From 610f2a0da40e0ef0635f87ec8451b80822b75bfa Mon Sep 17 00:00:00 2001 From: elserj Date: Thu, 1 Dec 2016 03:27:38 +0000 Subject: [PATCH] Add new mammal species svn path=/; revision=647 --- interactome_scripts/find_species.pl | 248 +++++++++++++++++++++++++--- 1 file changed, 224 insertions(+), 24 deletions(-) diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl index 24d1bf0..1fe1526 100755 --- a/interactome_scripts/find_species.pl +++ b/interactome_scripts/find_species.pl @@ -50,6 +50,10 @@ sub find_species { $species = "Capsicum_annuum"; }elsif ($temp =~ /Carica\_papaya/) { $species = "Carica_papaya"; + }elsif ($temp =~ /Castor_canadensis/) { + $species = "Castor_canadensis"; + }elsif ($temp =~ /Cavia_porcellus/) { + $species = "Cavia_porcellus"; }elsif ($temp =~ /Chlamy/) { $species = "Chlamydomonas_reinhardtii"; }elsif ($temp =~ /Cicer\_arietinum/) { @@ -66,8 +70,14 @@ sub find_species { $species = "Cucumis_sativus"; }elsif ($temp =~ /Danio/) { $species = "Danio_rerio"; + }elsif ($temp =~ /Dasypus_novemcinctus/) { + $species = "Dasypus_novemcinctus"; + }elsif ($temp =~ /Dipodomys_ordii/) { + $species = "Dipodomys_ordii"; }elsif ($temp =~ /Drosophila/) { $species = "Drosophila_melanogaster"; + }elsif ($temp =~ /Echinops_telfairi/) { + $species = "Echinops_telfairi"; }elsif ($temp =~ /Ectocarpus/) { $species = "Ectocarpus_siliculosus"; }elsif ($temp =~ /Elaphocordyceps\_capitata/) { @@ -78,6 +88,8 @@ sub find_species { $species = "Elaphocordyceps_paradoxa"; }elsif ($temp =~ /Epichloe_festucae/) { $species = "Epichloe\_festucae"; + }elsif ($temp = /Erinaceus_europaeus/) { + $species = "Erinaceus_europaeus"; }elsif ($temp =~ /Escherichia\_coli/) { $species = "Escherichia_coli"; }elsif ($temp =~ /Eucalyptus\_grandis/) { @@ -104,6 +116,8 @@ sub find_species { $species = "Homo_sapiens"; }elsif ($temp =~ /Hordeum\_vulgare/) { $species = "Hordeum_vulgare"; + }elsif ($temp =~ /Ictidomys_tridecemlineatus/) { + $species = "Ictidomys_tridecemlineatus"; }elsif ($temp =~ /Jatropha/) { $species = "Jatropha_curcas"; }elsif ($temp =~ /Kalanchoe\_laxiflora/) { @@ -114,6 +128,8 @@ sub find_species { $species = "Leersia_perrieri"; }elsif ($temp =~ /Linum\_usitatissimum/) { $species = "Linum_usitatissimum"; + }elsif ($temp =~ /Macropus_eugenii/) { + $species = "Macropus_eugenii"; }elsif ($temp =~ /Magnaporthe/) { $species = "Magnaporthe_grisea"; }elsif ($temp =~ /Malus/) { @@ -128,6 +144,8 @@ sub find_species { $species = "Mus_musculus"; }elsif ($temp =~ /Musa/) { $species = "Musa_acuminata"; + }elsif ($temp =~ /Mustela_putorious.furo/) { + $species = "Mustela_putorious.furo"; }elsif ($temp =~ /Nectria\_haematococca/) { $species = "Nectria_haematococca"; }elsif ($temp =~ /Nelumbo/) { @@ -138,6 +156,10 @@ sub find_species { $species = "Nostoc_punctiforme"; }elsif ($temp =~ /Oncorhynchus\_mykiss/) { $species = "Oncorhynchus\_mykiss"; + }elsif ($temp =~ /Ornithorhynchus_anatinus/) { + $species = "Ornithorhynchus_anatinus"; + }elsif ($temp =~ /Oryctolagus_cuniculus/) { + $species = "Oryctolagus_cuniculus"; }elsif ($temp =~ /Oryza\_australiensis/) { $species = "Oryza_australiensis"; }elsif ($temp =~ /Oryza\_barthii/) { @@ -182,6 +204,10 @@ sub find_species { $species = "Oryza_sativa.japonica.iplant"; }elsif ($temp =~ /Oryzias\_latipes/) { $species = "Oryzias\_latipes"; + }elsif ($temp =~ /Otolemur_garnettii/) { + $species = "Otolemur_garnettii"; + }elsif ($temp =~ /Pan_troglodytes/) { + $species = "Pan_troglodytes"; }elsif ($temp =~ /Pediculus/) { $species = "Pediculus_humanus"; }elsif ($temp =~ /Phaseolus\_vulgaris/) { @@ -202,8 +228,12 @@ sub find_species { $species = "Populus_trichocarpa.ver2"; }elsif ($temp =~ /Populus\_trichocarpa\.ver3/) { $species = "Populus_trichocarpa.ver3"; + }elsif ($temp =~ /Procavia_capensis/) { + $species = "Procavia_capensis"; }elsif ($temp =~ /Prunus/) { $species = "Prunus_persica"; + }elsif ($temp =~ /Pteropus_vampyrus/) { + $species = "Pteropus_vampyrus"; }elsif ($temp =~ /Rattus/) { $species = "Rattus_norvegicus"; }elsif ($temp =~ /Rhizopus/) { @@ -226,12 +256,16 @@ sub find_species { $species = "Solanum_tuberosum"; }elsif ($temp =~ /Solanum_lycopersicum/) { $species = "Solanum_lycopersicum"; + }elsif ($temp =~ /Sorex_araneus/) { + $species = "Sorex_araneus"; }elsif ($temp =~ /Sorghum/) { $species = "Sorghum_bicolor"; }elsif ($temp =~ /Synechocystis/) { $species = "Synechocystis_pcc6803"; }elsif ($temp =~ /Takifugu/) { $species = "Takifugu\_rubripes"; + }elsif ($temp =~ /Tarsius_syrichta/) { + $species = "Tarsius_syrichta"; }elsif ($temp =~ /Tetraodon/) { $species = "Tetraodon\_nigroviridis"; }elsif ($temp =~ /Theobroma\_cacao/) { @@ -320,6 +354,14 @@ sub find_gene { }elsif ($species eq "Carica_papaya") { my ($contig,$gene_id) = split(/\|/, $gene_header); $gene = $gene_id; + }elsif ($species eq "Castor_canadensis") { + my ($gene_info,$type,$gc,$gene_length) = split(/\s/, $gene_header); + my ($gene_number,$gene_id) = split(/::/, $gene_info); + my ($trinity_id, $m_number) = split(/\|/, $gene_id); + $gene = $trinity_id; #??? + }elsif ($species eq "Cavia_porcellus") { + 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 = $transcript; #??? @@ -345,10 +387,19 @@ sub find_gene { my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header); $transcript =~ s/transcript\://; $gene = $transcript; + }elsif ($species eq "Dasypus_novemcinctus") { + my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header); + $gene = $isoform; + }elsif ($species eq "Dipodomys_ordii") { + 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 = $transcript; + }elsif ($species eq "Echinops_telfairi") { + my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header); + $gene = $isoform; }elsif ($species eq "Ectocarpus_siliculosus") { my ($gene_id,$temp) = split(/\s+/, $gene_header); $gene = $gene_id; @@ -361,6 +412,9 @@ sub find_gene { }elsif ($species eq "Epichloe_festucae") { my ($gene_id, $temp) = split(/\s/, $gene_header); $gene = $gene_id; + }elsif ($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 "Escherichia_coli") { $gene = $gene_header; #??? }elsif ($species eq "Eucalyptus_grandis") { @@ -396,13 +450,15 @@ sub find_gene { }elsif ($species eq "Gossypium_hirsutum") { $gene = $gene_header; }elsif ($species eq "Homo_sapiens") { - my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header); - $transcript =~ s/transcript\://; - $gene = $transcript; + my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header); + $gene = $isoform }elsif ($species eq "Hordeum_vulgare") { my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header); $transcript =~ s/transcript\://; $gene = $transcript; + }elsif ($species eq "Ictidomys_tridecemlineatus") { + my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header); + $gene = $isoform }elsif ($species eq "Jatropha_curcas") { my ($gene_id, $temp) = split(/\s/,$gene_header); $gene = $gene_id; @@ -418,6 +474,9 @@ sub find_gene { }elsif ($species eq "Linum_usitatissimum") { my ($transcript,$gene_id) = split(/\|/, $gene_header); $gene = $gene_id; + }elsif ($species eq "Macropus_eugenii") { + my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header); + $gene = $isoform }elsif ($species eq "Magnaporthe_grisea") { my ($transcript,$gene_id,$temp) = split(/\s\|\s/, $gene_header); $gene = $transcript; @@ -434,11 +493,14 @@ sub find_gene { my ($gene_id,$transcript) = split(/\|/, $gene_header); $gene = $transcript; }elsif ($species eq "Mus_musculus") { - my ($protein,$type,$chrom,$gene_id,$transcript) = split(/\s/,$gene_header); - $gene = $protein; + my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header); + $gene = $isoform }elsif ($species eq "Musa_acuminata") { my ($protein,$type,$chrom,$gene_id,$transcript) = split(/\s/,$gene_header); $gene = $protein; + }elsif ($species eq "Mustela_putorius") { + my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header); + $gene = $isoform; }elsif ($species eq "Nectria_haematococca") { my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header); $transcript =~ s/transcript\://; @@ -455,9 +517,12 @@ sub find_gene { }elsif ($species eq "Oncorhynchus_mykiss") { my ($gi, $number, $type, $gene_id, $function) = split(/\|/,$gene_header); $gene = $number; - }elsif ($species eq "Leersia_perrieri") { - my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header); - $gene = $gene_id; + }elsif ($species eq "Ornithorhynchus_anatinus") { + my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header); + $gene = $isoform; + }elsif ($species eq "Oryctolagus_cuniculus") { + my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header); + $gene = $isoform; }elsif ($species eq "Oryza_australiensis") { my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header); $gene = $gene_id; @@ -526,6 +591,12 @@ sub find_gene { my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header); $transcript =~ s/transcript\://; $gene = $transcript; + }elsif ($species eq "Otolemur_garnettii") { + my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header); + $gene = $isoform; + }elsif ($species eq "Pan_troglodytes") { + 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 = $transcript; @@ -556,13 +627,18 @@ sub find_gene { }elsif ($species eq "Populus_trichocarpa.ver3") { my ($gene_id,$transcript_id) = split(/\|/,$gene_header); $gene = $transcript_id; + }elsif ($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 = $gene_id; + }elsif ($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 ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header); - $transcript =~ s/transcript\://; - $gene = $transcript; + my ($isoform, $type, $scaffold, $temp_gene, $transcript, $gene_biotype, $transcript_biotype, $gene_symbol, $description) = split(/\s/, $gene_header); + $gene = $isoform; }elsif ($species eq "Rhizopus_oryzae") { my ($jgi,$temp,$num,$gene_id) = split(/\|/, $gene_header); $gene = $num; @@ -593,6 +669,9 @@ sub find_gene { }elsif ($species eq "Solanum_tuberosum") { my ($locus_id,$prot_id) = split(/\|/,$gene_header); $gene = $prot_id; + }elsif ($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 = $transcript_id; @@ -603,6 +682,9 @@ sub find_gene { my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header); $transcript =~ s/transcript\://; $gene = $transcript; + }elsif ($species eq "Tarsius_syrichta") { + 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); $transcript =~ s/transcript\://; @@ -677,6 +759,17 @@ sub find_gene_synonym { }elsif ($species eq "Carica_papaya") { my ($contig,$gene_id) = split(/\|/, $gene_header); $synonym = $contig; + }elsif ($species eq "Castor_canadensis") { + my ($gene_info,$type,$gc,$gene_length) = split(/\s/, $gene_header); + my ($gene_number,$gene_id) = split(/::/, $gene_info); + my ($trinity_id, $m_number) = split(/\|/, $gene_id); + $synonym = "$gene_number,$m_number"; + }elsif ($species eq "Cavia_porcellus") { + 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"; }elsif ($species eq "Chlamydomonas_reinhardtii") { my ($locus,$transcript) = split(/\|/,$gene_header); $synonym = $locus; #??? @@ -698,12 +791,36 @@ sub find_gene_synonym { $gene_id =~ s/gene\://; $peptide =~ s/\:pep//; $synonym = "$peptide,$gene_id"; + }elsif ($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\://; + $transcript =~ s/transcript\://; + $gene_symbol =~ s/gene_symbol\://; + $synonym = "$temp_gene,$transcript,$gene_symbol"; + }elsif ($species eq "Dipodomys_ordii") { + my ($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"; }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,$gene_id"; + }elsif ($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\://; + $transcript =~ s/transcript\://; + $gene_symbol =~ s/gene_symbol\://; + $synonym = "$temp_gene,$transcript,$gene_symbol"; + }elsif ($species eq "Erinaceus_europaeus") { + my ($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"; }elsif ($species eq "Eucalyptus_grandis") { my ($gene_id,$transcript_id) = split(/\|/,$gene_header); $synonym = $gene_id; @@ -740,17 +857,23 @@ sub find_gene_synonym { my ($locus_id,$isomer) = split(/\|/,$gene_header); $synonym = $locus_id; }elsif ($species eq "Homo_sapiens") { - my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header); + 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_id =~ s/gene\://; - $peptide =~ s/\:pep//; - $synonym = "$peptide,$gene_id"; + $gene_symbol =~ s/gene_symbol\://; + $synonym = "$temp_gene,$transcript,$gene_symbol"; }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,$gene_id"; + }elsif ($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\://; + $transcript =~ s/transcript\://; + $gene_symbol =~ s/gene_symbol\://; + $synonym = "$temp_gene,$transcript,$gene_symbol"; }elsif ($species eq "Kalanchoe_laxiflora") { my ($gene_id, $peptide, $locus, $ID, $annot) = split(/\s/,$gene_header); $peptide =~ s/polypeptide\=//; @@ -760,6 +883,12 @@ sub find_gene_synonym { }elsif ($species eq "Linum_usitatissimum") { my ($transcript,$gene_id) = split(/\|/, $gene_header); $synonym = $transcript; + }elsif ($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\://; + $transcript =~ s/transcript\://; + $gene_symbol =~ s/gene_symbol\://; + $synonym = "$temp_gene,$transcript,$gene_symbol"; }elsif ($species eq "Magnaporthe_grissa") { my ($transcript,$gene_id,$temp) = split(/\s\|\s/, $gene_header); $synonym = $gene_id; @@ -776,17 +905,23 @@ sub find_gene_synonym { my ($gene_id,$transcript) = split(/\|/, $gene_header); $synonym = $gene_id; }elsif ($species eq "Mus_musculus") { - my ($protein,$type,$chrom,$gene_id,$transcript) = split(/\s/,$gene_header); + 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_id =~ s/gene\://; - $peptide =~ s/\:pep//; - $synonym = "$peptide,$gene_id"; + $gene_symbol =~ s/gene_symbol\://; + $synonym = "$temp_gene,$transcript,$gene_symbol"; }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,$gene_id"; + }elsif ($species eq "Mustela_putorius") { + 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"; }elsif ($species eq "Nectria_haematococca") { my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header); $transcript =~ s/transcript\://; @@ -802,6 +937,18 @@ sub find_gene_synonym { }elsif ($species eq "Oncorhynchus_mykiss") { my ($gi, $number, $type, $gene_id, $function) = split(/\|/,$gene_header); $synonym = $gene_id; + }elsif ($species eq "Ornithorhynchus_anatinus") { + 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"; + }elsif ($species eq "Oryctolagus_cuniculus") { + my ($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"; }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\://; @@ -820,6 +967,18 @@ sub find_gene_synonym { $gene_id =~ s/gene\://; $peptide =~ s/\:pep//; $synonym = "$peptide,$gene_id"; + }elsif ($species eq "Otolemur_garnettii") { + 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"; + }elsif ($species eq "Pan_troglodytes") { + my ($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"; }elsif ($species eq "Pediculus_humanus") { my ($gene_pa,$func,$func2,$unknown,$gene_id) = split(/[\|\s+]/, $gene_header); $gene_id =~ s/gene\://; @@ -844,15 +1003,27 @@ sub find_gene_synonym { }elsif ($species eq "Populus_trichocarpa.ver3") { my ($gene_id,$transcript_id) = split(/\|/,$gene_header); $synonym = $gene_id; + }elsif ($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\://; + $transcript =~ s/transcript\://; + $gene_symbol =~ s/gene_symbol\://; + $synonym = "$temp_gene,$transcript,$gene_symbol"; }elsif ($species eq "Prunus_persica") { my ($transcript,$gene_id) = split(/\|/,$gene_header); $synonym = $transcript; + }elsif ($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\://; + $transcript =~ s/transcript\://; + $gene_symbol =~ s/gene_symbol\://; + $synonym = "$temp_gene,$transcript,$gene_symbol"; }elsif ($species eq "Rattus_norvegicus") { - my ($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,$gene_id"; + my ($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"; }elsif ($species eq "Ricinus_communis") { my ($transcript,$model) = split(/\|/, $gene_header); $synonym = $model; @@ -880,6 +1051,12 @@ sub find_gene_synonym { }elsif ($species eq "Solanum_tuberosum") { my ($locus_id,$prot_id) = split(/\|/,$gene_header); $synonym = $locus_id; + }elsif ($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\://; + $transcript =~ s/transcript\://; + $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; @@ -889,6 +1066,12 @@ sub find_gene_synonym { $gene_id =~ s/gene\://; $peptide =~ s/\:pep//; $synonym = "$peptide,$gene_id"; + }elsif ($species eq "Tarsius_syrichta") { + 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"; }elsif ($species eq "Tetraodon_nigroviridis") { my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header); $transcript =~ s/transcript\://; @@ -954,6 +1137,8 @@ sub all_species_array { push (@spec_array, "Capsella_rubella"); push (@spec_array, "Capsicum_annuum"); push (@spec_array, "Carica_papaya"); + push (@spec_array, "Castor_canadensis"); + push (@spec_array, "Cavia_porcellus"); push (@spec_array, "Chlamydomonas_reinhardtii"); push (@spec_array, "Cicer_arietinum"); push (@spec_array, "Citrullus_lanatus"); @@ -962,12 +1147,16 @@ sub all_species_array { push (@spec_array, "Coffea_canephora"); push (@spec_array, "Cucumis_sativus"); push (@spec_array, "Danio_rerio"); + push (@spec_array, "Dasypus_novemcinctus"); + push (@spec_array, "Dipodomys_ordii"); push (@spec_array, "Drosophila_melanogaster"); + push (@spec_array, "Echinops_telfairi"); push (@spec_array, "Ectocarpus_siliculosus"); push (@spec_array, "Elaphocordyceps_capitata"); push (@spec_array, "Elaphocordyceps_ophioglossoides"); push (@spec_array, "Elaphocordyceps_paradoxa"); push (@spec_array, "Epichloe_festucae"); + push (@spec_array, "Erinaceus_europaeus"); push (@spec_array, "Escherichia_coli"); push (@spec_array, "Eucalyptus_grandis"); push (@spec_array, "Fragaria_vesca"); @@ -981,10 +1170,12 @@ sub all_species_array { push (@spec_array, "Gossypium_hirsutum"); push (@spec_array, "Homo_sapiens"); push (@spec_array, "Hordeum_vulgare"); + push (@spec_array, "Ictidomys_tridecemlineatus"); push (@spec_array, "Jatropha_curcas"); push (@spec_array, "Kalanchoe_laxiflora"); push (@spec_array, "Laccaria_bicolor"); push (@spec_array, "Linum_usitatissimum"); + push (@spec_array, "Macropus_eugenii"); push (@spec_array, "Magnaporthe_grissa"); push (@spec_array, "Malus_domestica"); push (@spec_array, "Manihot_esculenta"); @@ -992,11 +1183,14 @@ sub all_species_array { push (@spec_array, "Mimulus_guttatus"); push (@spec_array, "Mus_musculus"); push (@spec_array, "Musa_acuminata"); + push (@spec_array, "Mustela_putorius"); push (@spec_array, "Nectria_haematococca"); push (@spec_array, "Nelumbo_nucifera"); push (@spec_array, "Neurospora_crassa"); push (@spec_array, "Nostoc_punctiforme"); push (@spec_array, "Oncorhynchus_mykiss"); + push (@spec_array, "Ornithorhynchus_anatinus"); + push (@spec_array, "Oryctolagus_cuniculus"); push (@spec_array, "Oryza_australiensis"); push (@spec_array, "Oryza_barthii"); push (@spec_array, "Oryza_brachyantha"); @@ -1019,6 +1213,8 @@ sub all_species_array { push (@spec_array, "Oryza_sativa.japonica.IRGSP"); push (@spec_array, "Oryza_sativa.japonica.MSU"); push (@spec_array, "Oryzias_latipes"); + push (@spec_array, "Otolemur_garnettii"); + push (@spec_array, "Pan_troglodytes"); push (@spec_array, "Pediculus_humanus"); push (@spec_array, "Phaseolus_vulgaris"); push (@spec_array, "Phyllostachys_heterocycla"); @@ -1026,7 +1222,9 @@ sub all_species_array { push (@spec_array, "Phytophthora_infestans"); push (@spec_array, "Picea_abies"); push (@spec_array, "Populus_trichocarpa"); + push (@spec_array, "Procavia_capensis"); push (@spec_array, "Prunus_persica"); + push (@spec_array, "Pteropus_vampyrus"); push (@spec_array, "Rattus_norvegicus"); push (@spec_array, "Rhizopus_oryzae"); push (@spec_array, "Ricinus_communis"); @@ -1038,9 +1236,11 @@ sub all_species_array { push (@spec_array, "Setaria_italica"); push (@spec_array, "Solanum_tuberosum"); push (@spec_array, "Solanum_lycopersicum"); + push (@spec_array, "Sorex_araneus"); push (@spec_array, "Sorghum_bicolor"); push (@spec_array, "Synechocystis_pcc6803"); push (@spec_array, "Takifugu_rubripes"); + push (@spec_array, "Tarsius_syrichta"); push (@spec_array, "Tetraodon_nigroviridis"); push (@spec_array, "Theobroma_cacao"); push (@spec_array, "Tolypocladium_inflatum"); -- 2.34.1