From cab090e8d51d81f5e4a457a82775e43f9c514497 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 22 Sep 2011 09:52:43 +0000
Subject: [PATCH] add_xref now takes a hash instead of a list for easy
maintainance. Lots of docs and removal of old subroutines. perlcritic fixes.
---
.../xref_mapping/XrefParser/BaseParser.pm | 394 +++++++++---------
1 file changed, 187 insertions(+), 207 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index 6ccf5ec05a..26c604f315 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -18,12 +18,6 @@ my $add_dependent_xref_sth = undef;
my $get_xref_sth = undef;
my $add_synonym_sth = undef;
-#my $dbi;
-#my %dependent_sources;
-#my %taxonomy2species_id;
-#my %species_id2taxonomy;
-#my %name2species_id;
-#my %species_id2name;
my %xref_dependent_mapped;
@@ -40,7 +34,7 @@ sub new
my ($proto, $database, $is_verbose) = @_;
if((!defined $database)){# or (!$database->isa(XrefPArserDatabase)))
- croak "No database specfied";
+ croak 'No database specfied';
}
$verbose = $is_verbose;
my $dbi = $database->dbi;
@@ -76,8 +70,11 @@ sub get_filehandle
{
my ($self, $file_name) = @_;
- my $io;
+ my $io =undef;
+ if(!(defined $file_name) or $file_name eq ''){
+ confess "No file name";
+ }
my $alt_file_name = $file_name;
$alt_file_name =~ s/\.(gz|Z)$//x;
@@ -104,7 +101,7 @@ sub get_filehandle
if ( !defined $io ) { return }
if ($verbose) {
- print("Reading from '$file_name'...\n");
+ print "Reading from '$file_name'...\n" || croak 'Could not print out message';
}
return $io;
@@ -122,9 +119,11 @@ sub get_filehandle
sub get_source_id_for_source_name {
my ($self, $source_name,$priority_desc) = @_;
- my $sql = "SELECT source_id FROM source WHERE LOWER(name)='" . lc($source_name) . "'";
- if(defined($priority_desc)){
- $sql .= " AND LOWER(priority_description)='".lc($priority_desc)."'";
+ my $low_name = lc $source_name;
+ my $sql = "SELECT source_id FROM source WHERE LOWER(name)='$low_name'";
+ if(defined $priority_desc){
+ $low_name = lc $priority_desc;
+ $sql .= " AND LOWER(priority_description)='$low_name'";
$source_name .= " ($priority_desc)";
}
my $sth = $self->dbi->prepare($sql);
@@ -132,13 +131,13 @@ sub get_source_id_for_source_name {
my @row = $sth->fetchrow_array();
my $source_id;
if (@row) {
- $source_id = $row[0];
+ $source_id = $row[0];
} else {
carp "WARNING: There is no entity $source_name in the source-table of the xref database.\n";
carp "WARNING:. The external db name ($source_name) is hardcoded in the parser\n";
carp "WARNING: Couldn't get source ID for source name $source_name\n";
- $source_id = -1;
+ $source_id = '-1';
}
return $source_id;
}
@@ -157,7 +156,8 @@ sub get_source_ids_for_source_name_pattern {
my ($self, $source_name) = @_;
- my $sql = "SELECT source_id FROM source WHERE upper(name) LIKE '%".uc($source_name)."%'";
+ my $big_name = uc $source_name;
+ my $sql = "SELECT source_id FROM source WHERE upper(name) LIKE '%${big_name}%'";
my $sth = $self->dbi->prepare($sql);
my @sources;
@@ -179,18 +179,18 @@ sub get_source_name_for_source_id {
my ($self, $source_id) = @_;
my $source_name;
- my $sql = "SELECT name FROM source WHERE source_id= '" . $source_id. "'";
+ my $sql = "SELECT name FROM source WHERE source_id= '$source_id'";
my $sth = $self->dbi->prepare($sql);
$sth->execute();
my @row = $sth->fetchrow_array();
if (@row) {
- $source_name = $row[0];
+ $source_name = $row[0];
} else {
carp "There is no entity with source-id $source_id in the source-table of the \n";
carp "xref-database. The source-id and the name of the source-id is hard-coded in populate_metadata.sql\n" ;
carp "and in the parser\n";
carp "Couldn't get source name for source ID $source_id\n";
- $source_name = -1;
+ $source_name = '-1';
}
return $source_name;
}
@@ -207,30 +207,30 @@ sub get_valid_xrefs_for_dependencies{
my %dependent_2_xref;
- my $sql = "select source_id from source where LOWER(name) =?";
+ my $sql = 'select source_id from source where LOWER(name) =?';
my $sth = $self->dbi->prepare($sql);
my @dependent_sources;
- $sth->execute(lc($dependent_name));
+ $sth->execute(lc $dependent_name);
while(my @row = $sth->fetchrow_array()){
push @dependent_sources,$row[0];
}
my @sources;
foreach my $name (@reverse_ordered_source_list){
- $sth->execute(lc($name));
+ $sth->execute(lc $name);
while(my @row = $sth->fetchrow_array()){
push @sources,$row[0];
}
}
$sth->finish;
- my $dep_sql = (<<"DSS");
-SELECT d.master_xref_id, x2.accession
- FROM dependent_xref d, xref x1, xref x2
- WHERE x1.xref_id = d.master_xref_id AND
- x1.source_id = ? AND
- x2.xref_id = d.dependent_xref_id AND
- x2.source_id = ?
