Add new species and subroutines to use for common mart and ensembl downloads

svn path=/; revision=659

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 5dcb80d63f1770a3ec5129b9df0a67f205885e5c..fd38e361dbd1b37c1b7cdaf8acbc28c50a5e6b93 100755 (executable)
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -16,6 +16,8 @@ sub find_species {
                $species = "Aegilops_tauschii";
        }elsif ($temp =~ /Amborella\_trichopoda/) {
                $species = "Amborella_trichopoda";
+       }elsif ($temp =~ /Arabidopsis\_halleri/) {
+               $species = "Arabidopsis_halleri";
        }elsif ($temp =~ /Arabidopsis\_lyrata/) {
                $species = "Arabidopsis_lyrata";
        }elsif ($temp =~ /Arabidopsis\_thaliana/) {
@@ -24,6 +26,10 @@ sub find_species {
                $species = "Arachis_duranensis";
        }elsif ($temp =~ /Arachis\_ipaensis/) {
                $species = "Arachis_ipaensis";
+       }elsif ($temp =~ /Asparagus\_officinalis/) {
+               $species = "Asparagus_officinalis";
+       }elsif ($temp =~ /Azolla/) {
+               $species = "Azolla_filiculoides";
        }elsif ($temp =~ /Batrachochytrium/) {
                $species = "Batrachochytrium_dendrobatidis";
        }elsif ($temp =~ /Brachypodium\_distachyon/) {
@@ -42,7 +48,9 @@ sub find_species {
                $species = "Caenorhabditis_elegans";
        }elsif ($temp =~ /Cajanus\_cajan/) {
                $species = "Cajanus_cajan";
-       }elsif ($temp =~ /Cannabis/) {
+       }elsif ($temp =~ /Cannabis\_sativa\.CRBRx/) {
+               $species = "Cannabis_sativa.CRBRx";
+       }elsif ($temp =~ /Cannabis\_sativa\.Purple/) {
                $species = "Cannabis_sativa.Purple.Kush";
        }elsif ($temp =~ /Capsella/) {
                $species = "Capsella_rubella";
@@ -66,6 +74,8 @@ sub find_species {
                $species = "Cavia_porcellus";
        }elsif ($temp =~ /Chlamy/) {
                $species = "Chlamydomonas_reinhardtii";
+       }elsif ($temp =~ /Chondrus/) {
+               $species = "Chondrus_crispus";
        }elsif ($temp =~ /Cicer\_arietinum/) {
                $species = "Cicer_arietinum";
        }elsif ($temp =~ /Citrullus\_lanatus/) {
@@ -76,6 +86,10 @@ sub find_species {
                $species = "Citrus_sinensis";
        }elsif ($temp =~ /Coffea\_canephora/) {;
                $species = "Coffea_canephora";
+       }elsif ($temp =~ /Corchorus\_capsularis/) {
+               $species = "Corchorus_capsularis";
+       }elsif ($temp =~ /Corchorus\_olitorius/) {
+               $species = "Corchorus_olitorius";
        }elsif ($temp =~ /Cucumis\_sativus/) {
                $species = "Cucumis_sativus";
        }elsif ($temp =~ /Danio/) {
@@ -86,6 +100,8 @@ sub find_species {
                $species = "Dipodomys_ordii";
        }elsif ($temp =~ /Drosophila/) {
                $species = "Drosophila_melanogaster";
+       }elsif ($temp =~ /Durio/) {
+               $species = "Durio_zibethinus";
        }elsif ($temp =~ /Echinops_telfairi/) {
                $species = "Echinops_telfairi";
        }elsif ($temp =~ /Ectocarpus/) {
@@ -100,6 +116,8 @@ sub find_species {
                $species = "Epichloe\_festucae";
        }elsif ($temp =~ /Erinaceus_europaeus/) {
                $species = "Erinaceus_europaeus";
+       }elsif ($temp =~ /Erythranthe/) {
+               $species = "Erythranthe_guttata";
        }elsif ($temp =~ /Escherichia\_coli/) {
                $species = "Escherichia_coli";
        }elsif ($temp =~ /Eucalyptus\_grandis/) {
@@ -126,6 +144,10 @@ sub find_species {
                $species = "Homo_sapiens";
        }elsif ($temp =~ /Hordeum\_vulgare/) {
                $species = "Hordeum_vulgare";
+       }elsif ($temp =~ /Humulus\_lupulus\.haplotig/) {
+               $species = "Humulus_lupulus.haplotig";
+       }elsif ($temp =~ /Humulus\_lupulus\.primary/) {
+               $species = "Humulus_lupulus.primary";
        }elsif ($temp =~ /Ictidomys_tridecemlineatus/) {
                $species = "Ictidomys_tridecemlineatus";
        }elsif ($temp =~ /Jatropha/) {
@@ -148,6 +170,8 @@ sub find_species {
                $species = "Manihot_esculenta";
        }elsif ($temp =~ /Medicago/) {
                $species = "Medicago_truncatula";
+       }elsif ($temp =~ /Mentha\_longifolia/) {
+               $species = "Mentha_longifolia";
        }elsif ($temp =~ /Mimulus/) {
                $species = "Mimulus_guttatus";
        }elsif ($temp =~ /Mus\_musculus/) {
@@ -162,8 +186,12 @@ sub find_species {
                $species = "Nelumbo_nucifera";
        }elsif ($temp =~ /Neurospora/) {
                $species = "Neurospora_crassa";
+       }elsif ($temp =~ /Nicotiana/) {
+               $species = "Nicotiana_attenuata";
        }elsif ($temp =~ /Nostoc/) {
-               $species = "Nostoc_punctiforme";
+               $species = "Nostoc_punctiforme.pcc.73102";
+       }elsif ($temp =~ /Ocimum/) {
+               $species = "Ocimum_tenuiflorum";
        }elsif ($temp =~ /Oncorhynchus\_mykiss/) {
                $species = "Oncorhynchus\_mykiss";
        }elsif ($temp =~ /Ornithorhynchus_anatinus/) {
@@ -178,8 +206,8 @@ sub find_species {
                $species = "Oryza_brachyantha";
        }elsif ($temp =~ /Oryza\_glaberrima/) {
                $species = "Oryza_glaberrima";
-       }elsif ($temp =~ /Oryza\_glumaepatula/) {
-               $species = "Oryza_glumaepatula";
+       }elsif ($temp =~ /Oryza\_glumipatula/) {
+               $species = "Oryza_glumipatula";
        }elsif ($temp =~ /Oryza\_granulata/) {
                $species = "Oryza_granulata";
        }elsif ($temp =~ /Oryza\_kasalath/) {
@@ -198,10 +226,12 @@ sub find_species {
                $species = "Oryza_punctata";
        }elsif ($temp =~ /Oryza\_rufipogon/) {
                $species = "Oryza_rufipogon";
