diff --git a/misc-scripts/gene_description/gene-descriptions.pl b/misc-scripts/gene_description/gene-descriptions.pl
index e2ac1b46c0477485d12d9ed52e6135fc121535a9..a482f8668aaea269c94eaabe905d83e5850e8829 100755
--- a/misc-scripts/gene_description/gene-descriptions.pl
+++ b/misc-scripts/gene_description/gene-descriptions.pl
@@ -16,6 +16,7 @@
# 4 Problem with an Acc without description
use strict;
+use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Getopt::Long;
@@ -23,8 +24,8 @@ $| = 1;
# db_name used in the Ensembl core database (to be checked in table externalDB) and
# used in the protein mapping.
-my %protein_db_naming = ('swissprot' => "SWISSPROT",
- 'sptrembl' => "SPTREMBL",
+my %protein_db_naming = ('swissprot' => "Uniprot/SWISSPROT",
+ 'sptrembl' => "Uniprot/SPTREMBL",
'refseq' => "RefSeq");
my @databases_used_for_guessing_descriptions;
@@ -69,6 +70,7 @@ my ($host, $port, $dbname, $dbuser, $dbpass, $gene_description_file);
my $regexp_file;
my $debug = 0;
my $consortium = "";
+my $reg_conf;
unless (GetOptions('help' => \$help,
'host=s' => \$host,
@@ -79,7 +81,8 @@ unless (GetOptions('help' => \$help,
'r=s' => \$regexp_file,
'consortium' => \$consortium,
'load=s' => \$gene_description_file,
- 'debug' => \$debug)) {
+ 'debug' => \$debug,
+ 'reg_conf' => \$reg_conf)) {
die $usage;
}
@@ -121,6 +124,10 @@ if (defined $gene_description_file || defined $dbpass) {
die $usage;
}
+# Take values from ENSEMBL_REGISTRY environment variable or from ~/.ensembl_init
+# if no reg_conf file is given.
+Bio::EnsEMBL::Registry->load_all($reg_conf);
+
## Loading data to database if requested and exit
if (defined $gene_description_file) {
@@ -163,7 +170,7 @@ my $db_query = join ",",@databases_used_for_guessing_descriptions;
print STDERR "Preparing query...";
-my $sth = $db->prepare("
+my $sth = $db->dbc->prepare("
SELECT
tsl.translation_id,tsc.gene_id,xdb.db_name,x.dbprimary_acc,ix.query_identity,ix.target_identity
FROM
@@ -203,11 +210,17 @@ while (my ($ensp, $ensg, $db, $acc, $qy_percid, $tg_percid) = $sth->fetchrow_arr
$db eq $protein_db_naming{'refseq'})) {
if ($prev_qy_percid < $qy_percid) {
$desc = $sp_desc{"$db:$acc"};
+ if ($debug) {
+ print "debug1: $ensg $db, $desc, $acc, $qy_percid, $tg_percid\n";
+ }
$gene_desc{$ensg} = [ $db, $desc, $acc, $qy_percid, $tg_percid ]; # taking better SWISSPROT/RefSeq/Consortium desc.
next;
} elsif ($prev_qy_percid == $qy_percid &&
$prev_tg_percid < $tg_percid) {
$desc = $sp_desc{"$db:$acc"};
+ if ($debug) {
+ print "debug2: $ensg $db, $desc, $acc, $qy_percid, $tg_percid\n";
+ }
$gene_desc{$ensg} = [ $db, $desc, $acc, $qy_percid, $tg_percid ]; # taking better SWISSPROT/RefSeq/Consortium desc.