+ my $dep_sql = (<<'DSS');
+ SELECT d.master_xref_id, x2.accession
+ FROM dependent_xref d, xref x1, xref x2
+ WHERE x1.xref_id = d.master_xref_id AND
+ x1.source_id = ? AND
+ x2.xref_id = d.dependent_xref_id AND
+ x2.source_id = ?
DSS
$sth = $self->dbi->prepare($dep_sql);
@@ -252,28 +252,19 @@ DSS
# to master_xref_id for all of source names given
#####################################################
sub get_valid_xrefs_for_direct_xrefs{
- my ($self, $direct_name, @list) = @_;
+ my ($self, $direct_name, $separator) = @_;
my %direct_2_xref;
- my $sql = "select source_id from source where name like ?";
+ my $sql = 'select source_id from source where name like ?';
my $sth = $self->dbi->prepare($sql);
my @direct_sources;
- $sth->execute($direct_name."%");
+ $sth->execute("${direct_name}%");
while(my @row = $sth->fetchrow_array()){
push @direct_sources,$row[0];
}
- my @sources;
- foreach my $name (@list){
- $sth->execute($name);
- while(my @row = $sth->fetchrow_array()){
- push @sources,$row[0];
- }
- }
- $sth->finish;
-
my $gen_sql =(<<"GDS");
SELECT d.general_xref_id, d.ensembl_stable_id, 'TYPE', d.linkage_xref, x1.accession
FROM TABLE_direct_xref d, xref x1
@@ -285,18 +276,18 @@ GDS
my $i=0;
foreach my $type (qw(Gene Transcript Translation)){
my $t_sql = $gen_sql;
- my $table = lc($type);
- $t_sql =~ s/TABLE/$table/x;
- $t_sql =~ s/TYPE/$type/x;
+ my $table = lc $type;
+ $t_sql =~ s/TABLE/$table/xsm;
+ $t_sql =~ s/TYPE/$type/xsm;
$sth[$i++] = $self->dbi->prepare($t_sql);
}
foreach my $d (@direct_sources){
- for (my $ii =0; $i<3; $i++){
+ for my $ii (0..2) {
$sth[$ii]->execute($d);
- while(my @row = $sth[$ii]->fetchrow_array()){
- $direct_2_xref{$row[4]} = $row[0]."::".$row[1]."::".$row[2]."::".$row[3];
+ while(my ($gen_xref_id, $stable_id, $type, $link, $acc) = $sth[$ii]->fetchrow_array()){
+ $direct_2_xref{$acc} = $gen_xref_id.$separator.$stable_id.$separator.$type.$separator.$link;
}
}
}
@@ -315,7 +306,7 @@ sub label_to_acc{
# First cache synonyms so we can quickly add them later
my %synonyms;
- my $syn_sth = $self->dbi->prepare("SELECT xref_id, synonym FROM synonym");
+ my $syn_sth = $self->dbi->prepare('SELECT xref_id, synonym FROM synonym');
$syn_sth->execute();
my ($xref_id, $synonym);
@@ -329,7 +320,8 @@ sub label_to_acc{
my %valid_codes;
my @sources;
- my $sql = "select source_id from source where upper(name) like '%".uc($source_name)."%'";
+ my $big_name = uc $source_name;
+ my $sql = "select source_id from source where upper(name) like '%${big_name}%'";
my $sth = $self->dbi->prepare($sql);
$sth->execute();
while(my @row = $sth->fetchrow_array()){
@@ -368,7 +360,7 @@ sub get_valid_codes{
# First cache synonyms so we can quickly add them later
my %synonyms;
my $dbi = $self->dbi;
- my $syn_sth = $dbi->prepare("SELECT xref_id, synonym FROM synonym");
+ my $syn_sth = $dbi->prepare('SELECT xref_id, synonym FROM synonym');
$syn_sth->execute();
my ($xref_id, $synonym);
@@ -382,7 +374,8 @@ sub get_valid_codes{
my %valid_codes;
my @sources;
- my $sql = "select source_id from source where upper(name) like '%".uc($source_name)."%'";
+ my $big_name = uc $source_name;
+ my $sql = "select source_id from source where upper(name) like '%$big_name%'";
my $sth = $dbi->prepare($sql);
$sth->execute();
while(my @row = $sth->fetchrow_array()){
@@ -411,33 +404,39 @@ sub get_valid_codes{
sub upload_xref_object_graphs {
my ($self, $rxrefs) = @_;
- print "count = ".$#$rxrefs."\n" if($verbose);
+ my $count = scalar @{$rxrefs};
+ if($verbose) {
+ print "count = $count\n" || croak 'Could not print out count';
+ }
- if ($#$rxrefs > -1) {
+ if ($count) {
#################
# upload new ones
##################
- print "Uploading xrefs\n" if($verbose);
+ if ($verbose) {
+ print "Uploading xrefs\n"
+ || croak 'Could not print string';
+ }
#################################################################################