-       }elsif ($temp =~ /Oryza\_sativa.indica\.gramene/) {
-               $species = "Oryza_sativa.indica.gramene";
-       }elsif ($temp =~ /Oryza\_sativa.indica\.iplant/) {
-               $species = "Oryza_sativa.indica.iplant";
+       }elsif ($temp =~ /Oryza\_sativa\.AUS\.N22/) {
+               $species = "Oryza_sativa.AUS.N22";
+       }elsif ($temp =~ /Oryza\_sativa.indica\_/) {
+               $species = "Oryza_sativa.indica";
+       }elsif ($temp =~ /Oryza\_sativa.indica\.9311/) {
+               $species = "Oryza_sativa.indica.9311.OGE";
        }elsif ($temp =~ /Oryza\_sativa.indica.IR29/) {
                $species = "Oryza_sativa.indica.IR29";
        }elsif ($temp =~ /Oryza\_sativa.indica.pokkali/) {
@@ -210,6 +240,8 @@ sub find_species {
                $species = "Oryza_sativa.japonica.IRGSP";
        }elsif ($temp =~ /Oryza\_sativa.japonica.MSU/) {
                $species = "Oryza_sativa.japonica.MSU";
+       }elsif ($temp =~ /Oryza\_sativa.japonica.OGE/) {
+               $species = "Oryza_sativa.japonica.OGE";
        }elsif ($temp =~ /Oryza\_sativa.japonica\_iplant/) {
                $species = "Oryza_sativa.japonica.iplant";
        }elsif ($temp =~ /Oryzias\_latipes/) {
@@ -236,8 +268,8 @@ sub find_species {
                $species = "Pinus_taeda";
        }elsif ($temp =~ /Populus\_trichocarpa\.ver2/) {
                $species = "Populus_trichocarpa.ver2";
-       }elsif ($temp =~ /Populus\_trichocarpa\.ver3/) {
-               $species = "Populus_trichocarpa.ver3";
+       }elsif ($temp =~ /Populus\_trichocarpa/) {
+               $species = "Populus_trichocarpa";
        }elsif ($temp =~ /Procavia_capensis/) {
                $species = "Procavia_capensis";
        }elsif ($temp =~ /Prunus/) {
@@ -252,10 +284,12 @@ sub find_species {
                $species = "Ricinus_communis";
        }elsif ($temp =~ /cerevisiae/) {
                $species = "Saccharomyces_cerevisiae";
-       }elsif ($temp =~ /Salvia_hispancia\.salba/) {
-               $species = "Salvia_hispancia.salba";
+       }elsif ($temp =~ /Salvia_hispanica/) {
+               $species = "Salvia_hispanica";
        }elsif ($temp =~ /Salvia_splendens/) {
                $species = "Salvia_splendens";
+       }elsif ($temp =~ /Salvinia\_cucullata/) {
+               $species = "Salvinia_cucullata";
        }elsif ($temp =~ /pombe/) {
                $species = "Schizosaccharomyces_pombe";
        }elsif ($temp =~ /Selaginella/) {
@@ -271,7 +305,7 @@ sub find_species {
        }elsif ($temp =~ /Sorghum/) {
                $species = "Sorghum_bicolor";
        }elsif ($temp =~ /Synechocystis/) {
-               $species = "Synechocystis_pcc6803";
+               $species = "Synechocystis_sp.pcc.6803";
        }elsif ($temp =~ /Takifugu/) {
                $species = "Takifugu\_rubripes";
        }elsif ($temp =~ /Tarsius_syrichta/) {
@@ -286,6 +320,8 @@ sub find_species {
                $species = "Trichodesmium_erythraeum";
        }elsif ($temp =~ /Triticum\_aestivum/) {
                $species = "Triticum_aestivum";
+       }elsif ($temp =~ /Triticum\_dicoccoides/) {
+               $species = "Triticum_dicoccoides";
        }elsif ($temp =~ /Triticum\_monococcum\.DV92/) {
                $species = "Triticum_monococcum.DV92";
        }elsif ($temp =~ /Triticum\_monococcum\.G3116/) {
@@ -294,10 +330,20 @@ sub find_species {
                $species = "Triticum_turgidum";
        }elsif ($temp =~ /Triticum\_urartu/) {
                $species = "Triticum_urartu";
+       }elsif ($temp =~ /Utricularia/) {
+               $species = "Utricularia_gibba";
+       }elsif ($temp =~ /Vigna/) {
+               $species = "Vigna_radiata";
        }elsif ($temp =~ /Vitis\_vinifera/) {
                $species = "Vitis_vinifera";
        }elsif ($temp =~ /Zea\_mays/) {
                $species = "Zea_mays";
+       }elsif ($temp =~/Zoysia_japonica/) {
+               $species = "Zoysia_japonica.Nagirizaki";
+       }elsif ($temp =~/Zoysia_matrella/) {
+               $species = "Zoysia_matrella.Wakaba";
+       }elsif ($temp =~/Zoysia_pacifica/) {
+               $species = "Zoysia_pacifica.Zanpa";
        }else {
                die "Error: Species can not be found from file name $temp!";
        }
@@ -310,28 +356,35 @@ sub find_gene {
        my $species = $_[1];
        my $gene;
        if ($species eq "Aegilops_tauschii") {
-               my ($gene_id, $type, $location, $info) = split(/\s/, $gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Amborella_trichopoda") {
-               $gene = $gene_header;
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Arabidopsis_halleri") {
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Arabidopsis_lyrata") {
-               my ($name,$gene_id) = split(/\|/, $gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Arabidopsis_thaliana") {
-               my ($gene_id,$isomer) = split(/\|/, $gene_header);
-               $gene = $isomer;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Arachis_duranensis") {
-               my ($gene_id, $desc) = split(/\s/, $gene_header);
-               $gene = $gene_id;
+               my ($gene_info, $desc) = split(/\s/, $gene_header);
+               my ($spec, $random, $meth, $type, $spec2, $id, $transcript_no) = split(/\./, $gene_info);
+               $gene = "$spec2" . "." . "$id" . "." . "$transcipt_no";
+       }elsif ($species eq "Arachis_ipaensis") {
+               my ($gene_info, $desc) = split(/\s/, $gene_header);
+               my ($spec, $random, $meth, $type, $spec2, $id, $transcript_no) = split(/\./, $gene_info);
+               $gene = "$spec2" . "." . "$id" . "." . "$transcipt_no";
        }elsif ($species eq "Arachis_ipaensis") {
                my ($gene_id, $desc) = split(/\s/, $gene_header);
                $gene = $gene_id;
+       }elsif ($species eq "Asparagus_officinalis") {
