\n";
......@@ -52,12 +52,12 @@ open (OUT,">$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 (<CLONE>) {
# chomp;
# my ($embl_ac,$id) = split(/\t/,$_);
# print "$embl_ac\n";
# $embl_clone{$embl_ac}=1;
#}
while (<DBMAP>) {
......@@ -105,7 +105,7 @@ while (<XREF>) {
#Get the embl ACs for each SP and SPTREMBL proteins
#if ((($xrdb eq "SP") || ($xrdb eq "SPTREMBL")) && ($db eq "EMBL")) {
#print "$id\n";
#if ($embl_clone{$id}) {
#if ($embl_clone{$id}) {
# push(@{$sp2embl{$xrac}},$id);
#}
......@@ -117,7 +117,9 @@ while (<MAP>) {
#P01111 COBP00000000001 100 PRIMARY
my ($xr,$ens,$perc,$tag) = split (/\t/,$_);
if ($xr =~ /^\w+-\d{2}/) {
($xr) = $xr =~ /^(\w+)-\d{2}/;
}
#Hack to be taken away
#my ($en1,$en2) = $ens =~ /(\w{3})P(\d+)/;
#my $enst = $en1."T".$en2;
......@@ -161,10 +163,18 @@ while (<MAP>) {
#Print the know gene AC and its database
#print OUT "$ens\t$map{$xr}\t$xr\n";
#}
if (!defined $map{$xr}) {
print STDERR "can't find primary $xr\n";
}
print OUT "$ens\t$map{$xr}\t$xr\n";
#Print all of the external database it links to (eg: HUGO)
foreach my $both (@{$hash{$xr}}){
if (!defined $hash{$xr}) {
print STDERR "can't find Xref $xr\n";
}
($a,$b) = split(/&/,$both);
print OUT "$ens\t$a\t$b\n";
}
......
misc-scripts/protein_match/load_mapping.pl
View file @ f4359138
......@@ -12,18 +12,18 @@ my %scopid;
my %gene_map;
my %transcript_map;
my %spid;
my ($mapping, $hugosyn, $scopsyn, $out, $spsyn);
my ($mapping, $hugosyns, $scopsyn, $out, $spsyn);
#perl ../../src/ensembl-live/misc-scripts/protein_match/load_mapping.pl -mapping outputs/final_sorted.map -hugosyn secondary/ens4.txt -scopsyn secondary/dir.dom.scop.txt_1.53 -spid primary/hum_sp_sptrembl.pep
#perl ../../src/ensembl-live/misc-scripts/protein_match/load_mapping.pl -mapping outputs/final_sorted.map -hugosyn secondary/nomeid.txt -scopsyn secondary/dir.dom.scop.txt_1.53 -spid primary/hum_sp_sptrembl.pep
&GetOptions(
'mapping:s'=>\$mapping,
'hugosyn:s'=>\$hugosyn,
'hugosyn:s'=>\$hugosyns,
'scopsyn:s'=>\$scopsyn,
'spid:s'=>\$spsyn
);
my $dsn = "DBI:mysql:database=ensembl090_tmp;host=ecs1c";
my $dsn = "DBI:mysql:database=xrefs100_tmp;host=ecs1c";
my $db = DBI->connect("$dsn",'ensadmin') || die ("Could not connect to db!");
my $adaptor = Bio::EnsEMBL::DBSQL::DBEntryAdaptor->new($db);
......@@ -32,35 +32,42 @@ my $adaptor = Bio::EnsEMBL::DBSQL::DBEntryAdaptor->new($db);
print STDERR "Getting SP mapping\n";
#my $in = Bio::SeqIO->new(-file => $spsyn, '-format' =>'swiss');
my $in = Bio::SeqIO->new(-file => $spsyn, '-format' =>'swiss');
#while ( my $seq = $in->next_seq() ) {
my $ac;# = $seq->accession;
my $id;# = $seq->id;
while ( my $seq = $in->next_seq() ) {
my $ac = $seq->accession;
my $id = $seq->id;
