diff --git a/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm b/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
index 7fb3838057248bb7aa082c42b6793e36fff4020a..ed24106d2c0a410c09922de5d496107691ba2e05 100644
--- a/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
@@ -13,7 +13,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my $cpt = 0 ;
next if (/^File:/); # skip header
diff --git a/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm b/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm
index a9a37f555cb1d5e41ad41a246d58de310e82f52c..4fdbee3847ca3356f666b04deb1aa84f9d2bff93 100644
--- a/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm
@@ -13,7 +13,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my @xrefs;
diff --git a/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm b/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
index 641b724dfb620f7f435044cf89f56f8c939d24fa..76294ccfa7b7dd510afe7ec03531dff18bdc4fed 100644
--- a/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
@@ -14,7 +14,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
next if (/^File:/); # skip header
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index 231760080b9aba4f94649414c5eb64714adc8ce8..9050a702ed62ede99dd479adddf59b3442120374 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -169,7 +169,7 @@ sub run
print "Parsing local file '$local_file' with $parser\n";
eval "require XrefParser::$parser";
my $new = "XrefParser::$parser"->new();
- if($new->run($local_file, $source_id, $species_id)){
+ if($new->run($source_id, $species_id, $local_file)){
$summary{$parser}++;
}
else{
@@ -335,7 +335,7 @@ sub run
print "Parsing '" . join( "', '", @new_file ) . "' with $parser\n";
eval "require XrefParser::$parser";
my $new = "XrefParser::$parser"->new();
- if ( $new->run( $dir . '/' . $new_file[0], $source_id, $species_id ) )
+ if ( $new->run( $source_id, $species_id, $dir . '/' . $new_file[0] ) )
{
$summary{$parser}++;
}
@@ -992,10 +992,9 @@ sub md5sum
open( FILE, $file );
binmode(FILE);
- my $checksum = sprintf( "%d/%s",
- [ stat FILE ]->[7],
- substr( Digest::MD5->new()->addfile(*FILE)->hexdigest(), 0, 6 )
- );
+ my $checksum = sprintf( "%s/%d",
+ substr( Digest::MD5->new()->addfile(*FILE)->hexdigest(), 0, 6 ),
+ [ stat FILE ]->[7] );
close(FILE);
diff --git a/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
index e5fdc637b6f9bc760da46eb5c83d139b9b8a329e..37bd168af895ca1b276c47d702dd778dd4637c40 100644
--- a/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
@@ -13,7 +13,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my $ccds_io = $self->get_filehandle($file);
diff --git a/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm b/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
index 0d654293977f1263243e84416e5d79aa25d3f1b4..29eee0286f2aa0eefd55d9e0a27b4592eda9b8e0 100644
--- a/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
@@ -16,7 +16,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my $celera_gene_source_id = $self->get_source_id_for_source_name('Celera_Gene');
diff --git a/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm b/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm
index 061ad01da65fd7556258af882f54c0abcd304466..e6fd95fe60da14d7a1a645eb156a6a0014d353c0 100644
--- a/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm
@@ -14,7 +14,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my @xrefs;
diff --git a/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm b/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
index 750e46e1d1de67b1061058c1f1180bc4ab14f6b8..2f2d5e8870555b25f2f042035901c970d431681a 100644
--- a/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
@@ -23,9 +23,9 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
if(!defined($source_id)){
$source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
diff --git a/misc-scripts/xref_mapping/XrefParser/FastaParser.pm b/misc-scripts/xref_mapping/XrefParser/FastaParser.pm
index ebde3171f07a6e76721aeee2701c0d6429b36ff1..3073d09089cca015051a8769caeeaefb032ea950 100644
--- a/misc-scripts/xref_mapping/XrefParser/FastaParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/FastaParser.pm
@@ -14,7 +14,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my $sio = Bio::SeqIO->new(-format=>'fasta' , -file=>$file );
my $species_tax_id = $self->get_taxonomy_from_species_id($species_id);
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 31db32db96dec603e107e0fb83b9697e1cb97fe9..e90c86c1ecdf63a72fc368e4aeee869e8fb9310e 100644
--- a/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm
@@ -108,9 +108,9 @@ sub get_source{
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
my $species_name;
diff --git a/misc-scripts/xref_mapping/XrefParser/GOParser.pm b/misc-scripts/xref_mapping/XrefParser/GOParser.pm
index eac9d917f39f7828b875476065febf902a37bf28..3ff62e8fb45e2835e63dddb7726f061d8dda453f 100644
--- a/misc-scripts/xref_mapping/XrefParser/GOParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/GOParser.pm
@@ -25,9 +25,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
+
my %wrongtype;
if(!defined($source_id)){