# Start of sql needed to add xrefs, primary_xrefs, synonym, dependent_xrefs etc..
#################################################################################
my $dbi = $self->dbi;
- my $xref_sth = $dbi->prepare("INSERT INTO xref (accession,version,label,description,source_id,species_id, info_type) VALUES(?,?,?,?,?,?,?)");
- my $pri_insert_sth = $dbi->prepare("INSERT INTO primary_xref VALUES(?,?,?,?)");
- my $pri_update_sth = $dbi->prepare("UPDATE primary_xref SET sequence=? WHERE xref_id=?");
- my $syn_sth = $dbi->prepare("INSERT INTO synonym VALUES(?,?)");
- my $dep_sth = $dbi->prepare("INSERT INTO dependent_xref (master_xref_id, dependent_xref_id, linkage_annotation, linkage_source_id) VALUES(?,?,?,?)");
- my $xref_update_label_sth = $dbi->prepare("UPDATE xref SET label=? WHERE xref_id=?");
- my $xref_update_descr_sth = $dbi->prepare("UPDATE xref SET description=? WHERE xref_id=?");
- my $pair_sth = $dbi->prepare("INSERT INTO pairs VALUES(?,?,?)");
+ my $xref_sth = $dbi->prepare('INSERT INTO xref (accession,version,label,description,source_id,species_id, info_type) VALUES(?,?,?,?,?,?,?)');
+ my $pri_insert_sth = $dbi->prepare('INSERT INTO primary_xref VALUES(?,?,?,?)');
+ my $pri_update_sth = $dbi->prepare('UPDATE primary_xref SET sequence=? WHERE xref_id=?');
+ my $syn_sth = $dbi->prepare('INSERT INTO synonym VALUES(?,?)');
+ my $dep_sth = $dbi->prepare('INSERT INTO dependent_xref (master_xref_id, dependent_xref_id, linkage_annotation, linkage_source_id) VALUES(?,?,?,?)');
+ my $xref_update_label_sth = $dbi->prepare('UPDATE xref SET label=? WHERE xref_id=?');
+ my $xref_update_descr_sth = $dbi->prepare('UPDATE xref SET description=? WHERE xref_id=?');
+ my $pair_sth = $dbi->prepare('INSERT INTO pairs VALUES(?,?,?)');
# disable error handling here as we'll do it ourselves
- local $xref_sth->{RaiseError} = 0;
- local $xref_sth->{PrintError} = 0;
+ $xref_sth->{RaiseError} = 0;
+ $xref_sth->{PrintError} = 0;
#################################################################################
# End of sql needed to add xrefs, primary_xrefs, synonym, dependent_xrefs etc..
@@ -446,8 +445,9 @@ sub upload_xref_object_graphs {
foreach my $xref (@{$rxrefs}) {
my $xref_id=undef;
- if(!defined($xref->{ACCESSION})){
- print "your xref does not have an accession-number,so it can't be stored in the database\n";
+ if(!(defined $xref->{ACCESSION} )){
+ print "Your xref does not have an accession-number,so it can't be stored in the database\n"
+ || croak 'Could not write message';
return;
}
@@ -460,11 +460,11 @@ sub upload_xref_object_graphs {
$xref->{DESCRIPTION},
$xref->{SOURCE_ID},
$xref->{SPECIES_ID},
- $xref->{INFO_TYPE} || "MISC")){
+ $xref->{INFO_TYPE} || 'MISC')){
#
- # if we failed to add the xrefs it must already exist so go find the xref_id for this
+ # if we failed to add the xref it must already exist so go find the xref_id for this
#
- if(!defined($xref->{SOURCE_ID})){
+ if(!(defined $xref->{SOURCE_ID})){
print "your xref: $xref->{ACCESSION} does not have a source-id\n";
return;
}
@@ -473,8 +473,12 @@ sub upload_xref_object_graphs {
acc => $xref->{ACCESSION},
source_id => $xref->{SOURCE_ID},
species_id => $xref->{SPECIES_ID}} );
- $xref_update_label_sth->execute($xref->{LABEL},$xref_id) if (defined($xref->{LABEL}));
- $xref_update_descr_sth->execute($xref->{DESCRIPTION},$xref_id,) if (defined($xref->{DESCRIPTION}));
+ if(defined $xref->{LABEL} ) {
+ $xref_update_label_sth->execute($xref->{LABEL},$xref_id) ;
+ }
+ if(defined $xref->{DESCRIPTION} ){
+ $xref_update_descr_sth->execute($xref->{DESCRIPTION},$xref_id);
+ }
}
else{
#
@@ -490,7 +494,7 @@ sub upload_xref_object_graphs {
################
# Error checking
################
- if(!(defined($xref_id) and $xref_id)){
+ if(!((defined $xref_id) and $xref_id)){
print STDERR "xref_id is not set for :\n".
"$xref->{ACCESSION}\n$xref->{LABEL}\n".
"$xref->{DESCRIPTION}\n$xref->{SOURCE_ID}\n".