+               $gene = mart_gene($gene_header);
+       }elsif ($species eq "Azolla_filiculoides") {
+               $gene = $gene_header;
        }elsif ($species eq "Batrachochytrium_dendrobatidis") {
                my ($transcript,$gene_id,$info) = split(/\s\|\s/, $gene_header);
                $gene = $transcript;
        }elsif ($species eq "Brachypodium_distachyon") {
-               my ($gene_id,$isomer) = split(/\|/, $gene_header);
-               $gene = $isomer;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Brachypodium_sylvaticum.Corv") {
                my ($gene_id,$temp,$start,$end) = split(/\|/, $gene_header);
                $gene = $gene_id;
@@ -341,29 +394,28 @@ sub find_gene {
                my ($gene_id,$temp,$start,$end) = split(/\|/, $gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Brassica_oleracea") {
-               my ($protein,$type,$chrom,$gene_id,$transcript) = split(/\s/,$gene_header);
-               $gene = $protein;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Brassica_rapa") {
-               my ($gene_id,$transcript) = split(/\|/, $gene_header);
-               $gene = $transcript; #????
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Caenorhabditis_elegans") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-               $transcript =~ s/transcript\://;
-               $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Cajanus_cajan") {
-               my ($gene_id,$type,$locus,$temp) = split(/\s/, $gene_header);
-               $gene = $gene_id;
+               my ($gene_info, $desc) = split(/\s/, $gene_header);
+               my ($spec, $random, $meth, $type, $spec2, $spec_gene, $transcript_no) = split(/\./, $gene_info);
+               $gene = "$spec2" . "." . "$spec_gene" . "." . "$transcript_no";
        }elsif ($species eq "Cannabis_sativa.Purple.Kush") {
                my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header);
                $gene = $gene_id;
+       }elsif ($species eq "Cannabis_sativa.CRBRx") {
+               my ($isoform, $gene_id, $tempj) = split(/\s/, $gene_header);
+               $gene = $isoform;
        }elsif ($species eq "Capsella_rubella") {
-               my ($gene_id, $transcript) = split(/\|/, $gene_header);
-               $gene = $transcript;
+               $gene = mart_gene($gene_header);
        }elsif ($species eq "Capsicum_annuum") {
-               $gene = $gene_header;
-       }elsif ($species eq "Carica_papaya") {
-               my ($contig,$gene_id) = split(/\|/, $gene_header);
+               my ($gene_id, $temp) = split(/\|/, $gene_header);
                $gene = $gene_id;
+       }elsif ($species eq "Carica_papaya") {
+               $gene = mart_gene($gene_header);
        }elsif ($species eq "Castor_canadensis") {
                my ($gene_info,$type,$gc,$gene_length) = split(/\s/, $gene_header);
                my ($gene_number,$gene_id) = split(/::/, $gene_info);
@@ -390,30 +442,30 @@ sub find_gene {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform;
        }elsif ($species eq "Chlamydomonas_reinhardtii") {
-               my ($locus,$transcript) = split(/\|/,$gene_header);
-               $gene = $transcript; #???
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Chondrus_crispus") {
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Cicer_arietinum") {
-               my ($gi,$number,$ref,$gene_id,$function) = split(/\|/, $gene_header);
-               $gene = $gene_id;
+               $gene = mart_gene($gene_header);
        }elsif ($species eq "Citrullus_lanatus") {
                my ($gene_id, $type, $locus, $method) = split(/\s/, $gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Citrus_clementina") {
-               my ($transcript_id,$gene_id) = split(/\|/,$gene_header);
-               $gene = $gene_id;
+               $gene = mart_gene($gene_header);
        }elsif ($species eq "Citrus_sinensis") {
-               my ($transcript_id,$gene_id) = split(/\|/,$gene_header);
-               $gene = $gene_id;
+               $gene = mart_gene($gene_header);
        }elsif ($species eq "Coffea_canephora") {
                my ($gene_id, $function) = split(/\s/,$gene_header);
                $gene = $gene_id;
+       }elsif ($species eq "Corchorus_capsularis") {
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Corchorus_olitorius") {
+               my ($type, $gene_id, $gene_id_suffix, $function) = split(/[\|\s]+/, $gene_header);
+               $gene = $gene_id;
        }elsif ($species eq "Cucumis_sativus") {
-               my ($gene_id,$isomer) = split(/\|/,$gene_header);
-               $gene = $isomer;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Danio_rerio") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-               $transcript =~ s/transcript\://;
-               $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Dasypus_novemcinctus") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform;
@@ -421,9 +473,10 @@ sub find_gene {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform;
        }elsif ($species eq "Drosophila_melanogaster") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-               $transcript =~ s/transcript\://;
-               $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Durio_zibethinus") {
+               my ($gene_id, $type, $idk, $idk2, $quality) = split(/\s/, $gene_header);
+               $gene = $gene_id;
        }elsif ($species eq "Echinops_telfairi") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform;
@@ -442,15 +495,14 @@ sub find_gene {
        }elsif ($species eq "Erinaceus_europaeus") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform;
+       }elsif ($species eq "Erythranthe_guttata") {
+               $gene = mart_gene($gene_header);
        }elsif ($species eq "Escherichia_coli") {
                $gene = $gene_header; #???