$spid{$ac} = $id;
#}
}
open (HUGO, "$hugosyn") || die "Can't open file $mapping\n";
open (HUGO, "$hugosyns") || die "Can't open file $mapping\n";
while (<HUGO>) {
chomp;
#get red of the cariage return present in Hugos
$_ =~ s/\r//g;
my ($hgnc, $symbol, $alias, $withdrawn) = split (/\t/,$_);
#my ($hgnc, $symbol, $alias, $withdrawn) = split (/\t/,$_);
my @hug = split (/\t/,$_);
my $hgnc = $hug[0];
my $symbol = $hug[1];
my $alias = $hug[8];
my @aliases = split (/, /,$alias);
my @withdrawns = split (/, /,$withdrawn);
#my @withdrawns = split (/, /,$withdrawn);
$hugoid{$hgnc}=$symbol;
foreach my $al(@aliases) {
push(@{$hugosyn{$symbol}},$al);
push(@{$hugosyn{$hgnc}},$al);
}
foreach my $wi(@withdrawns) {
push(@{$hugosyn{$symbol}},$wi);
}
#foreach my $wi(@withdrawns) {
#push(@{$hugosyn{$symbol}},$wi);
#}
}
close (HUGO);
......@@ -76,7 +83,9 @@ while (<SCOP>) {
#Set up the display id
my $display = $pdb." ".$chain;
push (@{$scopid{$scopac}},$display);
#push (@{$scopid{$scopac}},$display);
$scopid{$scopac} = $display;
#push(@{$scopsyn{$scopac}},$pdb);
#push(@{$scopsyn{$scopac}},$chain);
......@@ -95,12 +104,12 @@ while (<MAPPING>) {
#Get SP mapping
#if (($db ne "HUGOSYMBOL") && ($db ne "SCOP") && ($db ne "SCOP1") && ($db ne "SCOP2") && ($db ne "HUGOID") && ($db ne "HUGOALIAS") && ($db ne "HUGOWITHDRAWN")) {
if (($db eq "EMBL") || ($db eq "EC") || ($db eq "OMIM") || ($db eq "REFSEQ") || ($db eq "LOCUS")) {
if (($db eq "EMBL_AC") || ($db eq "EMBL_PROT_AC") || ($db eq "EC") || ($db eq "OMIM") || ($db eq "REFSEQ") || ($db eq "LOCUS")) {
##############Temporary changes###########################
my ($ac1) = $ens =~ /COBP(\d+)/;
$ens = "COBT"."$ac1";
#my ($ac1) = $ens =~ /COBP(\d+)/;
#$ens = "COBT"."$ac1";
##########################################################
......@@ -111,7 +120,7 @@ while (<MAPPING>) {
-version => 1,
-release => 1,
-dbname => $db );
$adaptor->store($dbentry,$ens,"Gene");
$adaptor->store($dbentry,$ens,"Translation");
}
......@@ -129,15 +138,16 @@ while (<MAPPING>) {
-version => 1,
-release => 1,
-dbname => $db );
$adaptor->store($dbentry,$ens,"Translation");
}
if ($db eq "HUGOID") {
##################Temporary changes#######################
my ($ac1) = $ens =~ /COBP(\d+)/;
$ens = "COBT"."$ac1";
#my ($ac1) = $ens =~ /COBP(\d+)/;
#$ens = "COBT"."$ac1";
##########################################################
if (!defined $hugoid{$primary_ac}) {
print "Hugo primary Ac ($primary_ac) does not have an id\n";
}
......@@ -150,8 +160,12 @@ while (<MAPPING>) {
-version => 1,
-release => 1,
-dbname => $db );
if ($hugosyn{$primary_ac}) {
my @synonyms = @{$hugosyn{$primary_ac}};
#print STDERR "SYN: @synonyms\t$primary_ac\n";
foreach my $syn (@synonyms) {
