Raw content of XrefParser::Flybase_dmel_GFFv3_Parser
<![CDATA[# Parse UniProt (SwissProt & SPTrEMBL) files to create xrefs.
#
# Files actually contain both types of xref, distinguished by ID line;
#
# This module will read in the fly gff text file and make xrefs from the information in the file.
# First of all, it read knows what all the gene, transcript and translation types are, found in column 3 of the gff file:
# Gene = gene
# Transcript = mRNA ncRNA snRNA tRNA rRNA pseudogene snoRNA miRNA
# Translation = protein (could include CDS here but haven't ?)
#
# ID=FBgn => flybase_gene_id
# ID=FBtr => flybase_transcript_id
# ID=FBpp => flybase_polypeptide_id
# Name=CG0123 => FlyBaseName_gene
# Name=CG0123-RA => FlyBaseName_transcript
# Name=CG0123-PA => FlyBaseName_translations
# Dbxref=FlyBase:FBan => flybase_annotation_id
# Dbxref=FlyBase_Annotation_IDs:CG0123 => gadfly_gene_cgid
# Dbxref=FlyBase_Annotation_IDs:CG0123-RA => gadfly_transcript_cgid
# Dbxref=FlyBase_Annotation_IDs:CG0123-PA => gadfly_translation_id
# Alias= => flybase_synonym
#
# For each line in the gff file for the above list of genes, transcript and translations, the following happens:
# The unique_id is read in from ID= (FBgn, FBtr, FBpp). This is the direct xref for all xrefs of this entry.
# An xref is made for the entry, using the ID as the xref's accession. Synonyms from Alias= are added to this xref.
# The Name (Name=) is read in and added as an xref. Synonyms from Alias= are added to this xref.
# All entries from Dbxref= are added in as xrefs for the entry; they have no synonyms.
#2L gene [...] ID=CG11023;Dbxref=FlyBase:FBan0011023,FlyBase:FBgn0031208;gbunit=AE003590;synonym=CG11023
#2L mRNA [...] ID=CG11023-RA;Dbxref=FlyBase:FBtr008,FlyBase:FBgn003;dbxref_2nd=Gadfly:CG11023-RA;synonym=CG23-RA
#3R FlyBase gene 8084471 8128509 . + .
#ID=FBgn0003651;Name=svp;Alias=FBgn0011337,FBgn0011492,FBgn0011510,FBgn0038010,FBgn0063263;Ontology_term=SO:0000010,SO:0000087,GO:0004872,GO:0007270,GO:0042331,GO:0005515,GO:0007419,GO:0007503,GO:0045449,GO:0004879,GO:0003700,GO:0005634,GO:0007465,GO:0007462,GO:0007464,GO:0007510,GO:0005737,GO:0007507,GO:0007417,GO:0001700,GO:0006357,GO:0007165,GO:0043565,GO:0003707,GO:0008270,GO:0048749,GO:0001752;Dbxref=FlyBase:FBan0011502,FlyBase_Annotation_IDs:CG11502,INTERPRO:IPR013088,GB:AC007724,GB:AE003695,GB_protein:AAF54773,GB_protein:AAN13541,GB_protein:AAF54774,GB:AI108883,GB:AI402121,GB:AY075272,GB_protein:AAL68139,GB:AY119490,GB_protein:AAM50144,GB:AY129452,GB_protein:AAM76194,GB:BG633933,GB:BI167911,GB:CZ468719,GB:CZ472606,GB:CZ475640,GB:CZ475641,GB:CZ477001,GB:CZ482253,GB:CZ485541,GB:CZ485543,GB:G00472,GB:M28863,GB_protein:AAA62770,GB:M28864,GB_protein:AAA03014,UniProt/Swiss-Prot:P16375,UniProt/Swiss-Prot:P16376,UniProt/TrEMBL:Q8MRP3,INTERPRO:IPR000536,INTERPRO:IPR001628,INTERPRO:IPR001723,INTERPRO:IPR003068,INTERPRO:IPR008946,INTERPRO:IPR013629,dedb:9161,flygrid:66603,hybrigenics:521960,if:/newgene/sevenup.htm,orthologs:ensAG:ENSANGG00000002454,orthologs:ensAM:ENSAPMG00000000116,orthologs:ensCF:ENSCAFG00000008076,orthologs:ensDM:CG12744,orthologs:ensDR:ENSDARG00000017168,orthologs:ensFR:SINFRUG00000127451,orthologs:ensGG:ENSGALG00000007000,orthologs:ensHS:ENSG00000185551,orthologs:ensMM:ENSMUSG00000030551,orthologs:ensPT:ENSPTRG00000007484,orthologs:ensRN:ENSRNOG00000010308,orthologs:ensTN:GSTENG00006911001,orthologs:modCB:WBGene00030075;cyto_range=87B4-87B5;gbunit=AE014297;
package XrefParser::Flybase_dmel_GFFv3_Parser;
use strict;
use POSIX qw(strftime);
use File::Basename;
use Bio::EnsEMBL::Utils::Exception;
use base qw( XrefParser::BaseParser );
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(@_);
$self->external_source_db_name('flybase_gff');
# my @gff_obj =qw( CDS exon gene mRNA ncRNA pseudogene rRNA snRNA snoRNA tRNA );
# this array may need to change between releases so check that it's updated
my @gff_obj =qw( gene mRNA ncRNA snRNA tRNA rRNA pseudogene snoRNA miRNA);
$self->gff_object_types(\@gff_obj);
#
# hard-coded field separators out of gff
#
$self->gff_name("Name=");
$self->gff_ontology("Ontology_term=");
$self->gff_synonym("Alias=");