@@ -502,7 +506,7 @@ sub upload_xref_object_graphs {
# create entry in primary_xref table with sequence; if this is a "cumulative"
# entry it may already exist, and require an UPDATE rather than an INSERT
#############################################################################
- if(defined($xref->{SEQUENCE})){
+ if(defined $xref->{SEQUENCE} ){
if ( $self->primary_xref_id_exists($xref_id) ) {
$pri_update_sth->execute( $xref->{SEQUENCE}, $xref_id )
or croak( $dbi->errstr() );
@@ -526,7 +530,7 @@ sub upload_xref_object_graphs {
# if there are dependent xrefs, add xrefs and dependent xrefs for them
#######################################################################
foreach my $depref (@{$xref->{DEPENDENT_XREFS}}) {
- my %dep = %$depref;
+ my %dep = %{$depref};
#################
# Insert the xref
@@ -534,10 +538,10 @@ sub upload_xref_object_graphs {
$xref_sth->execute($dep{ACCESSION},
$dep{VERSION} || 0,
$dep{LABEL} || $dep{ACCESSION},
- $dep{DESCRIPTION} || "",
+ $dep{DESCRIPTION} || '',
$dep{SOURCE_ID},
$xref->{SPECIES_ID},
- "DEPENDENT");
+ 'DEPENDENT');
#####################################
# find the xref_id for dependent xref
@@ -548,7 +552,7 @@ sub upload_xref_object_graphs {
source_id => $dep{SOURCE_ID},
species_id => $xref->{SPECIES_ID}} );
- if(!defined($dep_xref_id) || $dep_xref_id ==0 ){
+ if(!(defined $dep_xref_id) || $dep_xref_id ==0 ){
print STDERR "acc = $dep{ACCESSION} \nlink = $dep{LINKAGE_SOURCE_ID} \n".$dbi->err."\n";
print STDERR "source = $dep{SOURCE_ID}\n";
}
@@ -574,7 +578,7 @@ sub upload_xref_object_graphs {
#################################################
# Add the pair data. refseq dna/pep pairs usually
#################################################
- if(defined($xref_id) and defined($xref->{PAIR})){
+ if(defined $xref_id and defined $xref->{PAIR} ){
$pair_sth->execute($xref->{SOURCE_ID},$xref->{ACCESSION},$xref->{PAIR});
}
@@ -582,9 +586,9 @@ sub upload_xref_object_graphs {
###########################
# tidy up statement handles
###########################
- $xref_sth->finish() if defined $xref_sth;
- $pri_insert_sth->finish() if defined $pri_insert_sth;
- $pri_update_sth->finish() if defined $pri_update_sth;
+ if(defined $xref_sth) {$xref_sth->finish()};
+ if(defined $pri_insert_sth) {$pri_insert_sth->finish()} ;
+ if(defined $pri_update_sth) {$pri_update_sth->finish()};
} # foreach xref
@@ -599,7 +603,7 @@ sub upload_xref_object_graphs {
######################################################################################
sub upload_direct_xrefs{
my ($self, $direct_xref) = @_;
- for my $dr(@$direct_xref) {
+ for my $dr(@{$direct_xref}) {
################################################
# Find the xref_id for this accession and source
@@ -613,8 +617,8 @@ sub upload_direct_xrefs{
$self->add_direct_xref($general_xref_id, $dr->{ENSEMBL_STABLE_ID},$dr->{ENSEMBL_TYPE},$dr->{LINKAGE_XREF});
}
else{
- print {*STDERR} "Problem Could not find accession ".$dr->{ACCESSION}." for source ".$dr->{SOURCE}.
- " soo not able ot add direct xref to ".$dr->{ENSEMBL_STABLE_ID}."\n";
+ print {*STDERR} 'Problem Could not find accession '.$dr->{ACCESSION}.' for source '.$dr->{SOURCE}.
+ ' so not able to add direct xref to '.$dr->{ENSEMBL_STABLE_ID}."\n";
}
}
return;
@@ -645,9 +649,9 @@ sub get_xref_sources {
my $self = shift;
my %sourcename_to_sourceid;
-
+
my $dbi = $self->dbi;
- my $sth = $dbi->prepare("SELECT name,source_id FROM source");
+ my $sth = $dbi->prepare('SELECT name,source_id FROM source');
$sth->execute() or croak( $dbi->errstr() );
while(my @row = $sth->fetchrow_array()) {
my $source_name = $row[0];
@@ -669,12 +673,12 @@ sub species_id2taxonomy {
my %species_id2taxonomy;
my $dbi = $self->dbi;
- my $sth = $dbi->prepare("SELECT species_id, taxonomy_id FROM species");
+ my $sth = $dbi->prepare('SELECT species_id, taxonomy_id FROM species');
$sth->execute() or croak( $dbi->errstr() );
while(my @row = $sth->fetchrow_array()) {
my $species_id = $row[0];
my $taxonomy_id = $row[1];
- if(defined($species_id2taxonomy{$species_id})){
+ if(defined $species_id2taxonomy{$species_id} ){
push @{$species_id2taxonomy{$species_id}}, $taxonomy_id;
}
else{
@@ -695,7 +699,7 @@ sub species_id2name {
my %species_id2name;
my $dbi = $self->dbi;
- my $sth = $dbi->prepare("SELECT species_id, name FROM species");
+ my $sth = $dbi->prepare('SELECT species_id, name FROM species');
$sth->execute() or croak( $dbi->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
my $species_id = $row[0];