        }elsif ($species eq "Eucalyptus_grandis") {
-               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
-               $gene = $transcript_id;
+               $gene = mart_gene($gene_header);
        }elsif ($species eq "Fragaria_vesca") {
-               my ($gene_id, $mrna_id) = split(/\|/, $gene_header);
-               $gene_id =~ s/\-v1\.0\-hybrid//;
-               $gene = $gene_id;
+               $gene = mart_gene($gene_header);
        }elsif ($species eq "Fusarium_graminearum") {
                my ($transcript, $gene_id, $info) = split(/\s\|\s/, $gene_header);
                $gene = $transcript;
@@ -469,20 +521,19 @@ sub find_gene {
                $transcript =~ s/transcript\://;
                $gene = $transcript;
        }elsif ($species eq "Glycine_max") {
-               my ($locus_id,$isomer) = split(/\|/,$gene_header);
-               $gene = $isomer;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Gossypium_raimondii") {
-               my ($locus_id,$isomer) = split(/\|/,$gene_header);
-               $gene = $isomer;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Gossypium_hirsutum") {
                $gene = $gene_header;
        }elsif ($species eq "Homo_sapiens") {
-               my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
-               $gene = $isoform
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Hordeum_vulgare") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-               $transcript =~ s/transcript\://;
-               $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Humulus_lupulus.haplotig") {
+               $gene = $gene_header;
+       }elsif ($species eq "Humulus_lupulus.primary") {
+               $gene = $gene_header;
        }elsif ($species eq "Ictidomys_tridecemlineatus") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform
@@ -496,11 +547,9 @@ sub find_gene {
                my ($source,$spec,$gene_id,$scaffold) = split(/\|/, $gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Leersia_perrieri") {
-               my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Linum_usitatissimum") {
-               my ($transcript,$gene_id) = split(/\|/, $gene_header);
-               $gene = $gene_id;
+               $gene = mart_gene($gene_header);
        }elsif ($species eq "Macropus_eugenii") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform
@@ -508,23 +557,20 @@ sub find_gene {
                my ($transcript,$gene_id,$temp) = split(/\s\|\s/, $gene_header);
                $gene = $transcript;
        }elsif ($species eq "Malus_domestica" ) {
-               my ($gene_id1,$gene_id2) = split(/\|/, $gene_header);
-               $gene = $gene_id2;
+               $gene = mart_gene($gene_header);
        }elsif ($species eq "Manihot_esculenta") {
-               my ($transcript,$gene_id) = split(/\|/, $gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Medicago_truncatula") {
-               my ($gene_id,$transcript) = split(/\|/, $gene_header);
-               $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Mentha_longifolia") {
+               $gene = $gene_header;
        }elsif ($species eq "Mimulus_guttatus") {
                my ($gene_id,$transcript) = split(/\|/, $gene_header);
                $gene = $transcript;
        }elsif ($species eq "Mus_musculus") {
-               my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
-               $gene = $isoform
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Musa_acuminata") {
-               my ($protein,$type,$chrom,$gene_id,$transcript) = split(/\s/,$gene_header);
-               $gene = $protein;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Mustela_putorius.furo") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform;
@@ -538,9 +584,13 @@ sub find_gene {
        }elsif ($species eq "Neurospora_crassa") {
                my ($transcript,$gene_id,$temp) = split(/\s\|\s/,$gene_header);
                $gene = $transcript;
-       }elsif ($species eq "Nostoc_punctiforme") {
-               my ($temp,$transcript,$source,$gene_id,$func) = split(/\|/, $gene_header);
-               $gene = $transcript;
+       }elsif ($species eq "Nicotiana_attenuata") {
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Nostoc_punctiforme.pcc.73102") {
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Ocimum_tenuiflorum") {
+               my ($gene_id, $number) = split(/\|/, $gene_header);
+               $gene = $gene_id;
        }elsif ($species eq "Oncorhynchus_mykiss") {
                my ($gi, $number, $type, $gene_id, $function) = split(/\|/,$gene_header);
                $gene = $number;
@@ -554,50 +604,40 @@ sub find_gene {
                my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Oryza_barthii") {
-               my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Oryza_brachyantha") {
-               my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Oryza_glaberrima") {
-               my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
-               $gene = $gene_id;
-       }elsif ($species eq "Oryza_glumaepatula") {
-               my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Oryza_glumipatula") {
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Oryza_granulata") {
                my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Oryza_kasalath") {
                $gene = $gene_header;
        }elsif ($species eq "Oryza_longistaminata") {
-               my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Oryza_meridionalis") {
-               my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Oryza_minuta") {
                my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Oryza_nivara") {
-               my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Oryza_officinalis") {
                my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Oryza_punctata") {
-               my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Oryza_rufipogon") {
-               my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
-               $gene = $gene_id;
-       }elsif ($species eq "Oryza_sativa.indica.iplant") {
-               my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
-               $gene = $gene_id;
-       }elsif ($species eq "Oryza_sativa.indica.gramene") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Oryza_sativa.indica") {
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Oryza_sativa.AUS.N22") {
+               $gene = $gene_header;
+       }elsif ($species eq "Oryza_sativa.indica.9311.OGE") {
+               $gene = $gene_header;
     }elsif ($species eq "Oryza_sativa.indica.IR29") {
        my ($gene_id,$position, $start, $length) = split(/\|/, $gene_header);
        $gene = $gene_id;
@@ -608,12 +648,12 @@ sub find_gene {