$self->gff_dbxref("Dbxref=");
#
# hard-coded source-names for different objects out of ./sql/populate_metadata.sql
#
# For Alias
$self->source_name_synonym('flybase_synonym'); # source for any Alias
# For Name
$self->source_name_name_prefix('FlyBaseName_'); # source for any Name
# For Dbxref
$self->source_name_fbgn('flybase_gene_id'); # source-name for ID=FBgn
$self->source_name_fbtr('flybase_transcript_id'); # source-name for ID=FBtr
$self->source_name_fbpp('flybase_polypeptide_id'); # source-name for ID=FBpp
$self->source_name_fban('flybase_annotation_id'); # source-name for ID=FBan
$self->source_name_gadfly_gene('gadfly_gene_cgid'); # For Dbxref=FlyBase_Annotation_IDs
$self->source_name_gadfly_transcript('gadfly_transcript_cgid'); # For Dbxref=FlyBase_Annotation_IDs
$self->source_name_gadfly_translation('gadfly_translation_cgid'); # For Dbxref=FlyBase_Annotation_IDs
$self->source_name_affymetrix('AFFY_DrosGenome1'); # For Dbxref=Affymetrix
$self->source_name_dgrc1('DGRC-1'); # For Dbxref=DGRC-1
$self->source_name_dgrc2('DGRC-2'); # For Dbxref=DGRC-2
$self->source_name_drsc('DRSC'); # For Dbxref=DRSC
$self->source_name_epd('EPD'); # For Dbxref=EPD
$self->source_name_flyreg('FlyReg'); # For Dbxref=FlyReg
$self->source_name_gb('EMBL'); # For Dbxref=GB
$self->source_name_gbprotein('protein_id'); # For Dbxref=GB_protein
$self->source_name_gcr('GPCR'); # For Dbxref=GCR
$self->source_name_gi('GI'); # For Dbxref=GI
$self->source_name_go('GO'); # For Dbxref=GO
$self->source_name_genomeRNAi('GenomeRNAi'); # For Dbxref=GenomeRNAi
$self->source_name_interpro('Interpro'); # For Dbxref=INTERPRO
$self->source_name_merops('MEROPS'); # For Dbxref=MEROPS
$self->source_name_miRBase('miRBase'); # For Dbxref=miRBase
$self->source_name_mitodrome('MitoDrome'); # For Dbxref=MitoDrome
$self->source_name_nrl3d('PDB'); # For Dbxref=NRL_3D
$self->source_name_pdb('PDB'); # For Dbxref=PDB
$self->source_name_rfam('RFAM'); # For Dbxref=Rfam
$self->source_name_tf('TransFac'); # For Dbxref=TF
$self->source_name_uniprotsp('Uniprot/SWISSPROT'); # For Dbxref=UniProt/Swiss-Prot
$self->source_name_uniprottr('Uniprot/SPTREMBL'); # For Dbxref=UniProt/TrEMBL
$self->source_name_bdgpinsituexpr('BDGP_insitu_expr'); # For Dbxref=bdgpinsituexpr
$self->source_name_dedb('DEDb'); # For Dbxref=dedb
$self->source_name_drosdel('DrosDel'); # For Dbxref=drosdel
$self->source_name_flygrid('FlyGrid'); # For Dbxref=flygrid
$self->source_name_hybrigenics('hybrigenics'); # For Dbxref=hybrigenics
$self->source_name_if('InteractiveFly'); # For Dbxref=if
$self->source_name_prefix_ensAGgene('Ens_Ag_gene'); # For Dbxref=ensAG
$self->source_name_prefix_ensAMgene('Ens_Am_gene'); # For Dbxref=ensAM
$self->source_name_prefix_ensCEgene('Ens_Ce_gene'); # For Dbxref=ensCE
$self->source_name_prefix_ensCFgene('Ens_Cf_gene'); # For Dbxref=ensCF
$self->source_name_prefix_ensDMgene('Ens_Dm_gene'); # For Dbxref=ensDM
$self->source_name_prefix_ensDRgene('Ens_Dr_gene'); # For Dbxref=ensDR
$self->source_name_prefix_ensFRgene('Ens_Fr_gene'); # For Dbxref=ensFR
$self->source_name_prefix_ensGGgene('Ens_Gg_gene'); # For Dbxref=ensGG
$self->source_name_prefix_ensHSgene('Ens_Hs_gene'); # For Dbxref=ensHS
$self->source_name_prefix_ensMMgene('Ens_Mm_gene'); # For Dbxref=ensMM
$self->source_name_prefix_ensPTgene('Ens_Pt_gene'); # For Dbxref=ensPT
$self->source_name_prefix_ensRNgene('Ens_Rn_gene'); # For Dbxref=ensRN
$self->source_name_prefix_ensTNgene('Ens_Tn_gene'); # For Dbxref=ensTN
$self->source_name_prefix_modCBgene('modCB_gene'); # For Dbxref=modCB
$self->source_name_prefix_modCEgene('modCE_gene'); # For Dbxref=modCE
$self->source_name_prefix_modDDgene('modDD_gene'); # For Dbxref=modDD
my @gene_types = qw (gene) ;
my @translation_types = qw (protein);
# The transcript_types may change from release to release so check that this list is up-to-date
my @transcript_types = qw (mRNA ncRNA snRNA tRNA rRNA pseudogene snoRNA miRNA);
$self->gene_types(\@gene_types) ;
$self->translation_types(\@translation_types) ;
$self->transcript_types(\@transcript_types) ;
$self->{'_xrefs'}=[];
$self->{'_direct_xrefs'}=[];
$self->{'_synonyms'}={};
return $self;
}
# --------------------------------------------------------------------------------
# large number of calls to SQL should now be speeded up as cached.
sub get_source{
my ($self, $name) =@_;
if(!defined($cache_source{$name})){
$cache_source{$name} = XrefParser::BaseParser->get_source_id_for_source_name($name)
}
return $cache_source{$name};
}
sub run {
my $self = shift if (defined(caller(1)));
my $source_id = shift;
my $species_id = shift;
my $files = shift;
my $release_file = shift;
$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 $species_name;
if(!defined($species_id)){
($species_id, $species_name) = get_species($file);
}
$self->species_id($species_id) ;
my $external_source_db_name = $self->external_source_db_name() ;
my $flybase_source_id = $self->get_source($external_source_db_name);
if(!$self->create_xrefs($flybase_source_id, $file)){
return 1;
}
my @xrefs = @{$self->xrefs};
$self->relink_synonyms_to_xrefs();
my @direct_xrefs = @{ $self->direct_xrefs } ;
# delete previous if running directly rather than via BaseParser
if (!defined(caller(1))) {
print "Deleting previous xrefs for these sources\n" if($verbose);
XrefParser::BaseParser->delete_by_source(\@xrefs);
}
print "... parsed.\n" if($verbose);
print STDERR "uploading ".scalar(@xrefs)." xrefs's\n" if($verbose);
XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs);
print STDERR "uploading ".scalar(@direct_xrefs)." direct-xrefs's\n" if($verbose);
XrefParser::BaseParser->upload_direct_xrefs(\@direct_xrefs);
return 0;
}
sub relink_synonyms_to_xrefs{
my $self = shift;
foreach my $x (@{$self->xrefs} ){
my $src_name = XrefParser::BaseParser->get_source_name_for_source_id($x->{SOURCE_ID});
if ($src_name =~ m/^FlyBaseName_/ || $src_name =~ m/^flybase_.*_id$/) {
$x->{SYNONYMS} = $self->get_synonyms($x->{ENSEMBL_STABLE_ID});
}
}
}
# --------------------------------------------------------------------------------
# Parse file into array of xref objects
# parse
sub create_xrefs {
my ($self, $flybase_source_id, $file) = @_;
print STDERR "starting to parse $file...." if($verbose);
my $gff_io = $self->get_filehandle($file);
if ( !defined $gff_io ) {
print STDERR "ERROR: Can't open the GFF file $file\n";
return 0;
}
while ( $_ = $gff_io->getline() ) {
chomp;
my @col = split /\t/;
if($col[3]){
# test if line contains information for object wanted (CDS,mRNA,gene,..)
if ( $self->line_contains_object_to_process( $col[2] ) ){
# work out if we have a gene, transcript or translation
my $type = $self->set_ensembl_object_type($col[2]);
# the 9th column contains all the attributes
my @desc = split /\;/,$col[8];
# the ID= is always the first element of this array
my $unique_id = shift @desc;
if(!$unique_id=~m/ID=/){
throw("parse-error: There seems to be no Identifier: $unique_id. Suspicous!");
# print "parse-error: There seems to be no Identifier: $unique_id. Suspicous!";
# return 0;
}
# for a gene, this will be FBgn, for a transcript this will be FBtr, etc
$unique_id =~s/ID=//g;
$self->make_id_xref($unique_id,$type);
# set up xref-entry for EVERY single item
foreach my $item (@desc) {
$self->set_flybase_synonyms($item,$unique_id);
# make all xrefs for type "Name=" in desc-field
# these are FlyBaseName_gene for genes, FlyBaseName_transcript for transcripts, etc
$self->make_name_xref($item,$unique_id,$type);
# make all xrefs for type "Name=" in desc-field
$self->make_dbxref_xref($item,$unique_id,$type);
}
}
} # we don't want to read the line otherwise
} # while ( $_ = $gff_io->getline() ) {
$gff_io->close();
return 1;
}
sub set_ensembl_object_type{
my ($self,$t) = @_ ; # $t is identifier in gff for object : CDS,mRNA,gene,pseudogene,snRNA,....
for my $hc (@{ $self->gene_types } ){
if ($t=~m/^$hc$/){
return 'gene';
}
}
for my $hc (@{ $self->translation_types } ){
if ($t=~m/^$hc$/){
return 'translation';
}
}
for my $hc (@{ $self->transcript_types} ){
if ($t=~m/^$hc$/){
return 'transcript';
}
}
}
sub make_dbxref_xref{
my ($self,$item,$unique_id,$type) = @_;
# item = attribute
# unique_id = ID
# type = gene, transcript, translation
my ($xref);
my $tg1 = $self->gff_dbxref ;
my $tg2 = $self->gff_ontology;
if ($item=~/$tg1/ || $item=~/$tg2/){ # Dbxref=
# split the xrefs up into a list
my $dbx1 = get_fields($item,$tg1);
my @dbx;
push @dbx, @{$dbx1} if $dbx1;
foreach my $dbx (@dbx) {
my $src_id = undef;
my $source_type = undef;
if ($dbx =~m/FlyBase:/){
$dbx =~s/FlyBase://g;
if($dbx=~m/FBgn/ and $type eq "gene"){
$src_id = $self->get_source($self->source_name_fbgn);
}elsif ($dbx =~m/FBtr/ and $type eq "transcript"){
$src_id = $self->get_source($self->source_name_fbtr);
}elsif ($dbx =~m/FBpp/ and $type eq "translation"){
$src_id = $self->get_source($self->source_name_fbpp);
}elsif ($dbx =~m/FBan/){
$src_id = $self->get_source($self->source_name_fban);
}
}elsif($dbx =~m/FlyBase_Annotation_IDs:/){
$dbx =~s/FlyBase_Annotation_IDs://g;
if($type eq "gene"){
$src_id = $self->get_source($self->source_name_gadfly_gene) ;
}
elsif($type eq "translation"){
$src_id = $self->get_source($self->source_name_gadfly_translation);
}
elsif($type eq "transcript"){
$src_id = $self->get_source($self->source_name_gadfly_transcript);
}
} elsif ($dbx =~m/Affymetrix:/) {
$dbx =~s/Affymetrix://g;
$src_id = $self->get_source($self->source_name_affymetrix) ;
} elsif ($dbx =~m/DGRC-1:/) {
$dbx =~s/DGRC-1://g;
$src_id = $self->get_source($self->source_name_dgrc1) ;
} elsif ($dbx =~m/DGRC-2:/) {
$dbx =~s/DGRC-2://g;
$src_id = $self->get_source($self->source_name_dgrc2);
} elsif ($dbx =~m/DRSC:/) {
$dbx =~s/DRSC://g;
$src_id = $self->get_source($self->source_name_drsc);
} elsif ($dbx =~m/EPD:/) {
$dbx =~s/EPD://g;
$src_id = $self->get_source($self->source_name_epd);
} elsif ($dbx =~m/FlyReg:/) {
$dbx =~s/FlyReg://g;
$src_id = $self->get_source($self->source_name_flyreg);
} elsif ($dbx =~m/GB:/) {
$dbx =~s/GB://g;
$src_id = $self->get_source($self->source_name_gb);
} elsif ($dbx =~m/GB_protein:/) {
$dbx =~s/GB_protein://g;
$src_id = $self->get_source($self->source_name_gbprotein);
} elsif ($dbx =~m/GCR:/) {
$dbx =~s/GCR://g;
$src_id = $self->get_source($self->source_name_gcr);
} elsif ($dbx =~m/GI:/) {
$dbx =~s/GI://g;
$src_id = $self->get_source($self->source_name_gi);
} elsif ($dbx =~m/GO:/) {
# this is an ontology_term
$dbx =~s/GO://g;
$src_id = $self->get_source($self->source_name_go);
} elsif ($dbx =~m/GenomeRNAi:/) {
$dbx =~s/GenomeRNAi://g;
$src_id = $self->get_source($self->source_name_genomeRNAi);
} elsif ($dbx =~m/INTERPRO:/) {
$dbx =~s/INTERPRO://g;
$src_id = $self->get_source($self->source_name_interpro);
} elsif ($dbx =~m/MEROPS:/) {
$dbx =~s/MEROPS://g;
$src_id = $self->get_source($self->source_name_merops);
} elsif ($dbx =~m/MIR:/) {
$dbx =~s/MIR://g;
$src_id = $self->get_source($self->source_name_miRBase);
} elsif ($dbx =~m/MITODROME:/) {
$dbx =~s/MITODROME://g;
$src_id = $self->get_source($self->source_name_mitodrome);
} elsif ($dbx =~m/NRL_3D:/) {
$dbx =~s/NRL_3D://g;
$src_id = $self->get_source($self->source_name_nrl3d);
} elsif ($dbx =~m/PDB:/) {
$dbx =~s/PDB://g;
$src_id = $self->get_source($self->source_name_pdb);
} elsif ($dbx =~m/Rfam:/) {
$dbx =~s/Rfam://g;
$src_id = $self->get_source($self->source_name_rfam);
} elsif ($dbx =~m/SO:/) {
# do nothing, we don't collect these
} elsif ($dbx =~m/TF:/) {
$dbx =~s/TF://g;
$src_id = $self->get_source($self->source_name_tf);
} elsif ($dbx =~m/UniProt\/Swiss-Prot:/) {
$dbx =~s/UniProt\/Swiss-Prot://g;
$src_id = $self->get_source($self->source_name_uniprotsp);
} elsif ($dbx =~m/UniProt\/TrEMBL:/) {
$dbx =~s/UniProt\/TrEMBL://g;
$src_id = $self->get_source($self->source_name_uniprottr);
} elsif ($dbx =~m/bdgpinsituexpr:/) {
$dbx =~s/bdgpinsituexpr://g;
$src_id = $self->get_source($self->source_name_bdgpinsituexpr);
} elsif ($dbx =~m/dedb:/) {
$dbx =~s/dedb://g;
$src_id = $self->get_source($self->source_name_dedb);
} elsif ($dbx =~m/drosdel:/) {
$dbx =~s/drosdel://g;
$src_id = $self->get_source($self->source_name_drosdel);
} elsif ($dbx =~m/flygrid:/) {
$dbx =~s/flygrid://g;
$src_id = $self->get_source($self->source_name_flygrid);
} elsif ($dbx =~m/hybrigenics:/) {
$dbx =~s/hybrigenics://g;
$src_id = $self->get_source($self->source_name_hybrigenics);
} elsif ($dbx =~m/if:/) {
$dbx =~s/if://g;
$src_id = $self->get_source($self->source_name_if);
} elsif ($dbx =~m/orthologs:ensAG:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensAGgene);
} elsif ($dbx =~m/orthologs:ensAM:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensAMgene);
} elsif ($dbx =~m/orthologs:ensCE:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensCEgene);
} elsif ($dbx =~m/orthologs:ensCF:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensCFgene);
} elsif ($dbx =~m/orthologs:ensDM:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensDMgene);
} elsif ($dbx =~m/orthologs:ensDR:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensDRgene);
} elsif ($dbx =~m/orthologs:ensFR:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensFRgene);
} elsif ($dbx =~m/orthologs:ensGG:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensGGgene);
} elsif ($dbx =~m/orthologs:ensHS:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensHSgene);
} elsif ($dbx =~m/orthologs:ensMM:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensMMgene);
} elsif ($dbx =~m/orthologs:ensPT:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensPTgene);
} elsif ($dbx =~m/orthologs:ensRN:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensRNgene);
} elsif ($dbx =~m/orthologs:ensTN:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_ensTNgene);
} elsif ($dbx =~m/orthologs:modCB:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_modCBgene);
} elsif ($dbx =~m/orthologs:modCE:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_modCEgene);
} elsif ($dbx =~m/orthologs:modDD:/) {
$dbx =~s/orthologs://g;
$src_id = $self->get_source($self->source_name_prefix_modDDgene);
} else {
warning("Dbxref type not recognised : $dbx");
}
if ($src_id){ # only add xref entry for FBgn FBtr...
my $xref ;
$xref->{ACCESSION} = $dbx ;
$xref->{LABEL} = $dbx;
$xref->{SOURCE_ID} = $src_id;
$xref->{SPECIES_ID} = $self->species_id();
#$xref->{SYNONYMS} = $self->get_synonyms($unique_id);
$self->add_xref($xref);
if ($type){
my $direct_xref;
$direct_xref = $xref ;
$direct_xref->{ENSEMBL_STABLE_ID} = $unique_id;
$direct_xref->{ENSEMBL_TYPE} = $type;
#$direct_xref->{LINKAGE_XREF}=undef;
$self->add_direct_xref($direct_xref) if $type ;
}
}
}
return;
}
}
sub set_flybase_synonyms {
my ($self,$item,$unique_id) = @_;
my $syn1 = $self->gff_synonym;
if ($item=~/$syn1/){
my $s1 = get_fields($item,$syn1);
my @syns;
push @syns, @{$s1} if $s1;
$self->add_synonym($unique_id,\@syns);
return \@syns;
}
return undef;
}
sub make_id_xref{
my ($self,$unique_id,$type) = @_;
my $xref=undef;
# make an xref
$xref->{ACCESSION} = $unique_id;
$xref->{LABEL} = $unique_id;
$xref->{SPECIES_ID} = $self->species_id();
$xref->{SYNONYMS} = $self->get_synonyms($unique_id);
my $type_s = $type;
if ($type eq "gene") {
$type_s = $self->source_name_fbgn();
} elsif ($type eq "transcript") {
$type_s = $self->source_name_fbtr();
} elsif ($type eq "translation") {
$type_s = $self->source_name_fbpp();
} else {
throw ("Type $type not recognised");
}
$xref->{SOURCE_ID} = $self->get_source($type_s);
$self->add_xref($xref);
# only allow Name on genes. This is a fix for Biomart really.
if (defined($xref) and $type){
my $direct_xref;
$direct_xref = $xref ;
$direct_xref->{ENSEMBL_STABLE_ID} = $unique_id;
$direct_xref->{ENSEMBL_TYPE} = $type;
$direct_xref->{LINKAGE_TYPE}='bla';
$direct_xref->{SYNONYMS} = $self->get_synonyms($unique_id);
$self->add_direct_xref($direct_xref);
}
return;
}
sub make_name_xref{
my ($self,$item,$unique_id,$type) = @_;
my $xref=undef;
my $target = $self->gff_name ;
if($item=~m/$target/){ ##Name=
#print "having $$gff_gene_name[0]\n" ;
# remove the Name= bit and split the names on a ','
my $gff_gene_name = get_fields ( $item, $target ) ;
throw("there is more than one id for item $item\n") if $$gff_gene_name[1];
$xref->{ACCESSION} = $$gff_gene_name[0];
$xref->{LABEL} = $$gff_gene_name[0];
$xref->{SPECIES_ID} = $self->species_id();
$xref->{SYNONYMS} = $self->get_synonyms($unique_id);
my $type_s = $type;
if($type eq "translation"){
$type_s = $type."s";
}
$xref->{SOURCE_ID} = $self->get_source($self->source_name_name_prefix().$type_s);
$self->add_xref($xref);
}
# only allow Name on genes. This is a fix for Biomart really.
if (defined($xref) and $type){
my $direct_xref;
$direct_xref = $xref ;
$direct_xref->{ENSEMBL_STABLE_ID} = $unique_id;
$direct_xref->{ENSEMBL_TYPE} = $type;
$direct_xref->{LINKAGE_TYPE}='bla';
$direct_xref->{SYNONYMS} = $self->get_synonyms($unique_id);
$self->add_direct_xref($direct_xref);
}
return;
}
sub get_fields {
my ($item,$target) =@_;
my @entrys;
if ($item =~m/$target/){
$item =~s/$target//g;
# check if there is more than one synonym / dbxref ...
if ($item =~/,/){
@entrys = split (/\,/,$item);
} else{
push @entrys, $item;
}
return \@entrys;
# if the item does not hold information of specific field
}else{
return undef;
}
}
sub source_name_name{
my $self = shift;
$self->{_source_name_name} = shift if @_ ;
return $self->{_source_name_name};
}
sub source_name_name_prefix{
my $self = shift;
$self->{_source_name_name_prefix} = shift if @_ ;
return $self->{_source_name_name_prefix};
}
sub source_name_synonym{
my $self = shift;
$self->{_source_name_synonym} = shift if @_ ;
return $self->{_source_name_synonym};
}
sub source_name_fbgn{
my $self = shift;
$self->{_source_name_gene} = shift if @_ ;
return $self->{_source_name_gene};
}
sub source_name_gadfly_gene{
my $self = shift;
$self->{_source_name_gadfly_gene} = shift if @_ ;
return $self->{_source_name_gadfly_gene};
}
sub source_name_gadfly_transcript{
my $self = shift;
$self->{_source_name_gadfly_transcript} = shift if @_ ;
return $self->{_source_name_gadfly_transcript};
}
sub source_name_gadfly_translation{
my $self = shift;
$self->{_source_name_gadfly_translation} = shift if @_ ;
return $self->{_source_name_gadfly_translation};
}
sub source_name_fbtr{
my $self = shift;
$self->{_source_name_transcript} = shift if @_ ;
return $self->{_source_name_transcript} ;
}
sub source_name_fbpp{
my $self = shift;
$self->{_source_name_fbpp} = shift if @_ ;
return $self->{_source_name_fbpp};
}
sub source_name_fban{
my $self = shift;
$self->{_sn_fban} = shift if @_ ;
return $self->{_sn_fban};
}
sub source_name_affymetrix {
my $self = shift;
$self->{_sn_affymetrix} = shift if @_ ;
return $self->{_sn_affymetrix};
}
sub source_name_dgrc1 {
my $self = shift;
$self->{_sn_dgrc1} = shift if @_ ;
return $self->{_sn_dgrc1};
}
sub source_name_dgrc2 {
my $self = shift;
$self->{_sn_dgrc2} = shift if @_ ;
return $self->{_sn_dgrc2};
}
sub source_name_drsc {
my $self = shift;
$self->{_sn_drsc} = shift if @_ ;
return $self->{_sn_drsc};
}
sub source_name_epd {
my $self = shift;
$self->{_sn_epd} = shift if @_ ;
return $self->{_sn_epd};
}
sub source_name_flyreg {
my $self = shift;
$self->{_sn_flyreg} = shift if @_ ;
return $self->{_sn_flyreg};
}
sub source_name_gb {
my $self = shift;
$self->{_sn_gb} = shift if @_ ;
return $self->{_sn_gb};
}
sub source_name_gbprotein {
my $self = shift;
$self->{_sn_gbprotein} = shift if @_ ;
return $self->{_sn_gbprotein};
}
sub source_name_gcr {
my $self = shift;
$self->{_sn_gcr} = shift if @_ ;
return $self->{_sn_gcr};
}
sub source_name_gi {
my $self = shift;
$self->{_sn_gi} = shift if @_ ;
return $self->{_sn_gi};
}
sub source_name_go {
my $self = shift;
$self->{_sn_go} = shift if @_ ;
return $self->{_sn_go};
}
sub source_name_genomeRNAi {
my $self = shift;
$self->{_sn_genomeRNAi} = shift if @_ ;
return $self->{_sn_genomeRNAi};
}
sub source_name_interpro {
my $self = shift;
$self->{_sn_interpro} = shift if @_ ;
return $self->{_sn_interpro};
}
sub source_name_merops {
my $self = shift;
$self->{_sn_merops} = shift if @_ ;
return $self->{_sn_merops};
}
sub source_name_miRBase {
my $self = shift;
$self->{_sn_miRBase} = shift if @_ ;
return $self->{_sn_miRBase};
}
sub source_name_mitodrome {
my $self = shift;
$self->{_sn_mitodrome} = shift if @_ ;
return $self->{_sn_mitodrome};
}
sub source_name_nrl3d {
my $self = shift;
$self->{_sn_nrl3d} = shift if @_ ;
return $self->{_sn_nrl3d};
}
sub source_name_pdb {
my $self = shift;
$self->{_sn_pdb} = shift if @_ ;
return $self->{_sn_pdb};
}
sub source_name_rfam {
my $self = shift;
$self->{_sn_rfam} = shift if @_ ;
return $self->{_sn_rfam};
}
sub source_name_tf {
my $self = shift;
$self->{_sn_tf} = shift if @_ ;
return $self->{_sn_tf};
}
sub source_name_uniprotsp {
my $self = shift;
$self->{_sn_uniprotsp} = shift if @_ ;
return $self->{_sn_uniprotsp};
}
sub source_name_uniprottr {
my $self = shift;
$self->{_sn_uniprottr} = shift if @_ ;
return $self->{_sn_uniprottr};
}
sub source_name_bdgpinsituexpr {
my $self = shift;
$self->{_sn_bdgpinsituexpr} = shift if @_ ;
return $self->{_sn_bdgpinsituexpr};
}
sub source_name_dedb {
my $self = shift;
$self->{_sn_dedb} = shift if @_ ;
return $self->{_sn_dedb};
}
sub source_name_drosdel {
my $self = shift;
$self->{_sn_drosdel} = shift if @_ ;
return $self->{_sn_drosdel};
}
sub source_name_flygrid {
my $self = shift;
$self->{_sn_flygrid} = shift if @_ ;
return $self->{_sn_flygrid};
}
sub source_name_hybrigenics {
my $self = shift;
$self->{_sn_hybrigenics} = shift if @_ ;
return $self->{_sn_hybrigenics};
}
sub source_name_if {
my $self = shift;
$self->{_sn_if} = shift if @_ ;
return $self->{_sn_if};
}
sub source_name_prefix_ensAGgene {
my $self = shift;
$self->{_sn_prefix_ensAG} = shift if @_ ;
return $self->{_sn_prefix_ensAG};
}
sub source_name_prefix_ensAMgene {
my $self = shift;
$self->{_sn_prefix_ensAM} = shift if @_ ;
return $self->{_sn_prefix_ensAM};
}
sub source_name_prefix_ensCEgene {
my $self = shift;
$self->{_sn_prefix_ensCE} = shift if @_ ;
return $self->{_sn_prefix_ensCE};
}
sub source_name_prefix_ensCFgene {
my $self = shift;
$self->{_sn_prefix_ensCF} = shift if @_ ;
return $self->{_sn_prefix_ensCF};
}
sub source_name_prefix_ensDMgene {
my $self = shift;
$self->{_sn_prefix_ensDM} = shift if @_ ;
return $self->{_sn_prefix_ensDM};
}
sub source_name_prefix_ensDRgene {
my $self = shift;
$self->{_sn_prefix_ensDR} = shift if @_ ;
return $self->{_sn_prefix_ensDR};
}
sub source_name_prefix_ensFRgene {
my $self = shift;
$self->{_sn_prefix_ensFR} = shift if @_ ;
return $self->{_sn_prefix_ensFR};
}
sub source_name_prefix_ensGGgene {
my $self = shift;
$self->{_sn_prefix_ensGG} = shift if @_ ;
return $self->{_sn_prefix_ensGG};
}
sub source_name_prefix_ensHSgene {
my $self = shift;
$self->{_sn_prefix_ensHS} = shift if @_ ;
return $self->{_sn_prefix_ensHS};
}
sub source_name_prefix_ensMMgene {
my $self = shift;
$self->{_sn_prefix_ensMM} = shift if @_ ;
return $self->{_sn_prefix_ensMM};
}
sub source_name_prefix_ensPTgene {
my $self = shift;
$self->{_sn_prefix_ensPT} = shift if @_ ;
return $self->{_sn_prefix_ensPT};
}
sub source_name_prefix_ensRNgene {
my $self = shift;
$self->{_sn_ensRN} = shift if @_ ;
return $self->{_sn_ensRN};
}
sub source_name_prefix_ensTNgene {
my $self = shift;
$self->{_sn_ensTN} = shift if @_ ;
return $self->{_sn_ensTN};
}
sub source_name_prefix_modCBgene {
my $self = shift;
$self->{_sn_modCB} = shift if @_ ;
return $self->{_sn_modCB};
}
sub source_name_prefix_modCEgene {
my $self = shift;
$self->{_sn_modCE} = shift if @_ ;
return $self->{_sn_modCE};
}
sub source_name_prefix_modDDgene {
my $self = shift;
$self->{_sn_modDD} = shift if @_ ;
return $self->{_sn_modDD};
}
sub gff_name{
my $self = shift;
$self->{_gff_name} = shift if @_ ;
return $self->{_gff_name};
}
sub gff_dbxref{
my $self = shift;
$self->{_gff_dbxref} = shift if @_ ;
return $self->{_gff_dbxref};
}
sub gff_synonym{
my $self = shift;
$self->{_gff_synonym} = shift if @_ ;
return $self->{_gff_synonym};
}
sub gff_ontology{
my $self = shift;
$self->{_gff_ontology} = shift if @_ ;
return $self->{_gff_ontology};
}
sub species_id {
my $self = shift;
$self->{_species_id} = shift if @_ ;
return $self->{_species_id};
}
sub xrefs{
my $self = shift;
$self->{_xrefs} = shift if @_ ;
return $self->{_xrefs};
}
sub add_xref{
my ($self,$add_xref) = @_;
push @{$self->xrefs() }, $add_xref;
return;
}
sub direct_xrefs{
my $self = shift;
$self->{_direct_xrefs} = shift if @_ ;
return $self->{_direct_xrefs};
}
sub add_direct_xref{
my ($self,$dr) = @_;
push @{$self->direct_xrefs() }, $dr;
return;
}
sub line_contains_object_to_process{
my ($self,$type_of_line) = @_; # shoud be mRNA, gene, pseudogene, CDS,...
for my $check_types ( @{$self->gff_object_types}) {
if ($check_types =~/^$type_of_line$/){
return 1;
}
}
return 0;
}
=pod
=head2 gff_object_types
Title : gff_object_types
Usage : $obj->gff_object_types(array-ref)
Function : contains gff-type-identifiers of gff-objects which have to be processed
Arguments : array-ref
Return-Val : array-ref
=cut
sub gff_object_types{
my $self = shift;
$self->{_gff_object_types} = shift if @_ ;
return $self->{_gff_object_types};
}
=pod
=head2 external_source_db_name
Title : external_source_db_name
Usage : $obj->external_source_db_name(external db name)
Function : returns name of hardcoded external source db name
Arguments : external db name
Return-Val : string
=cut
sub external_source_db_name{
my $self = shift;
$self->{_external_source_db_name} = shift if @_ ;
return $self->{_external_source_db_name};
}
# --------------------------------------------------------------------------------
# Get species (id and name) from file
# For UniProt files the filename is the taxonomy ID
sub get_species {
my ($file) = @_;
my ($taxonomy_id, $extension) = split(/\./, basename($file));
my $sth = XrefParser::BaseParser->dbi()->prepare("SELECT species_id,name FROM species WHERE taxonomy_id=?");
$sth->execute($taxonomy_id);
my ($species_id, $species_name);
while(my @row = $sth->fetchrow_array()) {
$species_id = $row[0];
$species_name = $row[1];
}
$sth->finish;
if (defined $species_name) {
print "Taxonomy ID " . $taxonomy_id . " corresponds to species ID " . $species_id . " name " . $species_name . "\n" if($verbose);
} else {
throw("Cannot find species corresponding to taxonomy ID " . $species_id . " - check species table\n");
}
return ($species_id, $species_name);
}
sub add_synonym{
my ($self,$unique_id,$synref) = @_;
#print "adding synonym for -$unique_id-:".join(" " , @$synref)."\n" ; ;
${$self->synonyms}{$unique_id}=$synref if($synref);
return;
}
sub get_synonyms{
my ($self,$unique_id) = @_;
return ${$self->synonyms}{$unique_id};
}
sub synonyms{
my $self = shift;
$self->{_synonyms} = shift if @_ ;
return $self->{_synonyms};
}
sub gene_types{
my $self = shift;
$self->{_gene_types} = shift if @_ ;
return $self->{_gene_types};
}
sub transcript_types{
my $self = shift;
$self->{_trans_types} = shift if @_ ;
return $self->{_trans_types};
}
sub translation_types{
my $self = shift;
$self->{_tl_types} = shift if @_ ;
return $self->{_tl_types};
}
1;
# Drosophila v5.3 : xrefs
# Gff_file external_db_id db_name
# ==
# Affymetrix 3120 AFFY_DrosGenome1
# DGRC-1 830 DGRC-1
# DGRC-2 831 DGRC-2
# DRSC 840 DRSC
# EPD 10100 EPD
# FlyBase 800 flybase_gene_id
# FlyBase_Annotation_IDs 804 flybase_annotation_id
# FlyReg 850 FlyReg
# GB 700 EMBL
# GB_protein 1700 protein_id
# GCR 10200 GPCR
# GI 10900 GI
# GO 1000 GO
# GenomeRNAi 860 GenomeRNAi
# INTERPRO 1200 Interpro
# MEROPS 10300 MEROPS
# MIR 10400 miRBase
# MITODROME 870 MitoDrome
# NRL_3D 1600 PDB
# PDB 1600 PDB
# Rfam 4200 RFAM
# TF 10500 TransFac
# UniProt/Swiss-Prot 2200 Uniprot/SWISSPROT
# UniProt/TrEMBL 2000 Uniprot/SPTREMBL
# bdgpinsituexpr 880 BDGP_insitu_expr
# dedb 890 DEDb
# drosdel 881 DrosDel
# flygrid 882 FlyGrid
# hybrigenics 883 hybrigenics
# if 884 InteractiveFly
# ensAG 6600 Ens_Ag_gene # Anopheles gambiae
# ensAM 6630 Ens_Am_gene # apis mellifera?
# ensCE 6660 Ens_Ce_gene # C Elegans
# ensCF 5700 Ens_Cf_gene # Canis familiaris
# ensDM 6690 Ens_Dm_gene #
# ensDR 5800 Ens_Dr_gene # Danio rerio
# ensFR 6720 Ens_Fr_gene # Takifugu rubripes
# ensGG 6400 Ens_Gg_gene # Gallus gallus
# ensHS 2700 Ens_Hs_gene # Homo sapiens
# ensMM 5000 Ens_Mm_gene # mus musculus
# ensPT 6750 Ens_Pt_gene # Pan troglodytes
# ensRN 6200 Ens_Rn_gene # Rattus norvegicus
# ensTN 6810 Ens_Tn_gene # Tetraodon nigroviridis
# modCB 10600 modCB # InParanoid Model organism database, Caenorhabditis briggsae
# modCE 10700 modCE # Caenorhabditis elegans
# modDD 10800 modDD # Dictyostelium discoideum
]]>