@@ -706,11 +710,11 @@ sub species_id2name {
##############################################
# Also populate the hash with all the aliases.
##############################################
- $sth = $dbi->prepare("SELECT species_id, aliases FROM species");
+ $sth = $dbi->prepare('SELECT species_id, aliases FROM species');
$sth->execute() or croak( $dbi->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
my $species_id = $row[0];
- foreach my $name ( split /,\s*/x, $row[1] ) {
+ foreach my $name ( split /,\s*/xms, $row[1] ) {
$species_id2name{$species_id} ||= [];
push @{$species_id2name{$species_id}}, $name;
}
@@ -726,20 +730,19 @@ sub species_id2name {
###########################################################################
sub get_xref_id {
my ($self, $arg_ref) = @_;
-# $sth, $error, $acc, $source, $species) = @_;
- my $sth = $arg_ref->{sth} || croak "Need a statement handle for get_xref_id";
- my $acc = $arg_ref->{acc} || croak "Need an accession for get_xref_id";
- my $source = $arg_ref->{source_id} || croak "Need an source_id for get_xref_id";
- my $species = $arg_ref->{species_id} || confess "Need an species_id for get_xref_id";
+ my $sth = $arg_ref->{sth} || croak 'Need a statement handle for get_xref_id';
+ my $acc = $arg_ref->{acc} || croak 'Need an accession for get_xref_id';
+ my $source = $arg_ref->{source_id} || croak 'Need an source_id for get_xref_id';
+ my $species = $arg_ref->{species_id} || confess 'Need an species_id for get_xref_id';
my $error = $arg_ref->{error};
my $id;
- if ($error and ($error == 1062)) { # duplicate (okay so get the original)
+ if ($error and ($error eq '1062')) { # duplicate (okay so get the original)
$id = $self->get_xref($acc, $source, $species);
}
elsif ($error){
- die "Error $error";
+ croak "Error $error";
}
else {
$id = $sth->{'mysql_insertid'};
@@ -759,11 +762,11 @@ sub primary_xref_id_exists {
my $exists = 0;
my $dbi = $self->dbi;
- my $sth = $dbi->prepare("SELECT xref_id FROM primary_xref WHERE xref_id=?");
+ my $sth = $dbi->prepare('SELECT xref_id FROM primary_xref WHERE xref_id=?');
$sth->execute($xref_id) or croak( $dbi->errstr() );
my @row = $sth->fetchrow_array();
my $result = $row[0];
- $exists = 1 if (defined $result);
+ if (defined $result) {$exists = 1; }
return $exists;
@@ -794,7 +797,7 @@ sub get_taxonomy_from_species_id{
sub get_direct_xref{
my ($self,$stable_id,$type,$link) = @_;
- $type = lc($type);
+ $type = lc $type;
my $dbi = $self->dbi;
my $sql = "select general_xref_id from ${type}_direct_xref d where ensembl_stable_id = ? and linkage_xref= ?";
@@ -819,8 +822,8 @@ sub get_xref{
#
# If the statement handle does nt exist create it.
#
- if(!defined($get_xref_sth)){
- my $sql = "select xref_id from xref where accession = ? and source_id = ? and species_id = ?";
+ if(!(defined $get_xref_sth) ){
+ my $sql = 'select xref_id from xref where accession = ? and source_id = ? and species_id = ?';
$get_xref_sth = $dbi->prepare($sql);
}
@@ -841,14 +844,22 @@ sub get_xref{
# else creates it and return the new xre_id
###########################################################
sub add_xref {
- my ( $self, $acc, $version, $label, $description, $source_id,
- $species_id, $info_type ) = @_;
+ my ( $self, $arg_ref) = @_;
+
+ my $acc = $arg_ref->{acc} || croak 'add_xref needs aa acc';
+ my $source_id = $arg_ref->{source_id} || croak 'add_xref needs a source_id';
+ my $species_id = $arg_ref->{species_id} || croak 'add_xref needs a species_id';
+ my $label = $arg_ref->{label} || $acc;
+ my $description = $arg_ref->{desc} || '';
+ my $version = $arg_ref->{version} || 0;
+ my $info_type = $arg_ref->{info_type} || 'MISC';
+
##################################################################
# See if it already exists. It so return the xref_id for this one.
##################################################################
my $xref_id = $self->get_xref($acc,$source_id, $species_id);
- if(defined($xref_id)){
+ if(defined $xref_id){
return $xref_id;
}
@@ -856,22 +867,22 @@ sub add_xref {
#######################################################################
# If the statement handle for the insertion of xrefs does not exist yet
# then create it
- ########################################################################
- if ( !defined($add_xref_sth) ) {
+ #######################################################################
+ if (!(defined $add_xref_sth) ) {
$add_xref_sth =
- $self->dbi->prepare( "INSERT INTO xref "
- . "(accession,version,label,description,source_id,species_id, info_type) "
- . "VALUES(?,?,?,?,?,?,?)" );
+ $self->dbi->prepare( 'INSERT INTO xref '
+ . '(accession,version,label,description,source_id,species_id, info_type) '
+ . 'VALUES(?,?,?,?,?,?,?)' );