next;
} else {
@@ -217,6 +230,9 @@ while (my ($ensp, $ensg, $db, $acc, $qy_percid, $tg_percid) = $sth->fetchrow_arr
if ($db eq $protein_db_naming{$consortium}) {
$desc = $sp_desc{"$db:$acc"};
+ if ($debug) {
+ print "debug3: $ensg $db, $desc, $acc, $qy_percid, $tg_percid\n";
+ }
$gene_desc{$ensg} = [ $db, $desc, $acc, $qy_percid, $tg_percid ]; # kick out the SWISSPROT/RefSeq/SPTREMBL desc -> priority to consortium desc
next;
}
@@ -224,6 +240,9 @@ while (my ($ensp, $ensg, $db, $acc, $qy_percid, $tg_percid) = $sth->fetchrow_arr
if ($db eq $protein_db_naming{'swissprot'} &&
$prevdb ne $protein_db_naming{$consortium}) {
$desc = $sp_desc{"$db:$acc"};
+ if ($debug) {
+ print "debug4: $ensg $db, $desc, $acc, $qy_percid, $tg_percid\n";
+ }
$gene_desc{$ensg} = [ $db, $desc, $acc, $qy_percid, $tg_percid ]; # kick out the RefSeq/SPTREMBL desc -> priority to SWISSPROT desc
next;
}
@@ -232,6 +251,9 @@ while (my ($ensp, $ensg, $db, $acc, $qy_percid, $tg_percid) = $sth->fetchrow_arr
$prevdb ne $protein_db_naming{'swissprot'} &&
$prevdb ne $protein_db_naming{$consortium}) {
$desc = $sp_desc{"$db:$acc"};
+ if ($debug) {
+ print "debug5: $ensg $db, $desc, $acc, $qy_percid, $tg_percid\n";
+ }
$gene_desc{$ensg} = [ $db, $desc, $acc, $qy_percid, $tg_percid ]; # kick out the SPTREMBL desc -> priority to RefSeq desc
next;
}
@@ -242,6 +264,9 @@ while (my ($ensp, $ensg, $db, $acc, $qy_percid, $tg_percid) = $sth->fetchrow_arr
if (compare_desc($prev_desc,$desc) < 0) {
# new desc is better
# warn "new better: $desc (old was: $prev_desc)\n";
+ if ($debug) {
+ print "debug6: $ensg $db, $desc, $acc, $qy_percid, $tg_percid\n";
+ }
$gene_desc{$ensg} = [ $db, $desc, $acc, $qy_percid, $tg_percid ];
next;
} else {
@@ -252,6 +277,9 @@ while (my ($ensp, $ensg, $db, $acc, $qy_percid, $tg_percid) = $sth->fetchrow_arr
}
} else {
$desc = $sp_desc{"$db:$acc"};
+ if ($debug) {
+ print "debug7: $ensg $db, $desc, $acc, $qy_percid, $tg_percid\n";
+ }
$gene_desc{$ensg} = [ $db, $desc, $acc, $qy_percid, $tg_percid ];
}
}
@@ -341,7 +369,7 @@ exit 3";
-user => $dbuser,
-pass => $dbpass);
- my $sth = $db->prepare("load data infile '$ENV{PWD}/gene_description_file.symlink' into table gene_description");
+ my $sth = $db->dbc->prepare("load data infile '$ENV{PWD}/gene_description_file.symlink' into table gene_description");
unless ($sth->execute()) {
unlink "$ENV{PWD}/gene_description_file.symlink";
@@ -417,17 +445,22 @@ sub parse_protein_database {
if ($line =~ /^DEFINITION\s+(\S.*\S)$/o) {
$desc .= $1;
+ print STDERR "desc1",$desc,"\n" if ($line =~ /^DEFINITION.*somatostatin precursor.*$/);
while (defined ($line = <PROTDBF>)) {
- last if ($line =~ /^ACCESSION\s+(\S+)\s*.*$/o);
+ if ($line =~ /^ACCESSION\s+(\S+)\s*.*$/o) {
+ # If xrefs have only NP_ uncomment the following line
+# $acc = $1;
+ last;
+ }
if ($line =~ /^\s+(\S.*\S)$/o) {
$desc .= " ". $1;
}
}
}
-
+
+ # Accession Number got in this line here during protein mapping
+ # not in ACCESSION line. If xrefs have only NP_ comment all the if
if ($line =~ /^DBSOURCE\s+(\S+)\s*.*$/o) {
-# Accession Number got in this line here during protein mapping
-# not in ACCESSION line.
if ($line =~ /^DBSOURCE\s+REFSEQ:\s+accession\s+(\S+)\.\d+$/o) {
$acc = $1;
} else {
@@ -439,8 +472,8 @@ Expecting to match this regexp /^DBSOURCE\\s+REFSEQ:\\s+accession\\s+(\\S+)\\.\\
}
if ($line =~ /^\/\/$/o) {
- $desc =~ s/\s*\[.*\]//g;
- $sp_desc{"$db:$acc"} = $desc;
+ #$desc =~ s/\s*\[.*\]//g;
+ $sp_desc{"$db:$acc"} = $desc;
$db = undef;
$acc = undef;
$desc = "";