                my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Oryza_sativa.japonica.IRGSP") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Oryza_sativa.japonica.MSU") {
-               my ($gene_id,$transcript) = split(/\|/,$gene_header);
-                $gene = $transcript;
+               my ($gene_id,$function) = split(/\s/,$gene_header);
+        $gene = $gene_id;
+    }elsif ($species eq "Oryza_sativa.japonica.OGE") {
+               $gene = $gene_header;
        }elsif ($species eq "Oryzias_latipes") {
                my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
             $transcript =~ s/transcript\://;
@@ -625,8 +665,7 @@ sub find_gene {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform;
     }elsif ($species eq "Phaseolus_vulgaris") {
-       my ($gene_id, $transcript) = split(/\|/,$gene_header);
-       $gene = $transcript;
+       $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Pediculus_humanus") {
                my ($gene_pa,$func,$func2,$unknown,$gene_id) = split(/[\|\s+]/, $gene_header);
                $gene = $gene_pa;
@@ -637,8 +676,7 @@ sub find_gene {
                my ($gene_id, $gene_model, $location, $dot, $strand, $dot2, $info) = split (/\|/, $gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Physcomitrella_patens") {
-               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
-               $gene = $transcript_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Phytophthora_infestans") {
                my ($transcript, $gene_id, $function) = split(/\s\|\s/,$gene_header);
                $gene = $transcript;
@@ -651,60 +689,48 @@ sub find_gene {
        }elsif ($species eq "Populus_trichocarpa.ver2") {
                my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
                $gene = $transcript_id;
-       }elsif ($species eq "Populus_trichocarpa.ver3") {
-               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
-               $gene = $transcript_id;
+       }elsif ($species eq "Populus_trichocarpa") {
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Procavia_capensis") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform;
        }elsif ($species eq "Prunus_persica") {
-               my ($transcript,$gene_id) = split(/\|/,$gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Pteropus_vampyrus") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform;
        }elsif ($species eq "Rattus_norvegicus") {
-               my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
-               $gene = $isoform;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Rhizopus_oryzae") {
                my ($jgi,$temp,$num,$gene_id) = split(/\|/, $gene_header);
                $gene = $num;
        }elsif ($species eq "Ricinus_communis") {
-               my ($transcript,$model) = split(/\|/, $gene_header);
-               $gene = $transcript;
+               $gene = mart_gene($gene_header);
        }elsif ($species eq "Saccharomyces_cerevisiae") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene = $transcript
-    }elsif ($species eq "Salvia_hispancia.salba") {
+               $gene = ensembl_gene($gene_header);
+    }elsif ($species eq "Salvia_hispanica") {
        $gene = $gene_header;
     }elsif ($species eq "Salvia_splendens") {
        $gene = $gene_header;
+    }elsif ($species eq "Salvinia_cucullata") {
+       $gene = $gene_header;
        }elsif ($species eq "Schizosaccharomyces_pombe") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene = $transcript
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Selaginella_moellendorffii") {
-               my ($locus_id,$prot_id) = split(/\|/,$gene_header);
-               $gene = $locus_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Setaria_italica") {
-               my ($locus_id,$prot_id) = split(/\|/,$gene_header);
-               $gene = $prot_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Solanum_lycopersicum") {
-               my ($locus_id,$prot_id) = split(/\|/,$gene_header);
-               $gene = $locus_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Solanum_tuberosum") {
-               my ($locus_id,$prot_id) = split(/\|/,$gene_header);
-               $gene = $prot_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Sorex_araneus") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform;
        }elsif ($species eq "Sorghum_bicolor") {
-               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
-               $gene = $transcript_id;
-       }elsif ($species eq "Synechocystis_pcc6803") {
-               my ($gene_id,$temp) = split(" ",$gene_header);
-               $gene = $gene_id; #???
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Synechocystis_sp.pcc.6803") {
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Takifugu_rubripes") {
                my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
         $transcript =~ s/transcript\://;
@@ -713,22 +739,17 @@ sub find_gene {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $gene = $isoform;
        }elsif ($species eq "Tetraodon_nigroviridis") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Theobroma_cacao") {
-               my ($gene_id,$transcript) = split(/\|/,$gene_header);
-               $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Tolypocladium_inflatum") {
                $gene = $gene_header;
        }elsif ($species eq "Trichodesmium_erythraeum") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Triticum_aestivum") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Triticum_dicoccoides") {
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Triticum_monococcum.DV92") {
                my ($gene_id,$temp) = split(/\|/,$gene_header);
                $gene = $gene_id;
@@ -739,16 +760,25 @@ sub find_gene {
                my ($gi,$temp,$gb,$gene_id,$strand,$start,$stop) = split(/[\|\s]+/, $gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Triticum_urartu") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Utricularia_gibba") {
+               my ($isoform, $gene_id) = split(/\|/, $gene_header);
+               $gene = $isoform;
+       }elsif ($species eq "Vigna_radiata") {
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Vitis_vinifera") {
-               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
-               $gene = $gene_id;
+               $gene = ensembl_gene($gene_header);
        }elsif ($species eq "Zea_mays") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene = $transcript;
+               $gene = ensembl_gene($gene_header);
+       }elsif ($species eq "Zoysia_japonica.Nagirizaki") {
+               my ($gene_id, $location, $strand) = split(/\s/, $gene_header);
+               $gene = $gene_id;
+       }elsif ($species eq "Zoysia_matrella.Wakaba") {
+               my ($gene_id, $location, $strand) = split(/\s/, $gene_header);
+               $gene = $gene_id;
+       }elsif ($species eq "Zoysia_pacifica.Zanpa") {
+               my ($gene_id, $location, $strand) = split(/\s/, $gene_header);
+               $gene = $gene_id;
                
        }else {
                die "Error: Gene id can not be found for species $species!";
@@ -762,30 +792,39 @@ sub find_gene_synonym {
        $gene_header =~ s/^>//; # strip off the header line identifier, if it isn't already
        my $species = $_[1];
        my $synonym;
-       if ($species eq "Batrachochytrium_dendrobatidis") {
+       if ($species eq "Aegilops_tauschii") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Amborella_trichopoda") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Arabidopsis_halleri") {
+               $gene = ensembl_synonym($gene_header);
+       }elsif ($species eq "Arabidopsis_lyrata") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Arabidopsis_thaliana") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Asparagus_officinalis") {
+               $synonym = mart_synonym($gene_header);
+       }elsif ($species eq "Batrachochytrium_dendrobatidis") {
                my ($transcript,$gene_id,$info) = split(/\s\|\s/, $gene_header);
                $synonym = $gene_id;
+       }elsif ($species eq "Brachypodium_distachyon") {
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Brassica_oleracea") {
-               my ($protein,$type,$chrom,$gene_id,$transcript) = split(/\s/,$gene_header);
-               $transcript =~ s/transcript\://;
-               $gene_id =~ s/gene\://;
-               $peptide =~ s/\:pep//;
-               $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Brassica_rapa") {
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Caenorhabditis_elegans") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-               $transcript =~ s/transcript\://;
-               $gene_id =~ s/gene\://;
-               $peptide =~ s/\:pep//;
-               $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Cajanus_cajan") {
                my ($gene_id,$type,$locus,$temp) = split(/\s/, $gene_header);
                $synonym = $locus;
-       }elsif ($species eq "Capsella_rubella") {
-               my ($gene_id, $transcript) = split(/\|/, $gene_header);
+       }elsif ($species eq "Cannabis_sativa") {
+               my ($isoform, $gene_id, $tempj) = split(/\s/, $gene_header);
                $synonym = $gene_id;
+       }elsif ($species eq "Capsella_rubella") {
+               $synonym = mart_synonym($gene_header);
        }elsif ($species eq "Carica_papaya") {
-               my ($contig,$gene_id) = split(/\|/, $gene_header);
-               $synonym = $contig;
+               $synonym = mart_synonym($gene_header);
        }elsif ($species eq "Castor_canadensis") {
                my ($gene_info,$type,$gc,$gene_length) = split(/\s/, $gene_header);
                my ($gene_number,$gene_id) = split(/::/, $gene_info);
@@ -809,26 +848,24 @@ sub find_gene_synonym {
                $gene_symbol =~ s/gene_symbol\://;
                $synonym = "$temp_gene,$transcript,$gene_symbol";
        }elsif ($species eq "Chlamydomonas_reinhardtii") {
-               my ($locus,$transcript) = split(/\|/,$gene_header);
-               $synonym = $locus; #???
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Chondrus_crispus") {
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Cicer_arietinum") {
-               my ($gi,$number,$ref,$gene_id,$function) = split(/\|/, $gene_header);
-               $synonym = $number;
+               $synonym = mart_synonym($gene_header);
        }elsif ($species eq "Citrus_clementina") {
-               my ($transcript_id,$gene_id) = split(/\|/,$gene_header);
-               $synonym = $transcript_id;
+               $synonym = mart_synonym($gene_header);
        }elsif ($species eq "Citrus_sinensis") {
-               my ($transcript_id,$gene_id) = split(/\|/,$gene_header);
-               $synonym = $transcript_id;
+               $synonym = mart_synonym($gene_header);
+       }elsif ($species eq "Corchorus_capsularis") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Corchorus_olitorius") {
+               my ($type, $gene_id, $gene_id_suffix, $function) = split(/[\|\s]+/, $gene_header);
+               $synonym = $gene_id_suffix;
        }elsif ($species eq "Cucumis_sativus") {
-               my ($gene_id,$isomer) = split(/\|/,$gene_header);
-               $synonym = $gene_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Danio_rerio") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-               $transcript =~ s/transcript\://;
-               $gene_id =~ s/gene\://;
-               $peptide =~ s/\:pep//;
-               $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Dasypus_novemcinctus") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $temp_gene =~ s/gene\://;
@@ -842,11 +879,7 @@ sub find_gene_synonym {
                $gene_symbol =~ s/gene_symbol\://;
                $synonym = "$temp_gene,$transcript,$gene_symbol";
        }elsif ($species eq "Drosophila_melanogaster") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-               $transcript =~ s/transcript\://;
-               $gene_id =~ s/gene\://;
-               $peptide =~ s/\:pep//;
-               $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Echinops_telfairi") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $temp_gene =~ s/gene\://;
@@ -859,14 +892,12 @@ sub find_gene_synonym {
                $transcript =~ s/transcript\://;
                $gene_symbol =~ s/gene_symbol\://;
                $synonym = "$temp_gene,$transcript,$gene_symbol";
+       }elsif ($species eq "Erythranthe_guttata") {
+               $synonym = mart_synonym($gene_header);
        }elsif ($species eq "Eucalyptus_grandis") {
-               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
-               $synonym = $gene_id;
+               $synonym = mart_synonym($gene_header);
        }elsif ($species eq "Fragaria_vesca") {
-               my ($gene_id, $mrna_id) = split(/\|/, $gene_header);
-               $gene_id =~ s/\-v1\.0\-hybrid//;
-               $mrna_id =~ s/\-v1\.0\-hybrid//;
-               $synonym = $mrna_id;
+               $synonym = mart_synonym($gene_header);
        }elsif ($species eq "Fusarium_graminearum") {
                my ($transcript, $gene_id, $info) = split(/\s\|\s/, $gene_header);
                $synonym = $gene_id;
@@ -889,23 +920,13 @@ sub find_gene_synonym {
                $peptide =~ s/\:pep//;
                $synonym = "$peptide,$gene_id";
        }elsif ($species eq "Glycine_max") {
-               my ($locus_id,$isomer) = split(/\|/,$gene_header);
-               $synonym = $locus_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Gossypium_raimondii") {
-               my ($locus_id,$isomer) = split(/\|/,$gene_header);
-               $synonym = $locus_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Homo_sapiens") {
-               my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
-               $temp_gene =~ s/gene\://;
-               $transcript =~ s/transcript\://;
-               $gene_symbol =~ s/gene_symbol\://;
-               $synonym = "$temp_gene,$transcript,$gene_symbol";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Hordeum_vulgare") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-               $transcript =~ s/transcript\://;
-               $gene_id =~ s/gene\://;
-               $peptide =~ s/\:pep//;
-               $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Ictidomys_tridecemlineatus") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $temp_gene =~ s/gene\://;
@@ -918,9 +939,10 @@ sub find_gene_synonym {
                $locus =~ s/locus\=//;
                $ID =~ s/ID\=//;
                $synonym = "$peptide,$locus,$ID";
+       }elsif ($species eq "Leersia_perrieri") {
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Linum_usitatissimum") {
-               my ($transcript,$gene_id) = split(/\|/, $gene_header);
-               $synonym = $transcript;
+               $synonym = mart_synonym($gene_header);
        }elsif ($species eq "Macropus_eugenii") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $temp_gene =~ s/gene\://;
@@ -931,29 +953,18 @@ sub find_gene_synonym {
                my ($transcript,$gene_id,$temp) = split(/\s\|\s/, $gene_header);
                $synonym = $gene_id;
        }elsif ($species eq "Malus_domestica" ) {
-               my ($gene_id1,$gene_id2) = split(/\|/, $gene_header);
-               $synonym = $gene_id1;
+               $synonym = mart_synonym($gene_header);
        }elsif ($species eq "Manihot_esculenta") {
-               my ($transcript,$gene_id) = split(/\|/, $gene_header);
-               $synonym = $transcript;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Medicago_truncatula") {
-               my ($gene_id,$transcript) = split(/\|/, $gene_header);
-               $synonym = $gene_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Mimulus_guttatus") {
                my ($gene_id,$transcript) = split(/\|/, $gene_header);
                $synonym = $gene_id;
        }elsif ($species eq "Mus_musculus") {
-               my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
-               $temp_gene =~ s/gene\://;
-               $transcript =~ s/transcript\://;
-               $gene_symbol =~ s/gene_symbol\://;
-               $synonym = "$temp_gene,$transcript,$gene_symbol";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Musa_acuminata") {
-               my ($protein,$type,$chrom,$gene_id,$transcript) = split(/\s/,$gene_header);
-               $transcript =~ s/transcript\://;
-               $gene_id =~ s/gene\://;
-               $peptide =~ s/\:pep//;
-               $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Mustela_putorius.furo") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $temp_gene =~ s/gene\://;
@@ -969,9 +980,10 @@ sub find_gene_synonym {
        }elsif ($species eq "Neurospora_crassa") {
                my ($transcript,$gene_id,$temp) = split(/\s\|\s/,$gene_header);
                $synonym = $gene_id;
-       }elsif ($species eq "Nostoc_punctiforme") {
-               my ($temp,$transcript,$source,$gene_id,$func) = split(/\|/, $gene_header);
-               $synonym = $gene_id;
+       }elsif ($species eq "Nicotiana_attenuata") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Nostoc_punctiforme.pcc.73102") {
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Oncorhynchus_mykiss") {
                my ($gi, $number, $type, $gene_id, $function) = split(/\|/,$gene_header);
                $synonym = $gene_id;
@@ -987,18 +999,28 @@ sub find_gene_synonym {
                $transcript =~ s/transcript\://;
                $gene_symbol =~ s/gene_symbol\://;
                $synonym = "$temp_gene,$transcript,$gene_symbol";
-    }elsif ($species eq "Oryza_sativa.indica.gramene") {
-        my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene_id =~ s/gene\://;
-        $peptide =~ s/\:pep//;
-        $synonym = "$peptide,$gene_id";
+       }elsif ($species eq "Oryza_barthii") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Oryza_brachyantha") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Oryza_glaberrima") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Oryza_glumipatula") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Oryza_longistaminata") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Oryza_meridionalis") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Oryza_nivara") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Oryza_punctata") {
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Oryza_rufipogon") {
+               $synonym = ensembl_synonym($gene_header);
+    }elsif ($species eq "Oryza_sativa.indica") {
+       $synonym = ensembl_synonym($gene_header);
     }elsif ($species eq "Oryza_sativa.japonica.IRGSP") {
-        my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene_id =~ s/gene\://;
-        $peptide =~ s/\:pep//;
-        $synonym = "$peptide,$gene_id";
+        $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Oryzias_latipes") {
                my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
         $transcript =~ s/transcript\://;
@@ -1022,25 +1044,19 @@ sub find_gene_synonym {
                $gene_id =~ s/gene\://;
                $synonym = $gene_id;
        }elsif ($species eq "Phaseolus_vulgaris") {
-               my ($gene_id, $transcript) = split(/\|/,$gene_header);
-               $synonym = $gene_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Phoenix_dactylifera") {
                my ($gene_id, $locus_tag, $product, $strand) = split(/\s\[/, $gene_header);
                $locus_tag =~ s/locus_tag=//;
                $locus_tag =~ s/"//g;
                $synonym = $locus_tag;
        }elsif ($species eq "Physcomitrella_patens") {
-               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
-               $synonym = $gene_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Phytophthora_infestans") {
                my ($transcript, $gene_id, $function) = split(/\s\|\s/,$gene_header);
                $synonym = $gene_id;
-       }elsif ($species eq "Populus_trichocarpa.ver2") {
-               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
-               $synonym = $gene_id;
-       }elsif ($species eq "Populus_trichocarpa.ver3") {
-               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
-               $synonym = $gene_id;
+       }elsif ($species eq "Populus_trichocarpa") {
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Procavia_capensis") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $temp_gene =~ s/gene\://;
@@ -1048,8 +1064,7 @@ sub find_gene_synonym {
                $gene_symbol =~ s/gene_symbol\://;
                $synonym = "$temp_gene,$transcript,$gene_symbol";
        }elsif ($species eq "Prunus_persica") {
-               my ($transcript,$gene_id) = split(/\|/,$gene_header);
-               $synonym = $transcript;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Pteropus_vampyrus") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $temp_gene =~ s/gene\://;
@@ -1057,38 +1072,21 @@ sub find_gene_synonym {
                $gene_symbol =~ s/gene_symbol\://;
                $synonym = "$temp_gene,$transcript,$gene_symbol";
        }elsif ($species eq "Rattus_norvegicus") {
-               my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
-               $temp_gene =~ s/gene\://;
-               $transcript =~ s/transcript\://;
-               $gene_symbol =~ s/gene_symbol\://;
-               $synonym = "$temp_gene,$transcript,$gene_symbol";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Ricinus_communis") {
-               my ($transcript,$model) = split(/\|/, $gene_header);
-               $synonym = $model;
+               $synonym = mart_synonym($gene_header);
        }elsif ($species eq "Saccharomyces_cerevisiae") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene_id =~ s/gene\://;
-        $peptide =~ s/\:pep//;
-        $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Schizosaccharomyces_pombe") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene_id =~ s/gene\://;
-        $peptide =~ s/\:pep//;
-        $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Selaginella_moellendorffii") {
-               my ($locus_id,$prot_id) = split(/\|/,$gene_header);
-               $synonym = $prot_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Setaria_italica") {
-               my ($locus_id,$prot_id) = split(/\|/,$gene_header);
-               $synonym = $locus_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Solanum_lycopersicum") {
-               my ($locus_id,$prot_id) = split(/\|/,$gene_header);
-               $synonym = $locus_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Solanum_tuberosum") {
-               my ($locus_id,$prot_id) = split(/\|/,$gene_header);
-               $synonym = $locus_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Sorex_araneus") {
                my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header);
                $temp_gene =~ s/gene\://;
@@ -1096,8 +1094,9 @@ sub find_gene_synonym {
                $gene_symbol =~ s/gene_symbol\://;
                $synonym = "$temp_gene,$transcript,$gene_symbol";
        }elsif ($species eq "Sorghum_bicolor") {
-               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
-               $synonym = $gene_id;
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Synechocystis_sp.pcc.6803") {
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Takifugu_rubripes") {
                my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
         $transcript =~ s/transcript\://;
@@ -1111,40 +1110,26 @@ sub find_gene_synonym {
                $gene_symbol =~ s/gene_symbol\://;
                $synonym = "$temp_gene,$transcript,$gene_symbol";
        }elsif ($species eq "Tetraodon_nigroviridis") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene_id =~ s/gene\://;
-        $peptide =~ s/\:pep//;
-        $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Theobroma_cacao") {
-               my ($gene_id,$transcript) = split(/\|/,$gene_header);
-               $synonym = $gene_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Trichodesmium_erythraeum") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene_id =~ s/gene\://;
-        $peptide =~ s/\:pep//;
-        $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Triticum_aestivum") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene_id =~ s/gene\://;
-        $peptide =~ s/\:pep//;
-        $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Triticum_dicoccoides") {
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Triticum_urartu") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-               $transcript =~ s/transcript\://;
-               $gene_id =~ s/gene\://;
-               $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
+       }elsif ($species eq "Utricularia_gibba") {
+               my ($isoform, $gene_id) = split(/\|/, $gene_header);
+               $synonym = $gene_id;
+       }elsif ($species eq "Vigna_radiata") {
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Vitis_vinifera") {
-               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
-               $synonym = $transcript_id;
+               $synonym = ensembl_synonym($gene_header);
        }elsif ($species eq "Zea_mays") {
-               my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
-        $transcript =~ s/transcript\://;
-        $gene_id =~ s/gene\://;
-        $peptide =~ s/\:pep//;
-        $synonym = "$peptide,$gene_id";
+               $synonym = ensembl_synonym($gene_header);
                
        }else {
                $synonym = "null";
@@ -1178,6 +1163,7 @@ sub all_species_array {
        push (@spec_array, "Castor_canadensis");
        push (@spec_array, "Cavia_porcellus");
        push (@spec_array, "Chlamydomonas_reinhardtii");
+       push (@spec_array, "Chondrus_crispus");
        push (@spec_array, "Cicer_arietinum");
        push (@spec_array, "Citrullus_lanatus");
        push (@spec_array, "Citrus_clementina");
@@ -1432,4 +1418,36 @@ sub find_taxon {
        return $taxon;
 }      
 
+sub ensembl_gene {
+               my $gene_header = $_[0];
+               my ($gene, $type, $contig, $gene_alias, $transcript, $biotype, $description) = split(/\s/, $gene_header);
+               $transcipt =~ s/transcript\://;
+               return $transcript;
+}
+
+sub ensembl_synonym {
+               my $gene_header = $_[0];
+               my ($gene, $type, $contig, $gene_alias, $transcript, $biotype, $description) = split(/\s/, $gene_header);
+        $gene_alias =~ s/gene\://;
+        my $synonym = "$gene,$gene_alias";
+               return $synonym;
+}
+
+sub mart_gene {
+               my $gene_header = $_[0];
+               my ($gene, $transcript, $synonyms) = split(/\|/, $gene_header);
+               return $transcript;
+}
+
+sub mart_synonym {
+               my $gene_header = $_[0];
+               my ($gene, $transcript, $synonyms) = split(/\|/, $gene_header);
+               if ($synonyms eq "") {
+                               my $synonym = "$gene";
+                               return $synonym;
+               }else{
+                               my $synonym = "$gene,$synonyms";
+                               return $synonym;
+               }
+}
 1;