}
######################################################################
# If the description is more than 255 characters, chop it off and add
# an indication that it has been truncated to the end of it.
######################################################################
- if (defined($description) && (length($description) > 255 ) ) {
+ if (defined $description && ((length $description) > 255 ) ) {
my $truncmsg = ' /.../';
- substr( $description, 255 - length($truncmsg),
- length($truncmsg), $truncmsg );
+ substr $description, 255 - (length $truncmsg),
+ length $truncmsg, $truncmsg;
}
@@ -893,11 +904,11 @@ sub add_xref {
sub add_to_direct_xrefs{
my ($self, $arg_ref) = @_;
- my $stable_id = $arg_ref->{stable_id} || croak ("Need a direct_xref on which this xref linked too" );
- my $type = $arg_ref->{type} || croak ("Need a table type on which to add");
- my $acc = $arg_ref->{acc} || croak ("Need an accession of this direct xref" );
- my $source_id = $arg_ref->{source_id} || croak ("Need a source_id for this direct xref" );
- my $species_id = $arg_ref->{species_id} || croak ("Need a species_id for this direct xref" );
+ my $stable_id = $arg_ref->{stable_id} || croak ('Need a direct_xref on which this xref linked too' );
+ my $type = $arg_ref->{type} || croak ('Need a table type on which to add');
+ my $acc = $arg_ref->{acc} || croak ('Need an accession of this direct xref' );
+ my $source_id = $arg_ref->{source_id} || croak ('Need a source_id for this direct xref' );
+ my $species_id = $arg_ref->{species_id} || croak ('Need a species_id for this direct xref' );
my $version = $arg_ref->{version} || 0;
my $label = $arg_ref->{label} || $acc;
my $description = $arg_ref->{desc};
@@ -908,11 +919,10 @@ sub add_to_direct_xrefs{
######################
# Get statement handle
######################
- if(!defined($add_xref_sth)){
- my $sql = (<<"AXX");
-INSERT INTO xref
- (accession,version,label,description,source_id,species_id, info_type)
- VALUES (?,?,?,?,?,?,?)
+ if(!(defined $add_xref_sth)){
+ my $sql = (<<'AXX');
+ INSERT INTO xref (accession,version,label,description,source_id,species_id, info_type)
+ VALUES (?,?,?,?,?,?,?)
AXX
$add_xref_sth = $dbi->prepare($sql);
}
@@ -921,10 +931,10 @@ AXX
# If the acc already has an xrefs find it else cretae a new one
###############################################################
my $direct_id = $self->get_xref($acc, $source_id, $species_id);
- if(!defined($direct_id)){
+ if(!(defined $direct_id)){
$add_xref_sth->execute(
$acc, $version || 0, $label,
- $description, $source_id, $species_id, "DIRECT"
+ $description, $source_id, $species_id, 'DIRECT'
) or croak("$acc\t$label\t\t$source_id\t$species_id\n");
}
@@ -933,7 +943,7 @@ AXX
#########################
# Now add the direct info
#########################
- $self->add_direct_xref($direct_id, $stable_id, $type, "");
+ $self->add_direct_xref($direct_id, $stable_id, $type, '');
return;
}
@@ -949,23 +959,23 @@ sub add_direct_xref {
#######################################################
# Create statement handles if they do not exist already
########################################################
- if (!defined($add_direct_xref_sth{$ensembl_type})){
- my $add_gene_direct_xref_sth = $dbi->prepare("INSERT INTO gene_direct_xref VALUES(?,?,?)");
- my $add_tr_direct_xref_sth = $dbi->prepare("INSERT INTO transcript_direct_xref VALUES(?,?,?)");
- my $add_tl_direct_xref_sth = $dbi->prepare("INSERT INTO translation_direct_xref VALUES(?,?,?)");
- $add_direct_xref_sth{"gene"} = $add_gene_direct_xref_sth;
- $add_direct_xref_sth{"transcript"} = $add_tr_direct_xref_sth;
- $add_direct_xref_sth{"translation"} = $add_tl_direct_xref_sth;
- $add_direct_xref_sth{"Gene"} = $add_gene_direct_xref_sth;
- $add_direct_xref_sth{"Transcript"} = $add_tr_direct_xref_sth;
- $add_direct_xref_sth{"Translation"} = $add_tl_direct_xref_sth;
+ if (!(defined $add_direct_xref_sth{$ensembl_type})){
+ my $add_gene_direct_xref_sth = $dbi->prepare('INSERT INTO gene_direct_xref VALUES(?,?,?)');
+ my $add_tr_direct_xref_sth = $dbi->prepare('INSERT INTO transcript_direct_xref VALUES(?,?,?)');
+ my $add_tl_direct_xref_sth = $dbi->prepare('INSERT INTO translation_direct_xref VALUES(?,?,?)');
+ $add_direct_xref_sth{'gene'} = $add_gene_direct_xref_sth;
+ $add_direct_xref_sth{'transcript'} = $add_tr_direct_xref_sth;
+ $add_direct_xref_sth{'translation'} = $add_tl_direct_xref_sth;
+ $add_direct_xref_sth{'Gene'} = $add_gene_direct_xref_sth;
+ $add_direct_xref_sth{'Transcript'} = $add_tr_direct_xref_sth;
+ $add_direct_xref_sth{'Translation'} = $add_tl_direct_xref_sth;
}
##############################
# Make sure type is recognised
##############################
- if(!defined($add_direct_xref_sth{$ensembl_type})){
- croak "ERROR add_direct_xref_sth does not exist for $ensembl_type ???\n";
+ if(!(defined $add_direct_xref_sth{$ensembl_type})){
+ croak "ERROR add_direct_xref_sth does not exist for $ensembl_type ???";
}
else{
##########################
@@ -983,10 +993,10 @@ sub add_direct_xref {
sub add_dependent_xref{
my ($self, $arg_ref) = @_;
- my $master_xref = $arg_ref->{master_xref_id} || croak( "Need a master_xref_id on which this xref depends on" );
- my $acc = $arg_ref->{acc} || croak( "Need an accession of this dependent xref" );
- my $source_id = $arg_ref->{source_id} || croak( "Need a source_id for this dependent xref" );
- my $species_id = $arg_ref->{species_id} || croak( "Need a species_id for this dependent xref" );
+ my $master_xref = $arg_ref->{master_xref_id} || croak( 'Need a master_xref_id on which this xref depends on' );
+ my $acc = $arg_ref->{acc} || croak( 'Need an accession of this dependent xref' );
+ my $source_id = $arg_ref->{source_id} || croak( 'Need a source_id for this dependent xref' );
+ my $species_id = $arg_ref->{species_id} || croak( 'Need a species_id for this dependent xref' );
my $version = $arg_ref->{version} || 0;
my $label = $arg_ref->{label} || $acc;
my $description = $arg_ref->{desc};
@@ -997,16 +1007,16 @@ sub add_dependent_xref{
########################################
# Create/Get the statement handle needed
########################################
- if(!defined($add_xref_sth)){
- my $sql = (<<"IXR");
+ if(!(defined $add_xref_sth)){
+ my $sql = (<<'IXR');
INSERT INTO xref
(accession,version,label,description,source_id,species_id, info_type)
VALUES (?,?,?,?,?,?,?)
IXR
$add_xref_sth = $dbi->prepare($sql);
}
- if(!defined($add_dependent_xref_sth)){
- my $sql = (<<"ADX");
+ if(!(defined $add_dependent_xref_sth)){
+ my $sql = (<<'ADX');
INSERT INTO dependent_xref
(master_xref_id,dependent_xref_id,linkage_annotation,linkage_source_id)
VALUES (?,?,?,?)
@@ -1019,10 +1029,10 @@ ADX
# else create it and get the new xref_id
####################################################
my $dependent_id = $self->get_xref($acc, $source_id, $species_id);
- if(!defined($dependent_id)){
+ if(!(defined $dependent_id)){
$add_xref_sth->execute(
$acc, $version, $label,
- $description, $source_id, $species_id, "DEPENDENT"
+ $description, $source_id, $species_id, 'DEPENDENT'
) or croak("$acc\t$label\t\t$source_id\t$species_id\n");
}
$dependent_id = $self->get_xref($acc, $source_id, $species_id);
@@ -1030,7 +1040,7 @@ ADX
################################################
# Croak if we have failed to create.get the xref
################################################
- if(!defined($dependent_id)){
+ if(!(defined $dependent_id)){
croak("$acc\t$label\t\t$source_id\t$species_id\n");
}
@@ -1038,11 +1048,11 @@ ADX
# If the dependency has not already been set ( is already in hash xref_dependent_mapped)
# then add it
########################################################################################
- if(!defined($xref_dependent_mapped{$master_xref."|".$dependent_id})){
+ if(!(defined $xref_dependent_mapped{"$master_xref|$dependent_id"})){
$add_dependent_xref_sth->execute( $master_xref, $dependent_id, $linkage,
$source_id )
or croak("$master_xref\t$dependent_id\t$linkage\t$source_id");
- $xref_dependent_mapped{$master_xref."|".$dependent_id} = 1;
+ $xref_dependent_mapped{"$master_xref|$dependent_id"} = 1;
}
return $dependent_id;
@@ -1057,13 +1067,13 @@ sub add_to_syn_for_mult_sources{
my ($self, $acc, $sources, $syn, $species_id) = @_;
my $dbi = $self->dbi;
- if(!defined($add_synonym_sth)){
- $add_synonym_sth = $dbi->prepare("INSERT INTO synonym VALUES(?,?)");
+ if(!(defined $add_synonym_sth)){
+ $add_synonym_sth = $dbi->prepare('INSERT INTO synonym VALUES(?,?)');
}
- foreach my $source_id (@$sources){
+ foreach my $source_id (@{$sources}){
my $xref_id = $self->get_xref($acc, $source_id, $species_id);
- if(defined($xref_id)){
+ if(defined $xref_id){
$add_synonym_sth->execute( $xref_id, $syn )
or croak( $dbi->errstr() . "\n $xref_id\n $syn\n" );
}
@@ -1079,11 +1089,11 @@ sub add_to_syn{
my ($self, $acc, $source_id, $syn, $species_id) = @_;
my $dbi = $self->dbi;
- if(!defined($add_synonym_sth)){
- $add_synonym_sth = $dbi->prepare("INSERT INTO synonym VALUES(?,?)");
+ if(!(defined $add_synonym_sth)){
+ $add_synonym_sth = $dbi->prepare('INSERT INTO synonym VALUES(?,?)');
}
my $xref_id = $self->get_xref($acc, $source_id, $species_id);
- if(defined($xref_id)){
+ if(defined $xref_id){
$add_synonym_sth->execute( $xref_id, $syn )
or croak( $dbi->errstr() . "\n $xref_id\n $syn\n" );
}
@@ -1102,8 +1112,8 @@ sub add_synonym{
my ($self, $xref_id, $syn) = @_;
my $dbi=$self->dbi;
- if(!defined($add_synonym_sth)){
- $add_synonym_sth = $dbi->prepare("INSERT INTO synonym VALUES(?,?)");
+ if(!(defined $add_synonym_sth)){
+ $add_synonym_sth = $dbi->prepare('INSERT INTO synonym VALUES(?,?)');
}
$add_synonym_sth->execute( $xref_id, $dbi->quote($syn) )
@@ -1127,10 +1137,10 @@ SELECT xref.accession, xref.label
WHERE source.name LIKE '$name%' AND
xref.source_id = source.source_id
GLA
- if(defined($prio_desc)){
+ if(defined $prio_desc){
$sql .= " and source.priority_description like '$prio_desc'";
}
- if(defined($species_id)){
+ if(defined $species_id){
$sql .= " and xref.species_id = $species_id";
}
my $sub_sth = $self->dbi->prepare($sql);
@@ -1153,10 +1163,10 @@ SELECT xref.accession, synonym.synonym
xref.source_id = source.source_id
GLS
- if(defined($prio_desc)){
+ if(defined $prio_desc){
$sql .= " AND source.priority_description LIKE '$prio_desc'";
}
- if(defined($species_id)){
+ if(defined $species_id){
$sql .= " AND xref.species_id = $species_id";
}
$sub_sth = $self->dbi->prepare($sql);
@@ -1185,10 +1195,10 @@ sub get_label_to_desc{
WHERE source.name LIKE '$name%' AND
xref.source_id = source.source_id
GDH
- if(defined($prio_desc)){
+ if(defined $prio_desc){
$sql .= " and source.priority_description like '$prio_desc'";
}
- if(defined($species_id)){
+ if(defined $species_id){
$sql .= " and xref.species_id = $species_id";
}
my $sub_sth = $self->dbi->prepare($sql);
@@ -1210,10 +1220,10 @@ GDH
xref.source_id = source.source_id
GDS
- if(defined($prio_desc)){
+ if(defined $prio_desc){
$syn_sql .= " AND source.priority_description LIKE '$prio_desc'";
}
- if(defined($species_id)){
+ if(defined $species_id){
$syn_sql .= " AND xref.species_id = $species_id";
}
$sub_sth = $self->dbi->prepare($syn_sql);
@@ -1227,36 +1237,6 @@ GDS
}
-#
-#
-#
-#sub get_accession_from_label{
-# my ($self, $name) = @_;
-
-# my $sql = "select xref.accession from xref where xref.label like '$name'";
-# my $sub_sth = $self->dbi->prepare($sql);
-
-# $sub_sth->execute();
-# while(my @row = $sub_sth->fetchrow_array()) {
-# return $row[0];
-# }
-# return;
-#}
-
-#sub get_sub_list{
-# my ($self, $name) = @_;
-# my @list=();
-
-# my $sql = "select xref.accession from xref where xref.accession like '$name%'";
-# my $sub_sth = $self->dbi->prepare($sql);
-
-# $sub_sth->execute();
-# while(my @row = $sub_sth->fetchrow_array()) {
-# push @list, $row[0];
-# }
-# return @list;
-#}
-
########################################
# Set release for a particular source_id.
########################################
@@ -1264,10 +1244,9 @@ sub set_release{
my ($self, $source_id, $s_release ) = @_;
my $sth =
- $self->dbi->prepare(
- "UPDATE source SET source_release=? WHERE source_id=?");
+ $self->dbi->prepare('UPDATE source SET source_release=? WHERE source_id=?');
- print "Setting release to '$s_release' for source ID '$source_id'\n" if($verbose);
+ if($verbose) { print "Setting release to '$s_release' for source ID '$source_id'\n"; }
$sth->execute( $s_release, $source_id );
return;
@@ -1294,7 +1273,7 @@ GDM
my $dependent_xref;
$sth->bind_columns(\$master_xref,\$dependent_xref);
while($sth->fetch){
- $xref_dependent_mapped{$master_xref."|".$dependent_xref}=1;
+ $xref_dependent_mapped{"$master_xref|$dependent_xref"}=1;
}
$sth->finish;
return;
@@ -1310,6 +1289,7 @@ sub get_ext_synonyms{
my $source_name = shift;
my %ext_syns;
my %seen; # can be in more than once fro each type of external source.
+ my $separator = qw{:};
my $sql =(<<"GES");
SELECT x.accession, x.label, sy.synonym
@@ -1326,12 +1306,12 @@ GES
my $count = 0;
while($sth->fetch){
- if(!defined($seen{$acc.":".$syn})){
+ if(!(defined $seen{$acc.$separator.$syn})){
push @{$ext_syns{$acc}}, $syn;
push @{$ext_syns{$label}}, $syn;
$count++;
}
- $seen{$acc.":".$syn} = 1;
+ $seen{$acc.$separator.$syn} = 1;
}
$sth->finish;
@@ -1357,17 +1337,17 @@ sub parsing_finished_store_data {
# identity_xref object_xref_id
my %table_and_key =
- ( 'xref' => "xref_id", 'object_xref' => "object_xref_id" );
+ ( 'xref' => 'xref_id', 'object_xref' => 'object_xref_id' );
foreach my $table ( keys %table_and_key ) {
my $sth = $self->dbi->prepare(
- "select MAX(" . $table_and_key{$table} . ") from $table" );
+ 'select MAX(' . $table_and_key{$table} . ") from $table" );
$sth->execute;
my $max_val;
$sth->bind_columns( \$max_val );
$sth->fetch;
$sth->finish;
- $self->add_meta_pair( "PARSED_" . $table_and_key{$table},
+ $self->add_meta_pair( 'PARSED_' . $table_and_key{$table},
$max_val || 1 );
}
return;
--
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