diff --git a/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm b/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm
index c207105f6f59a021f48aa228a9a5cf04612bb02f..584e21658c495d88ffa4df062a69576d62784c55 100644
--- a/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm
@@ -25,10 +25,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
print STDERR "source = $source_id\tspecies = $species_id\n";
if(!defined($source_id)){
diff --git a/misc-scripts/xref_mapping/XrefParser/HUGO_CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/HUGO_CCDSParser.pm
index ca172bf50fc9e812e9a35040305bfb78cd17eb84..16177b5b39509d1797f86afcd3030ec7a4e05851 100644
--- a/misc-scripts/xref_mapping/XrefParser/HUGO_CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HUGO_CCDSParser.pm
@@ -11,7 +11,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my $hugo_io = $self->get_filehandle($file);
diff --git a/misc-scripts/xref_mapping/XrefParser/HUGO_ENSGParser.pm b/misc-scripts/xref_mapping/XrefParser/HUGO_ENSGParser.pm
index 664904ff7b2a76571c54d5d2d61567d325df6a4b..19165282428ac53666c4edf4f9ad66492ce61a68 100644
--- a/misc-scripts/xref_mapping/XrefParser/HUGO_ENSGParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HUGO_ENSGParser.pm
@@ -11,7 +11,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my $hugo_io = $self->get_filehandle($file);
diff --git a/misc-scripts/xref_mapping/XrefParser/IPIParser.pm b/misc-scripts/xref_mapping/XrefParser/IPIParser.pm
index 0f62360f245130421eda59deebf2653fb691fdca..ecf97b478cf1ba54f601728b9ebb8a29b4c3e08a 100644
--- a/misc-scripts/xref_mapping/XrefParser/IPIParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/IPIParser.pm
@@ -13,7 +13,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my @xrefs;
diff --git a/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm b/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm
index d959b579b031b67f1d0479714068d2007e5273e2..55beefae90bcc12b206b181c83f6b4bd08b33f38 100644
--- a/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm
@@ -14,7 +14,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my @xrefs;
diff --git a/misc-scripts/xref_mapping/XrefParser/InterproParser.pm b/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
index ec834915f588ea4ec461486c0dad9f3ccbd50596..65c55130eb1f744e636f0df3fd077c7e056c5d3a 100644
--- a/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
@@ -27,10 +27,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
-
+
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
print STDERR "source = $source_id\tspecies = $species_id\n";
if(!defined($source_id)){
diff --git a/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm b/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm
index 4cb15cd0a24308d053b52e850132b2a053db0b28..f76003ffcca3f3a21c6861d1fe980e875791dae1 100644
--- a/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm
@@ -13,7 +13,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my $source_name = $self->get_source_name_for_source_id ($source_id) ;
diff --git a/misc-scripts/xref_mapping/XrefParser/MGDParser.pm b/misc-scripts/xref_mapping/XrefParser/MGDParser.pm
index 85b9aa5dc9ee6e44e9ec6a4bf0e0c701442c591e..e3261decc9ad5e921b97e40d875c2a9bd3b275f0 100644
--- a/misc-scripts/xref_mapping/XrefParser/MGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MGDParser.pm
@@ -28,10 +28,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
if(!defined($source_id)){
$source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
diff --git a/misc-scripts/xref_mapping/XrefParser/MIMParser.pm b/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
index c634c09925bfd4ab0ce565d2da499c6cff08041b..b380b7b4185ce2462a92fdd9e8a2860516d73d01 100644
--- a/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
@@ -23,9 +23,11 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
+
my $general_source_id = shift;
my $species_id = shift;
+ my $file = shift;
+
my %old_to_new;
my %removed;
my $source_id;
diff --git a/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm b/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
index a56b1542273569331c3a9d88f300911b7b3fa217..75ded6d1a460888807ec0144afbb41b5af09dc57 100644
--- a/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
@@ -14,7 +14,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my $ottt_io = $self->get_filehandle($file);
diff --git a/misc-scripts/xref_mapping/XrefParser/RGDParser.pm b/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
index 8f147c02a872ba075f321c0725b3c4f496ac7232..ef4326cda9bf75c319191e25a82256370c839d3a 100644
--- a/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
@@ -27,11 +27,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
+
my $source_id = shift;
my $species_id = shift;
-
-
+ my $file = shift;
if(!defined($source_id)){
$source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
index efad047380aed159c2d2a0c28e45132fa184c991..e5e13aad268d52540a0ba62c0bcd8f371cb19243 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
@@ -27,9 +27,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
+
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
if ($source_id < 1) {
$source_id = XrefParser::BaseParser->get_source_id_for_filename(basename($file));
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm
index 1625701a107635e9c9b0ff88feb4ab1d9884970e..5bd810b9e2ff7d8f7e3a7e6f7f85ba7268823fa9 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm
@@ -27,9 +27,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
+
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
my $peptide_source_id = XrefParser::BaseParser->get_source_id_for_source_name('RefSeq_peptide');
my $dna_source_id = XrefParser::BaseParser->get_source_id_for_source_name('RefSeq_dna');
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
index 96a376aae496f78e6d0fe8c88516e32bc9359ede..bf6166a81b7f12ccde280862821faa36332d259d 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
@@ -10,7 +10,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my $refseq_io = $self->get_filehandle($file);
diff --git a/misc-scripts/xref_mapping/XrefParser/SGDParser.pm b/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
index 8d1f89f6048b25450932068e035e786935990296..5c20c87410bec7578cb15b10e47a872b69b7c113 100644
--- a/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
@@ -23,9 +23,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
+
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
if(!defined($source_id)){
$source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
diff --git a/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm b/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
index 8ff59a44db6505d279f4d0de31b075a5b865641a..6b164dbb5864fe6e17c238b24fd886380229eaac 100644
--- a/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
@@ -23,10 +23,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
if(!defined($source_id)){
$source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
diff --git a/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm b/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm
index 2f8e585ec8fbc2ecef2404067241a84c5af04782..e0ae092804fd6e70edd5c360d45aa15722c4f51f 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm
@@ -27,9 +27,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
+
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
my $unigene_source_id = XrefParser::BaseParser->get_source_id_for_source_name('UniGene');
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
index e15ad5a66af43f16facfb4762f96cd2f97338c6e..a1921fcde8c04af0f2f7fdf3a0dc7b70aa08d9f4 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
@@ -35,9 +35,11 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
+
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
+
my $species_name;
my ($sp_source_id, $sptr_source_id);
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm
index 9001395c4939a591c76c42a7b5ab5a9492a5900d..d1ac12981e7a80c28d2ef1bfd150b9b894f73937 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm
@@ -18,7 +18,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my @xrefs;
diff --git a/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm b/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
index df059b421c7397528fe472262845993760d4fa86..afd31f047ffd93fa8179d9b1abf19fba3dcf5af6 100644
--- a/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
@@ -10,7 +10,7 @@ my $syn_sth;
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my @xrefs = $self->create_xrefs($source_id, $species_id, $file);
diff --git a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
index 8f27dbfb86498248455b28ec487185a5b7b8e5b7..8086a7ae9cf09a1d8fa709ae29d3ad78ed5ad398 100644
--- a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
@@ -17,7 +17,7 @@ my $dep_sth;
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
print STDERR "WORMPep source = $source_id\tspecies = $species_id\n";
diff --git a/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm b/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm
index 02c1e7591f2c2abfab11efd910fa23ee74d7d239..f11b9dfddd41852d5cd2e7750e3e7583e4d92b49 100644
--- a/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm
@@ -15,7 +15,7 @@ use base qw( XrefParser::BaseParser );
sub run {
- my ($self, $file, $source_id, $species_id) = @_;
+ my ($self, $source_id, $species_id, $file) = @_;
my @xrefs;
diff --git a/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm b/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
index 83ceda1bcf863de0e29543ffd99dcc03e9c48025..3bf3d9219c1a6af7f3936d13f1de57dd71184efe 100644
--- a/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
@@ -23,9 +23,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
+
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
if(!defined($source_id)){
$source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
diff --git a/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm b/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
index 8ca57774fbb6a66d9f91bc75fd118613e3cfca04..a0478ba73a91d4709613124860cb8df7bb2ae640 100644
--- a/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
@@ -23,10 +23,10 @@ if (!defined(caller())) {
sub run {
my $self = shift if (defined(caller(1)));
- my $file = shift;
my $source_id = shift;
my $species_id = shift;
+ my $file = shift;
if(!defined($source_id)){
$source_id = XrefParser::BaseParser->get_source_id_for_filename($file);