if ($syn =~ /\S+/) {
......@@ -161,24 +175,27 @@ while (<MAPPING>) {
}
$adaptor->store($dbentry,$ens,"Gene");
$adaptor->store($dbentry,$ens,"Translation");
}
if ($db eq "SCOP") {
if ($db eq "SCOP") {
my $dspl;
#############tmp########################
my ($ac1) = $ens =~ /COBP(\d+)/;
$ens = "COBT"."$ac1";
#my ($ac1) = $ens =~ /COBP(\d+)/;
#$ens = "COBT"."$ac1";
########################################
$dspl = $scopid{$primary_ac};
if (!defined $scopid{$primary_ac}) {
print "SCOP primary Ac ($primary_ac) does not have an id\n";
($dspl) = $primary_ac =~ /\w{1}(\w{4})/;
}
my $dbentry = Bio::EnsEMBL::DBEntry->new
( -adaptor => $adaptor,
-primary_id => $primary_ac,
-display_id => $scopid{$primary_ac},
-display_id => $dspl,
-version => 1,
-release => 1,
-dbname => $db );
......@@ -190,7 +207,7 @@ if ($db eq "SCOP") {
}
}
}
$adaptor->store($dbentry,$ens,"Gene");
$adaptor->store($dbentry,$ens,"Translation");
}
......@@ -198,3 +215,10 @@ if ($db eq "SCOP") {
misc-scripts/protein_match/process_pmach.pl
View file @ f4359138
......@@ -32,27 +32,27 @@ my ($ens,$sp,$refseq,$pdb);
);
&runpmatch();
#&postprocesspmatch($sp);
&postprocesspmatch($sp);
&postprocesspmatch($refseq);
#&postprocesspmatch($pdb);
#&finalprocess($sp);
&postprocesspmatch($pdb);
&finalprocess($sp);
&finalprocess($refseq);
#&finalprocess($pdb);
&finalprocess($pdb);
#perl ../../../src/ensembl-live/misc-scripts/protein_match/process_pmach.pl -ens ../primary/TGWpep -sp ../primary/SPTr.human.expanded -refseq ../primary/hs2.fsa -pdb ../primary/scop.fas
#perl ../../../src/ensembl-live/misc-scripts/protein_match/process_pmach.pl -ens ../primary/SPAN_pepfile -sp ../primary/SPTr.human.expanded -refseq ../primary/hs2.fsa -pdb ../primary/scop_human.fas
sub runpmatch {
print STDERR "Running pmatch\n";
#Run pmatch and store the data in files which will be kept for debugging
#my $pmatch1 = "/nfs/griffin2/rd/bin.ALPHA/pmatch -T 14 $sp $ens > ens_sp_rawpmatch";
my $pmatch1 = "/nfs/griffin2/rd/bin.ALPHA/pmatch -T 14 $sp $ens > ens_sp_rawpmatch";
my $pmatch2 = "/nfs/griffin2/rd/bin.ALPHA/pmatch -T 14 $refseq $ens > ens_refseq_rawpmatch";
#my $pmatch3 = "/nfs/griffin2/rd/bin.ALPHA/pmatch -T 14 $pdb $ens > ens_pdb_rawpmatch";
my $pmatch3 = "/nfs/griffin2/rd/bin.ALPHA/pmatch -T 14 $pdb $ens > ens_pdb_rawpmatch";
#system($pmatch1); # == 0 or die "$0\Error running '$pmatch1' : $!";
system($pmatch1); # == 0 or die "$0\Error running '$pmatch1' : $!";
system($pmatch2); #== 0 or die "$0\Error running '$pmatch2' : $!";
#system($pmatch3); #== 0 or die "$0\Error running '$pmatch2' : $!";
system($pmatch3); #== 0 or die "$0\Error running '$pmatch2' : $!";
}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment