From 98a44bc7b5764b7f3e4b742a5aa36eeb9c69e17a Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 14 Jul 2011 14:50:30 +0000
Subject: [PATCH] perlcritic level 5 fixes
---
.../xref_mapping/XrefParser/AedesCAPParser.pm | 3 +-
.../XrefParser/AedesGenBankParser.pm | 3 +-
.../xref_mapping/XrefParser/AgilentParser.pm | 3 +-
.../xref_mapping/XrefParser/AnoXcelParser.pm | 14 +-
.../XrefParser/AnophelesSymbolParser.pm | 3 +-
.../xref_mapping/XrefParser/BaseParser.pm | 124 +++++++++---------
.../xref_mapping/XrefParser/CCDSParser.pm | 2 +-
.../xref_mapping/XrefParser/CeleraParser.pm | 3 +-
.../XrefParser/CeleraProteinParser.pm | 2 +-
.../XrefParser/CeleraTranscriptParser.pm | 2 +-
.../xref_mapping/XrefParser/CodelinkParser.pm | 3 +-
.../xref_mapping/XrefParser/DBASSParser.pm | 4 +-
.../xref_mapping/XrefParser/EG_DBParser.pm | 16 +--
.../XrefParser/EntrezGeneParser.pm | 17 +--
.../xref_mapping/XrefParser/FantomParser.pm | 18 +--
.../xref_mapping/XrefParser/FastaParser.pm | 3 +-
.../XrefParser/Flybase_dmel_GFFv3_Parser.pm | 28 +---
.../xref_mapping/XrefParser/GOParser.pm | 17 +--
.../xref_mapping/XrefParser/GOSlimParser.pm | 2 +-
.../xref_mapping/XrefParser/HGNCParser.pm | 16 +--
.../xref_mapping/XrefParser/HPAParser.pm | 3 +-
.../xref_mapping/XrefParser/IKMCParser.pm | 3 +-
.../xref_mapping/XrefParser/IPIParser.pm | 3 +-
.../xref_mapping/XrefParser/IlluminaParser.pm | 3 +-
.../XrefParser/IlluminaWGParser.pm | 3 +-
.../xref_mapping/XrefParser/ImmunoDBParser.pm | 18 +--
.../XrefParser/InterproGoParser.pm | 3 +-
.../xref_mapping/XrefParser/InterproParser.pm | 25 +---
.../XrefParser/IxodesCAPParser.pm | 3 +-
.../xref_mapping/XrefParser/JGI_Parser.pm | 3 +-
.../XrefParser/JGI_ProteinParser.pm | 2 +-
.../xref_mapping/XrefParser/MGDParser.pm | 35 ++---
.../xref_mapping/XrefParser/MGIParser.pm | 17 +--
.../XrefParser/MGI_Desc_Parser.pm | 15 +--
.../xref_mapping/XrefParser/MIMParser.pm | 17 +--
.../xref_mapping/XrefParser/Mim2GeneParser.pm | 17 +--
.../xref_mapping/XrefParser/OTTTParser.pm | 12 +-
.../xref_mapping/XrefParser/PHIbaseParser.pm | 20 +--
.../xref_mapping/XrefParser/RGDParser.pm | 18 +--
.../XrefParser/RefSeqGPFFParser.pm | 23 +---
.../xref_mapping/XrefParser/RefSeqParser.pm | 20 +--
.../XrefParser/RefSeq_CCDSParser.pm | 2 +-
.../xref_mapping/XrefParser/SGDParser.pm | 14 +-
.../xref_mapping/XrefParser/SegmentParser.pm | 17 +--
.../xref_mapping/XrefParser/UCSCParser.pm | 3 +-
.../xref_mapping/XrefParser/UniGeneParser.pm | 25 +---
.../XrefParser/UniProtDirectParser.pm | 16 +--
.../xref_mapping/XrefParser/UniProtParser.pm | 23 +---
.../UniProtParser_descriptions_only.pm | 20 +--
.../XrefParser/UniProtVarSplicParser.pm | 3 +-
.../XrefParser/VBCommunitySymbolParser.pm | 17 +--
.../XrefParser/VBExternalDescriptionParser.pm | 14 +-
.../xref_mapping/XrefParser/VBPubMedParser.pm | 15 +--
.../XrefParser/VBRNADescriptionParser.pm | 15 +--
.../XrefParser/VBribosomalParser.pm | 14 +-
.../xref_mapping/XrefParser/VbDirectParser.pm | 6 +-
.../xref_mapping/XrefParser/VbGFF3Parser.pm | 9 +-
.../XrefParser/WilsonAffyParser.pm | 3 +-
.../xref_mapping/XrefParser/WormPepParser.pm | 3 +-
.../XrefParser/XenopusJamboreeParser.pm | 3 +-
.../xref_mapping/XrefParser/ZFINDescParser.pm | 22 +---
.../xref_mapping/XrefParser/ZFINParser.pm | 18 +--
.../XrefParser/curated_transcriptParser.pm | 15 +--
.../xref_mapping/XrefParser/ncRNAParser.pm | 17 +--
.../xref_mapping/XrefParser/ncRNA_DBParser.pm | 15 +--
65 files changed, 159 insertions(+), 696 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/AedesCAPParser.pm b/misc-scripts/xref_mapping/XrefParser/AedesCAPParser.pm
index 33e72cefbb..5986301bc9 100644
--- a/misc-scripts/xref_mapping/XrefParser/AedesCAPParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AedesCAPParser.pm
@@ -20,8 +20,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm b/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
index 3699a7e221..feb2241a22 100644
--- a/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
@@ -13,8 +13,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm b/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm
index 3ee69d8651..0f5d42fc23 100644
--- a/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm
@@ -13,8 +13,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/AnoXcelParser.pm b/misc-scripts/xref_mapping/XrefParser/AnoXcelParser.pm
index 2e40b0a109..514a070809 100644
--- a/misc-scripts/xref_mapping/XrefParser/AnoXcelParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AnoXcelParser.pm
@@ -13,21 +13,9 @@ use base qw( XrefParser::BaseParser );
# AGAP004678-PA AGAP004678-RA 2L:203866-204956:1 AGAP004678
#...
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: AnoXcelParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm b/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
index 59e24b7f3e..b6f94919fb 100644
--- a/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
@@ -14,8 +14,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index add99cbada..281cdede6d 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -1,6 +1,8 @@
package XrefParser::BaseParser;
use strict;
+use warnings;
+use Bio::EnsEMBL::Utils::Exception;
use Carp;
use DBI;
@@ -17,7 +19,6 @@ use URI::file;
use Text::Glob qw( match_glob );
use LWP::UserAgent;
-use Bio::EnsEMBL::Utils::Exception;
my $base_dir = File::Spec->curdir();
@@ -45,9 +46,7 @@ my ( $host, $port, $dbname, $user,
# Get info about files to be parsed from the database
sub run {
- my $self = shift;
-
- ( $host, $port, $dbname,
+ ( my $self, $host, $port, $dbname,
$user, $pass, my $speciesr,
my $sourcesr, $checkdownload, $create,
$release, $cleanup, $drop_db,
@@ -352,7 +351,7 @@ sub run {
# second the number of primary xrefs
$group_sql = "SELECT count(*), s.name from source s, primary_xref px, xref x where s.source_id = x.source_id and px.xref_id = x.xref_id group by s.name";
- my $sum_sth = $dbi->prepare($group_sql);
+ $sum_sth = $dbi->prepare($group_sql);
$sum_sth->execute();
$sum_sth->bind_columns(\$sum_count, \$sum_name);
@@ -371,7 +370,7 @@ sub run {
# third the number of dependent xrefs
$group_sql = "SELECT count(*), s.name from source s, dependent_xref dx, xref x where s.source_id = x.source_id and dx.dependent_xref_id = x.xref_id group by s.name";
- my $sum_sth = $dbi->prepare($group_sql);
+ $sum_sth = $dbi->prepare($group_sql);
$sum_sth->execute();
$sum_sth->bind_columns(\$sum_count, \$sum_name);
@@ -395,7 +394,7 @@ sub run {
$group_sql = "SELECT count(*), s.name from source s, ".$type."_direct_xref dx, xref x where s.source_id = x.source_id and dx.general_xref_id = x.xref_id group by s.name";
- my $sum_sth = $dbi->prepare($group_sql);
+ $sum_sth = $dbi->prepare($group_sql);
$sum_sth->execute();
$sum_sth->bind_columns(\$sum_count, \$sum_name);
@@ -415,7 +414,7 @@ sub run {
# seventh the number of coordinate xrefs
$group_sql = "SELECT count(*), s.name from source s, coordinate_xref cx where s.source_id = cx.source_id group by s.name";
- my $sum_sth = $dbi->prepare($group_sql);
+ $sum_sth = $dbi->prepare($group_sql);
$sum_sth->execute();
$sum_sth->bind_columns(\$sum_count, \$sum_name);
@@ -433,7 +432,7 @@ sub run {
# eigth the number of synonyms
$group_sql = "select count(*), s.name from source s, xref x, synonym o where s.source_id = x.source_id and x.xref_id = o.xref_id group by s.name";
- my $sum_sth = $dbi->prepare($group_sql);
+ $sum_sth = $dbi->prepare($group_sql);
$sum_sth->execute();
$sum_sth->bind_columns(\$sum_count, \$sum_name);
@@ -500,7 +499,7 @@ sub run {
# second the number of primary xrefs
$group_sql = "SELECT count(*), s.name from source s, primary_xref px, xref x where s.source_id = x.source_id and px.xref_id = x.xref_id group by s.name";
- my $sum_sth = $dbi->prepare($group_sql);
+ $sum_sth = $dbi->prepare($group_sql);
$sum_sth->execute();
$sum_sth->bind_columns(\$sum_count, \$sum_name);
@@ -515,7 +514,7 @@ sub run {
# third the number of dependent xrefs
$group_sql = "SELECT count(*), s.name from source s, dependent_xref dx, xref x where s.source_id = x.source_id and dx.dependent_xref_id = x.xref_id group by s.name";
- my $sum_sth = $dbi->prepare($group_sql);
+ $sum_sth = $dbi->prepare($group_sql);
$sum_sth->execute();
$sum_sth->bind_columns(\$sum_count, \$sum_name);
@@ -533,7 +532,7 @@ sub run {
$group_sql = "SELECT count(*), s.name from source s, ".$type."_direct_xref dx, xref x where s.source_id = x.source_id and dx.general_xref_id = x.xref_id group by s.name";
- my $sum_sth = $dbi->prepare($group_sql);
+ $sum_sth = $dbi->prepare($group_sql);
$sum_sth->execute();
$sum_sth->bind_columns(\$sum_count, \$sum_name);
@@ -548,7 +547,7 @@ sub run {
# seventh the number of coordinate xrefs
$group_sql = "SELECT count(*), s.name from source s, coordinate_xref cx where s.source_id = cx.source_id group by s.name";
- my $sum_sth = $dbi->prepare($group_sql);
+ $sum_sth = $dbi->prepare($group_sql);
$sum_sth->execute();
$sum_sth->bind_columns(\$sum_count, \$sum_name);
@@ -562,7 +561,7 @@ sub run {
# eigth the number of synonyms
$group_sql = "select count(*), s.name from source s, xref x, synonym o where s.source_id = x.source_id and x.xref_id = o.xref_id group by s.name";
- my $sum_sth = $dbi->prepare($group_sql);
+ $sum_sth = $dbi->prepare($group_sql);
$sum_sth->execute();
$sum_sth->bind_columns(\$sum_count, \$sum_name);
@@ -586,7 +585,7 @@ sub run {
# remove last working directory
# TODO reinstate after debugging
#rmtree $dir;
-
+ return 1;
} ## end sub run
# ------------------------------------------------------------------------------
@@ -599,9 +598,7 @@ sub run {
# if there was an error.
sub fetch_files {
- my $self = shift;
-
- my ( $dest_dir, @user_uris ) = @_;
+ my ($self, $dest_dir, @user_uris ) = @_;
my @processed_files;
@@ -838,7 +835,7 @@ sub get_filehandle
or carp("Can not open file '$file_name'");
}
- if ( !defined $io ) { return undef }
+ if ( !defined $io ) { return }
print "Reading from '$file_name'...\n" if($verbose);
@@ -885,7 +882,7 @@ sub get_source_id_for_filename {
}
sub rename_url_file{
- return undef;
+ return;
}
# Get species ID for a particular file; matches url field
@@ -1246,7 +1243,7 @@ sub upload_xref_object_graphs {
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";
- return undef;
+ return;
}
# Create entry in xref table and note ID
if(! $xref_sth->execute($xref->{ACCESSION},
@@ -1258,7 +1255,7 @@ sub upload_xref_object_graphs {
$xref->{INFO_TYPE} || "MISC")){
if(!defined($xref->{SOURCE_ID})){
print "your xref: $xref->{ACCESSION} does not have a source-id\n";
- return undef;
+ return;
}
$xref_id = $self->insert_or_select($xref_sth, $dbi->err, $xref->{ACCESSION}, $xref->{SOURCE_ID}, $xref->{SPECIES_ID});
$xref_update_label_sth->execute($xref->{LABEL},$xref_id) if (defined($xref->{LABEL}));
@@ -1351,6 +1348,7 @@ sub upload_direct_xrefs{
$self->add_direct_xref($general_xref_id, $dr->{ENSEMBL_STABLE_ID},$dr->{ENSEMBL_TYPE},$dr->{LINKAGE_XREF});
}
}
+ return;
}
sub add_meta_pair {
@@ -1361,7 +1359,7 @@ sub add_meta_pair {
my $sth = $dbi->prepare('insert into meta (meta_key, meta_value, date) values("'.$key.'", "'.$value.'", now())');
$sth->execute;
$sth->finish;
-
+ return;
}
@@ -1410,7 +1408,7 @@ sub taxonomy2species_id {
my $species_id = $row[0];
my $taxonomy_id = $row[1];
if( my $ori =$taxonomy2species_id{$taxonomy_id} ){
- die( "Taxon $taxonomy_id already used for species $ori. ".
+ croak ( "Taxon $taxonomy_id already used for species $ori. ".
"Cannot assign to species $species_id as well. ".
"Consider using the species_id2taxonomy call instead. ".
"Called by ". join( ', ', (caller(0))[1..2] ) );
@@ -1476,7 +1474,7 @@ sub name2species_id {
my $species_id = $row[0];
foreach my $name ( split /,\s*/, $row[1] ) {
if ( my $ori = $name2species_id{$name} ) {
- die( "Name $name already used for species $ori. ".
+ croak ( "Name $name already used for species $ori. ".
"Cannot assign to species $species_id as well. ".
"Consider using the species_id2name call instead. ".
"Called by ". join( ', ', (caller(0))[1..2] ) );
@@ -1546,14 +1544,14 @@ sub update_source
# inherited set_release() method.
$dbi->prepare($sql)->execute() || croak( $dbi->errstr() );
+ return;
}
# --------------------------------------------------------------------------------
sub dbi2{
- my $self = shift;
- my ($host, $port, $user, $dbname, $pass) = @_;
+ my ($self, $host, $port, $user, $dbname, $pass) = @_;
my $dbi2 = undef;
if ( !defined $dbi2 || !$dbi2->ping() ) {
@@ -1565,7 +1563,7 @@ sub dbi2{
DBI->connect( $connect_string, $user, $pass,
# { 'RaiseError' => 1 } )
)
- or warn( "Can't connect to database: " . $DBI::errstr ) and return undef;
+ or warn( "Can't connect to database: " . $DBI::errstr ) and return;
$dbi2->{'mysql_auto_reconnect'} = 1; # Reconnect on timeout
}
@@ -1603,14 +1601,14 @@ sub md5sum
{
my $file = shift;
- if ( !open( FILE, $file ) ) { return undef }
- binmode(FILE);
+ open my $FH, "<", $file or return;
+ binmode($FH);
my $checksum = sprintf( "%s/%d",
- substr( Digest::MD5->new()->addfile(*FILE)->hexdigest(), 0, 6 ),
- [ stat FILE ]->[7] );
+ substr( Digest::MD5->new()->addfile(*$FH)->hexdigest(), 0, 6 ),
+ [ stat $FH ]->[7] );
- close(FILE);
+ close($FH);
return $checksum;
}
@@ -1737,7 +1735,7 @@ sub delete_by_source {
$dep_sth->finish() if defined $dep_sth;
$xref_sth->finish() if defined $xref_sth;
# $p_xref_sth->finish() if defined $p_xref_sth;
-
+ return;
}
# --------------------------------------------------------------------------------
@@ -1769,7 +1767,7 @@ sub validate_sources {
# --------------------------------------------------------------------------------
-sub show_valid_sources() {
+sub show_valid_sources {
my $species = shift;
my $dbi = dbi();
@@ -1779,7 +1777,7 @@ sub show_valid_sources() {
while (my @row = $sth->fetchrow_array()) {
print $row[0] . "\n";
}
-
+ return;
}
# --------------------------------------------------------------------------------
@@ -1811,7 +1809,7 @@ sub validate_species {
# --------------------------------------------------------------------------------
-sub show_valid_species() {
+sub show_valid_species {
my $dbi = dbi();
my $sth = $dbi->prepare("SELECT name, aliases FROM species");
@@ -1820,7 +1818,7 @@ sub show_valid_species() {
while (my @row = $sth->fetchrow_array()) {
print STDERR $row[0] . " (aliases: " . $row[1] . ")\n";
}
-
+ return;
}
sub get_taxonomy_from_species_id{
@@ -1849,7 +1847,7 @@ sub get_direct_xref{
if(my @row = $direct_sth->fetchrow_array()) {
return $row[0];
}
- return undef;
+ return;
}
@@ -1865,7 +1863,7 @@ sub get_xref{
if(my @row = $get_xref_sth->fetchrow_array()) {
return $row[0];
}
- return undef;
+ return;
}
sub add_xref {
@@ -1904,14 +1902,14 @@ sub add_xref {
sub add_to_direct_xrefs{
my ($self,$direct_xref,$type, $acc,$version,$label,$description,$linkage,$source_id,$species_id) = @_;
- $direct_xref || die( "Need a direct_xref on which this xref linked too" );
- $acc || die( "Need an accession of this dependent xref" );
+ $direct_xref || croak( "Need a direct_xref on which this xref linked too" );
+ $acc || croak( "Need an accession of this dependent xref" );
$version ||= 0;
$label ||= $acc;
$description ||= undef;
$linkage ||= undef;
- $source_id || die( "Need a source_id for this dependent xref" );
- $species_id || die( "Need a species_id for this dependent xref" );
+ $source_id || croak( "Need a source_id for this dependent xref" );
+ $species_id || croak( "Need a species_id for this dependent xref" );
if(!defined($add_xref_sth)){
$add_xref_sth = dbi->prepare("
@@ -1932,19 +1930,20 @@ VALUES
$direct_id = $self->get_xref($acc, $source_id, $species_id);
$self->add_direct_xref($direct_id, $direct_xref, $type, "");
+ return;
}
sub add_to_xrefs{
my ($self,$master_xref,$acc,$version,$label,$description,$linkage,$source_id,$species_id) = @_;
- $master_xref || die( "Need a master_xref_id on which this xref depends" );
- $acc || die( "Need an accession of this dependent xref" );
+ $master_xref || croak( "Need a master_xref_id on which this xref depends" );
+ $acc || croak( "Need an accession of this dependent xref" );
$version ||= 0;
$label ||= $acc;
$description ||= undef;
$linkage ||= undef;
- $source_id || die( "Need a source_id for this dependent xref" );
- $species_id || die( "Need a species_id for this dependent xref" );
+ $source_id || croak( "Need a source_id for this dependent xref" );
+ $species_id || croak( "Need a species_id for this dependent xref" );
if(!defined($add_xref_sth)){
$add_xref_sth = dbi->prepare("
@@ -1997,7 +1996,7 @@ sub add_to_syn_for_mult_sources{
$found = 1;
}
}
-
+ return;
}
@@ -2016,6 +2015,7 @@ sub add_to_syn{
warn ( "Could not find acc $acc in "
. "xref table source = $source_id of species $species_id\n" );
}
+ return;
}
@@ -2031,6 +2031,7 @@ sub add_synonym{
$add_synonym_sth->execute( $xref_id, $syn )
or croak( $dbi->errstr() . "\n $xref_id\n $syn\n" );
+ return;
}
@@ -2061,6 +2062,7 @@ sub add_direct_xref {
else{
$add_direct_xref_sth{$ensembl_type}->execute($general_xref_id, $ensembl_stable_id, $linkage_type);
}
+ return;
}
# ------------------------------------------------------------------------------
@@ -2089,7 +2091,7 @@ sub create {
catfile( $sql_dir, 'sql', 'populate_metadata.sql' );
my $ini_file = catfile( $sql_dir, 'xref_config.ini' );
- $| = 1; # flush stdout
+ local $| = 1; # flush stdout
# Figure out whether to run 'xref_config2sql.pl' or not by comparing
# the timestamps on 'xref_config.ini' and 'sql/populate_metadata.sql'.
@@ -2101,7 +2103,7 @@ sub create {
catfile( 'sql', 'populate_metadata.sql' ) );
print("==> Should I re-run 'xref_config2sql.pl' for you? [y/N]: ");
- my $reply = <STDIN>;
+ my $reply = <ARGV>;
chomp $reply;
if ( lc( substr( $reply, 0, 1 ) ) eq 'y' ) {
@@ -2140,7 +2142,7 @@ sub create {
if ( $create && !$drop_db ) {
print "WARNING: about to drop database $dbname on $host:$port; yes to confirm, otherwise exit: ";
- my $p = <STDIN>;
+ my $p = <ARGV>;
chomp $p;
if ($p eq "yes") {
$dbh->do( "DROP DATABASE $dbname" );
@@ -2179,6 +2181,7 @@ sub create {
. "$dbname < $metadata_file";
system($cmd) == 0
or croak("Cannot execute the following command (exit $?):\n$cmd\n");
+ return;
}
sub get_label_to_acc{
@@ -2212,7 +2215,7 @@ sub get_label_to_acc{
if(defined($species_id)){
$sql .= " and xref.species_id = $species_id";
}
- my $sub_sth = dbi->prepare($sql);
+ $sub_sth = dbi->prepare($sql);
$sub_sth->execute();
while(my @row = $sub_sth->fetchrow_array()) {
@@ -2254,7 +2257,7 @@ sub get_label_to_desc{
if(defined($species_id)){
$sql .= " and xref.species_id = $species_id";
}
- my $sub_sth = dbi->prepare($sql);
+ $sub_sth = dbi->prepare($sql);
$sub_sth->execute();
while(my @row = $sub_sth->fetchrow_array()) {
@@ -2280,7 +2283,7 @@ sub get_accession_from_label{
while(my @row = $sub_sth->fetchrow_array()) {
return $row[0];
}
- return undef;
+ return;
}
@@ -2305,8 +2308,7 @@ sub get_sub_list{
sub set_release
{
- my $self = shift;
- my ( $source_id, $release ) = @_;
+ my ($self, $source_id, $release ) = @_;
my $dbi = dbi();
@@ -2317,6 +2319,7 @@ sub set_release
print "Setting release to '$release' for source ID '$source_id'\n" if($verbose);
$sth->execute( $release, $source_id );
+ return;
}
sub get_dependent_mappings {
@@ -2336,7 +2339,7 @@ sub get_dependent_mappings {
$xref_dependent_mapped{$master_xref."|".$dependent_xref}=1;
}
$sth->finish;
-
+ return;
}
sub get_ext_synonyms{
@@ -2402,7 +2405,7 @@ sub parsing_finished_store_data{
$self->add_meta_pair("PARSED_".$table_and_key{$table}, $max_val);
$sth->finish;
}
-
+ return;
}
@@ -2420,7 +2423,7 @@ sub reset_to_just_parsed{
# set process_status to "parsing_finished"
-
+return;
}
@@ -2428,6 +2431,7 @@ sub reset_to_mapping_finished{
my $self= shift;
$self->reset_to_parsed();
#set process_status to "mapping_finished"
+ return;
}
# --------------------------------------------------------------------------------
diff --git a/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
index df16975c46..a57a837235 100644
--- a/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
@@ -13,7 +13,7 @@ use base qw( XrefParser::BaseParser );
sub run_script {
- my $self = shift if (defined(caller(1)));
+ my $self = shift;
my $file = shift;
my $source_id = shift;
my $species_id = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm b/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
index d2e38ad5b2..d4c54d1b35 100644
--- a/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
@@ -16,8 +16,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/CeleraProteinParser.pm b/misc-scripts/xref_mapping/XrefParser/CeleraProteinParser.pm
index a51cc21403..6b71d99084 100644
--- a/misc-scripts/xref_mapping/XrefParser/CeleraProteinParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CeleraProteinParser.pm
@@ -6,7 +6,7 @@ use base qw( XrefParser::CeleraParser );
# See CeleraParser for details
-sub get_sequence_type()
+sub get_sequence_type
{
return 'peptide';
}
diff --git a/misc-scripts/xref_mapping/XrefParser/CeleraTranscriptParser.pm b/misc-scripts/xref_mapping/XrefParser/CeleraTranscriptParser.pm
index fb08e9f140..c2f5473471 100644
--- a/misc-scripts/xref_mapping/XrefParser/CeleraTranscriptParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CeleraTranscriptParser.pm
@@ -6,7 +6,7 @@ use base qw( XrefParser::CeleraParser );
# See CeleraParser for details
-sub get_sequence_type()
+sub get_sequence_type
{
return 'dna';
}
diff --git a/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm b/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm
index e314556b60..d987126916 100644
--- a/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm
@@ -14,8 +14,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm b/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
index e1ec0267c8..4efd8e988b 100644
--- a/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
@@ -20,8 +20,7 @@ my $source_id;
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
@@ -30,7 +29,6 @@ sub run {
my $filename = @{$files}[0];
-# my ( $source_id, $species_id, $filename, $rel_url,$verbose ) = @_;
my $file_io = $self->get_filehandle($filename);
if ( !defined($file_io) ) {
diff --git a/misc-scripts/xref_mapping/XrefParser/EG_DBParser.pm b/misc-scripts/xref_mapping/XrefParser/EG_DBParser.pm
index ee69800373..a535ba4109 100644
--- a/misc-scripts/xref_mapping/XrefParser/EG_DBParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/EG_DBParser.pm
@@ -8,22 +8,8 @@ use base qw( XrefParser::BaseParser );
use strict;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
-
-#my $dbi2;
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: EG_DBParser.pm file <source_id> <species_id> <verbose>\n\n";
- exit(1);
- }
-
- run(@ARGV);
-}
-
sub run_script {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $file = shift;
my $source_id = shift;
my $species_id = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm b/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
index 4811ab0000..b7ce3e4259 100644
--- a/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
@@ -6,24 +6,9 @@ use File::Basename;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: EntrezGeneParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/FantomParser.pm b/misc-scripts/xref_mapping/XrefParser/FantomParser.pm
index 8184144e26..e049d77338 100644
--- a/misc-scripts/xref_mapping/XrefParser/FantomParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/FantomParser.pm
@@ -7,25 +7,9 @@ use File::Spec::Functions;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: FantomParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/FastaParser.pm b/misc-scripts/xref_mapping/XrefParser/FastaParser.pm
index 4cbc9c369e..2979e1d152 100644
--- a/misc-scripts/xref_mapping/XrefParser/FastaParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/FastaParser.pm
@@ -14,8 +14,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm b/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm
index 3beecdac6b..0f06ab57b9 100644
--- a/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm
@@ -46,23 +46,6 @@ my %cache_source =();
my $verbose;
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: Flybase_dmel_GFFv3_Parser.pm file.gff\n";
- print scalar(@ARGV);
- exit(1);
- }
-
- run($ARGV[0], -1);
-
-}
-
-# --------------------------------------------------------------------------------
-
sub new {
my $proto = shift;
my $self = $proto->SUPER::new(@_);
@@ -177,8 +160,7 @@ sub get_source{
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
@@ -186,10 +168,6 @@ sub run {
$verbose = shift;
my $file = @{$files}[0];
-# my $self = shift if (defined(caller(1)));
-# my $source_id = shift;
-# my $species_id = shift;
-# my $file = shift;
my $species_name;
@@ -530,7 +508,7 @@ sub set_flybase_synonyms {
$self->add_synonym($unique_id,\@syns);
return \@syns;
}
- return undef;
+ return;
}
sub make_id_xref{
@@ -619,7 +597,7 @@ sub get_fields {
# if the item does not hold information of specific field
}else{
- return undef;
+ return;
}
}
diff --git a/misc-scripts/xref_mapping/XrefParser/GOParser.pm b/misc-scripts/xref_mapping/XrefParser/GOParser.pm
index bcaaa991eb..3f7c7c4738 100644
--- a/misc-scripts/xref_mapping/XrefParser/GOParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/GOParser.pm
@@ -8,24 +8,9 @@ use File::Basename;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: GoParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/GOSlimParser.pm b/misc-scripts/xref_mapping/XrefParser/GOSlimParser.pm
index 27e27fc0ac..861e32f3ff 100644
--- a/misc-scripts/xref_mapping/XrefParser/GOSlimParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/GOSlimParser.pm
@@ -11,7 +11,7 @@ my $reg = "Bio::EnsEMBL::Registry";
sub run_script {
- my $self = shift if (defined(caller(1)));
+ my $self = shift;
my $file = shift;
my $source_id = shift;
my $species_id = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm b/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
index b80e1ccfcc..674828b6a8 100644
--- a/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
@@ -9,23 +9,9 @@ my $xref_sth ;
my $dep_sth;
my $syn_sth;
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: HGNCParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run(@ARGV);
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files_ref = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/HPAParser.pm b/misc-scripts/xref_mapping/XrefParser/HPAParser.pm
index 86213a1d22..5b9b41572c 100644
--- a/misc-scripts/xref_mapping/XrefParser/HPAParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HPAParser.pm
@@ -15,8 +15,7 @@ use base qw( XrefParser::BaseParser);
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/IKMCParser.pm b/misc-scripts/xref_mapping/XrefParser/IKMCParser.pm
index 8418befa85..3b01292c9a 100644
--- a/misc-scripts/xref_mapping/XrefParser/IKMCParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/IKMCParser.pm
@@ -16,8 +16,7 @@ sub new {
}
sub run_script {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $file = shift;
my $source_id = shift;
my $species_id = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/IPIParser.pm b/misc-scripts/xref_mapping/XrefParser/IPIParser.pm
index 49a276def6..9925f5253c 100644
--- a/misc-scripts/xref_mapping/XrefParser/IPIParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/IPIParser.pm
@@ -13,8 +13,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm b/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm
index b0a1d86724..9ca3123d5e 100644
--- a/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm
@@ -14,8 +14,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/IlluminaWGParser.pm b/misc-scripts/xref_mapping/XrefParser/IlluminaWGParser.pm
index cf063fea76..aaa2cc6228 100644
--- a/misc-scripts/xref_mapping/XrefParser/IlluminaWGParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/IlluminaWGParser.pm
@@ -7,8 +7,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/ImmunoDBParser.pm b/misc-scripts/xref_mapping/XrefParser/ImmunoDBParser.pm
index 8f647862b9..dbaa82911e 100644
--- a/misc-scripts/xref_mapping/XrefParser/ImmunoDBParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ImmunoDBParser.pm
@@ -5,24 +5,8 @@ use POSIX qw(strftime);
use File::Basename;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: ImmunoDBParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/InterproGoParser.pm b/misc-scripts/xref_mapping/XrefParser/InterproGoParser.pm
index cb0e84f2a8..f2a8dba9f3 100644
--- a/misc-scripts/xref_mapping/XrefParser/InterproGoParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/InterproGoParser.pm
@@ -6,8 +6,7 @@ use vars qw(@ISA);
@ISA = qw(XrefParser::BaseParser);
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/InterproParser.pm b/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
index d0794e6d77..f538aa9a12 100644
--- a/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
@@ -3,31 +3,14 @@ package XrefParser::InterproParser;
use strict;
use POSIX qw(strftime);
use File::Basename;
-
+
use base qw( XrefParser::BaseParser );
-
+
my $xref_sth ;
my $dep_sth;
-
-
-
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: InterproParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run(@ARGV);
-}
-
-
-sub run {
- my $self = shift if (defined(caller(1)));
+sub run {
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files_ref = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/IxodesCAPParser.pm b/misc-scripts/xref_mapping/XrefParser/IxodesCAPParser.pm
index 2a888a14af..c2a2f1232a 100644
--- a/misc-scripts/xref_mapping/XrefParser/IxodesCAPParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/IxodesCAPParser.pm
@@ -13,8 +13,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm b/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm
index cb32def5a1..7ceed6ea14 100644
--- a/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm
@@ -13,8 +13,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/JGI_ProteinParser.pm b/misc-scripts/xref_mapping/XrefParser/JGI_ProteinParser.pm
index 90afb658b7..b290559173 100644
--- a/misc-scripts/xref_mapping/XrefParser/JGI_ProteinParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/JGI_ProteinParser.pm
@@ -7,7 +7,7 @@ use base qw( XrefParser::JGI_Parser );
# See JGI_Parser for details
-sub get_sequence_type() {
+sub get_sequence_type {
return 'peptide';
}
diff --git a/misc-scripts/xref_mapping/XrefParser/MGDParser.pm b/misc-scripts/xref_mapping/XrefParser/MGDParser.pm
index 709aa4c3f8..8bb8c80b30 100644
--- a/misc-scripts/xref_mapping/XrefParser/MGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MGDParser.pm
@@ -1,34 +1,17 @@
package XrefParser::MGDParser;
-
+
use strict;
+use warnings;
use POSIX qw(strftime);
use File::Basename;
-
+
use base qw( XrefParser::BaseParser );
-
+
my $xref_sth ;
my $dep_sth;
-
-
-
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: MGDParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
@@ -38,14 +21,18 @@ sub run {
my $file = @{$files}[0];
die "No longer used. MGI is taken form the uniprot file\n";
+}
+1;
+
+__END__
if(!defined($source_id)){
$source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
}
if(!defined($species_id)){
$species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
- }
-
+ }
+
my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
diff --git a/misc-scripts/xref_mapping/XrefParser/MGIParser.pm b/misc-scripts/xref_mapping/XrefParser/MGIParser.pm
index cab7091c0e..c48e3d1bf8 100644
--- a/misc-scripts/xref_mapping/XrefParser/MGIParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MGIParser.pm
@@ -6,24 +6,9 @@ use DBI;
use base qw(XrefParser::BaseParser);
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: MGIParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm b/misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm
index 8d29ef3ec6..1c6fe5b661 100644
--- a/misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm
@@ -9,22 +9,9 @@ use strict;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
-#my $dbi2;
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: MGI_Desc_Parser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run(@ARGV);
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/MIMParser.pm b/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
index d78e5a086a..c5b5296526 100644
--- a/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
@@ -6,24 +6,9 @@ use File::Basename;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: MIMParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $general_source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/Mim2GeneParser.pm b/misc-scripts/xref_mapping/XrefParser/Mim2GeneParser.pm
index 008e0a4ddf..c6f093dfe3 100644
--- a/misc-scripts/xref_mapping/XrefParser/Mim2GeneParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/Mim2GeneParser.pm
@@ -6,24 +6,9 @@ use File::Basename;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: Mim2GeneParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm b/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
index b1b848842b..dc42b67c7b 100644
--- a/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
@@ -7,19 +7,9 @@ use base qw( XrefParser::BaseParser );
use strict;
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: OTTTParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run(@ARGV);
-}
sub run_script {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $file = shift;
my $source_id = shift;
my $species_id = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/PHIbaseParser.pm b/misc-scripts/xref_mapping/XrefParser/PHIbaseParser.pm
index 9bb8f76ae2..13bfd128c5 100644
--- a/misc-scripts/xref_mapping/XrefParser/PHIbaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/PHIbaseParser.pm
@@ -8,29 +8,11 @@ use XML::LibXML;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: PhibaseParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- print STDERR "ARGV[0]: $ARGV[0]\n";
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
- #my $phi_xml_file = shift;
my $files = shift;
my $verbose = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/RGDParser.pm b/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
index a35e5deef5..3df95f851c 100644
--- a/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
@@ -9,25 +9,9 @@ use base qw( XrefParser::BaseParser );
my $xref_sth ;
my $dep_sth;
-
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: RGDParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
index 32acd1d3fb..1a93281505 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
@@ -8,28 +8,11 @@ use File::Basename;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: RefSeqGPFFParser.pm file.SPC <source_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0], -1);
-
-}
-
-# --------------------------------------------------------------------------------
-
my $verbose;
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files_ref = shift;
@@ -135,7 +118,7 @@ sub create_xrefs {
if ( !defined $refseq_io ) {
print STDERR "ERROR: Can't open RefSeqGPFF file $file\n";
- return undef;
+ return;
}
my @xrefs;
@@ -161,7 +144,7 @@ sub create_xrefs {
}else{
print STDERR "Could not work out sequence type for $file\n";
- return undef;
+ return;
}
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm
index e631e31a0a..019d3d2060 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm
@@ -10,26 +10,10 @@ use base qw( XrefParser::BaseParser );
my $verbose;
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: RefSeqParser.pm file.SPC <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0], -1);
-
-}
-
-# --------------------------------------------------------------------------------
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files_ref = shift;
@@ -130,7 +114,7 @@ sub create_xrefs {
if ( !defined $refseq_io ) {
print STDERR "ERROR: Can't open RefSeq file $file\n";
- return undef;
+ return;
}
my @xrefs;
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
index fe64316796..3a89d7f2c2 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
@@ -10,7 +10,7 @@ use base qw( XrefParser::BaseParser );
sub run_script {
- my $self = shift if (defined(caller(1)));
+ my $self = shift;
my $file = shift;
my $source_id = shift;
my $species_id = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/SGDParser.pm b/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
index 44d4e37653..e32c2d724a 100644
--- a/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
@@ -9,21 +9,9 @@ use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: SGDParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files_ref = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm b/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
index 3d87d28a71..623fb18739 100644
--- a/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
@@ -6,23 +6,8 @@ use File::Basename;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: SegmentParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files_ref = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/UCSCParser.pm b/misc-scripts/xref_mapping/XrefParser/UCSCParser.pm
index 50645bf7ba..d8b3c244bd 100644
--- a/misc-scripts/xref_mapping/XrefParser/UCSCParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UCSCParser.pm
@@ -8,8 +8,7 @@ use warnings;
use base qw( XrefParser::CoordinateParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm b/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm
index 574d5e3c6a..ef664a438c 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm
@@ -10,26 +10,9 @@ use base qw( XrefParser::BaseParser );
my $verbose;
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: UniGeneParser.pm file.SPC <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0], -1);
-
-}
-
-# --------------------------------------------------------------------------------
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
@@ -112,7 +95,7 @@ sub get_desc{
if ( !defined $desc_io ) {
print STDERR "ERROR: Can't open $data_file\n";
- return undef;
+ return;
}
while ( $_ = $desc_io->getline() ) {
@@ -147,14 +130,14 @@ sub create_xrefs {
# my %name2species_id = map{ $_=>$species_id } @names;
if ( !defined( $self->get_desc($data_file) ) ) {
- return undef;
+ return;
}
my $unigene_io = $self->get_filehandle($uniq_file);
if ( !defined $unigene_io ) {
print STDERR "Can't open RefSeq file $uniq_file\n";
- return undef;
+ return;
}
#>gnl|UG|Hs#S19185843 Homo sapiens N-acetyltransferase 2 (arylamine N-acetyltransferase)
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm
index f81c3311ee..e0f1123ceb 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm
@@ -10,26 +10,12 @@ use base qw( XrefParser::BaseParser );
# All assumed to be linked to translation
my $verbose;
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print "\nUsage: RefSeqParser.pm file.SPC <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0], -1);
-
-}
# --------------------------------------------------------------------------------
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
index 2d82b3c578..8163af5bbf 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
@@ -18,28 +18,9 @@ use base qw( XrefParser::BaseParser );
my $verbose;
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 3) {
- print STDERR "\nUsage: UniProtParser.pm file.SPC <source_id> <species_id>\n\n";
- print STDERR scalar(@ARGV);
- exit(1);
- }
-
- run($ARGV[0], -1);
-
-}
-
-# --------------------------------------------------------------------------------
-
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
@@ -199,7 +180,7 @@ sub create_xrefs {
%{ $self->get_valid_codes( "mim_morbid", $species_id ) };
my $uniprot_io = $self->get_filehandle($file);
- if ( !defined $uniprot_io ) { return undef }
+ if ( !defined $uniprot_io ) { return }
my @xrefs;
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtParser_descriptions_only.pm b/misc-scripts/xref_mapping/XrefParser/UniProtParser_descriptions_only.pm
index 0e233f0d8e..66100abe2b 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtParser_descriptions_only.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtParser_descriptions_only.pm
@@ -15,29 +15,13 @@ use File::Basename;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 3) {
- print STDERR "\nUsage: UniProtParser.pm file.SPC <source_id> <species_id>\n\n";
- print STDERR scalar(@ARGV);
- exit(1);
- }
-
- run($ARGV[0], -1);
-
-}
-
my $verbose;
# --------------------------------------------------------------------------------
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
@@ -177,7 +161,7 @@ sub create_xrefs {
print "Predicted SpTREMBL source id for $file: $sptr_pred_source_id\n" if($verbose);
my $uniprot_io = $self->get_filehandle($file);
- if ( !defined $uniprot_io ) { return undef }
+ if ( !defined $uniprot_io ) { return }
my @xrefs;
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm
index 2ac20eb65c..efb7a1e82e 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm
@@ -18,8 +18,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/VBCommunitySymbolParser.pm b/misc-scripts/xref_mapping/XrefParser/VBCommunitySymbolParser.pm
index cd8f89ed4f..02dc38fb93 100644
--- a/misc-scripts/xref_mapping/XrefParser/VBCommunitySymbolParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VBCommunitySymbolParser.pm
@@ -6,24 +6,9 @@ use File::Basename;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: VBCommunitySymbolParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/VBExternalDescriptionParser.pm b/misc-scripts/xref_mapping/XrefParser/VBExternalDescriptionParser.pm
index 804edce1a9..38da9125ef 100644
--- a/misc-scripts/xref_mapping/XrefParser/VBExternalDescriptionParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VBExternalDescriptionParser.pm
@@ -13,21 +13,9 @@ use base qw( XrefParser::BaseParser );
# AAEL010223 phosphatidylserine decarboxylase
# ...
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: VBExternalDescription.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/VBPubMedParser.pm b/misc-scripts/xref_mapping/XrefParser/VBPubMedParser.pm
index b21e682ebb..a4fff87462 100644
--- a/misc-scripts/xref_mapping/XrefParser/VBPubMedParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VBPubMedParser.pm
@@ -12,22 +12,9 @@ use base qw( XrefParser::BaseParser );
#1961751 AAEL006563 gene AAEL006563 Inferred from UniProt entry VCP_AEDAE (P42660)
#2052024 AAEL006424 gene AAEL006424 Inferred from UniProt entry ALL2_AEDAE (P18153)
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: VBPubMed.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/VBRNADescriptionParser.pm b/misc-scripts/xref_mapping/XrefParser/VBRNADescriptionParser.pm
index a939e46434..f721c9a803 100644
--- a/misc-scripts/xref_mapping/XrefParser/VBRNADescriptionParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VBRNADescriptionParser.pm
@@ -12,22 +12,9 @@ use base qw( XrefParser::BaseParser );
# AGAP013556 U6 spliceosomal RNA [Source: RFAM 9.0]
# etc.
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: VBRNADescription.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm b/misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm
index f37bcaf41e..719af0eae6 100644
--- a/misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm
@@ -13,21 +13,9 @@ use base qw( XrefParser::BaseParser );
# MOS10003 AGAP001910 gene Rps3 40S ribosomal protein S3
# ...
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: VBribosomalParser.pm.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm b/misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm
index de97986c48..1c8013b33e 100644
--- a/misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm
@@ -19,14 +19,14 @@ sub run {
my ($self, $file, $source_id, $species_id) = @_;
- open (INFILE, "<$file");
+ open my $FH, "<", $file || return;
my $i=0;
print STDERR "source: ".$source_id."\tspecies: ".$species_id."\n";
my $type = "transcript";
- while (my $ln = <INFILE>) {
+ while (my $ln = <$FH>) {
chomp($ln);
my ($probe,$id, $version, $description, $ensembl_id) = split("\t",$ln);
$i++;
@@ -40,7 +40,7 @@ sub run {
print $i." VB direct xrefs succesfully parsed\n" if($verbose);
- close(INFILE);
+ close($FH);
return 0;
diff --git a/misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.pm b/misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.pm
index 7e516a65d3..ce4fe5dcb5 100644
--- a/misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.pm
@@ -12,8 +12,7 @@ use base qw( XrefParser::CoordinateParser );
# Parser for GFF3-format probe mappings from Vectorbase
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
@@ -22,9 +21,9 @@ sub run {
my $file = @{$files}[0];
- open (INFILE, "<$file");
+ open ($FH, "<", $file) || return 1;
my $i=0; my $type = "transcript";
- while (my $ln = <INFILE>) {
+ while (my $ln = <$FH>) {
# # parse GFF line:
chomp($ln); $i++;
my ($seqid, $source, $type, $start, $end, $score, $strand, $phase, $attributes) = split("\t",$ln);
@@ -76,7 +75,7 @@ sub run {
}
}
print STDERR $i." VB GFF3 xrefs succesfully parsed\n" if($verbose);
- close(INFILE);
+ close($FH);
return 0;
} ## end sub run
diff --git a/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm b/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
index 9eb1ee65e6..b3c29c2432 100644
--- a/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
@@ -10,8 +10,7 @@ my $syn_sth;
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
index e86d288af1..49e55340d6 100644
--- a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
@@ -17,8 +17,7 @@ my $dep_sth;
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm b/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm
index a646eff138..0ff6fef022 100644
--- a/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm
@@ -11,8 +11,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/ZFINDescParser.pm b/misc-scripts/xref_mapping/XrefParser/ZFINDescParser.pm
index f42493093a..ab03b01198 100644
--- a/misc-scripts/xref_mapping/XrefParser/ZFINDescParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ZFINDescParser.pm
@@ -7,25 +7,10 @@ use File::Spec::Functions;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: ZFINDescParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
@@ -42,7 +27,7 @@ sub run {
}
- open(FH,"<$file") || die "could not open file $file";
+ open( my $FH, "<", $file) || die "could not open file $file";
#e.g.
@@ -53,7 +38,7 @@ sub run {
my $count =0;
my $withdrawn = 0;
- while ( <FH> ) {
+ while ( <$FH> ) {
chomp;
my ($zfin, $desc, $label) = split (/\t/,$_);
@@ -65,6 +50,7 @@ sub run {
$count++;
}
}
+ close($FH);
if($verbose){
print "\t$count xrefs added, $withdrawn withdrawn entries ignored\n";
diff --git a/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm b/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
index 9ba745b102..a00cb1d867 100644
--- a/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
@@ -7,25 +7,9 @@ use File::Spec::Functions;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: ZFINParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
index 0518e8b16a..d5da63aeb2 100644
--- a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
@@ -9,21 +9,8 @@ use Bio::EnsEMBL::Registry;
my $reg = "Bio::EnsEMBL::Registry";
-#my $dbi2;
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: curated_transcriptParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run(@ARGV);
-}
-
sub run_script {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $file = shift;
my $source_id = shift;
my $species_id = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm b/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
index 7e4b80eceb..06cad2bc89 100644
--- a/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
@@ -6,24 +6,9 @@ use File::Basename;
use base qw( XrefParser::BaseParser );
-# --------------------------------------------------------------------------------
-# Parse command line and run if being run directly
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: ncRNAParser.pm file <source_id> <species_id>\n\n";
- exit(1);
- }
-
- run($ARGV[0]);
-
-}
-
sub run {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $source_id = shift;
my $species_id = shift;
my $files = shift;
diff --git a/misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.pm b/misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.pm
index 1f2bc3f787..ba8b8cb414 100644
--- a/misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.pm
@@ -9,21 +9,8 @@ use strict;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
-#my $dbi2;
-
-if (!defined(caller())) {
-
- if (scalar(@ARGV) != 1) {
- print STDERR "\nUsage: ncRNA_DBParser.pm file <source_id> <species_id> <verbose>\n\n";
- exit(1);
- }
-
- run(@ARGV);
-}
-
sub run_script {
- my $self = shift if (defined(caller(1)));
-
+ my $self = shift;
my $file = shift;
my $source_id = shift;
my $species_id = shift;
--
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