From: elserj <elserj@localhost>
Date: Tue, 14 May 2019 21:55:22 +0000 (+0000)
Subject: Script to generate fasta_taxon_mapping.txt file for iprscan
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=31742c1b9e91b7ba842cd5317244597980816fce;p=old-jaiswallab-svn%2F.git

Script to generate fasta_taxon_mapping.txt file for iprscan

svn path=/; revision=663
---

diff --git a/interactome_scripts/create_taxon_mapping.pl b/interactome_scripts/create_taxon_mapping.pl
new file mode 100755
index 0000000..45c3884
--- /dev/null
+++ b/interactome_scripts/create_taxon_mapping.pl
@@ -0,0 +1,20 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+if(-e "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl") {
+	require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
+}elsif(-e "$ENV{HOME}/bin/find_species.pl") {
+	require "$ENV{HOME}/bin/find_species.pl";
+}
+
+my @files = glob(*.fa);
+open(OUTFILE, ">fasta_taxon_mapping.txt";
+
+foreach my $file (@files){
+		my $species = find_species($file);
+		my $taxon = find_taxon($species);
+		print OUTFILE "$file\t$taxon\n";
+}
+close(OUTFILE);
diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 10716bc..f7ff442 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -1299,10 +1299,13 @@ sub find_taxon {
 	my %taxon_hash = (
 		'Aegilops_tauschii', '37682',
 		'Amborella_trichopoda', '13333',
+		'Arabidopsis_halleri', '81970',
 		'Arabidopsis_lyrata' , '59689',
 		'Arabidopsis_thaliana', '3702',
 		'Arachis_duranensis', '130453',
 		'Arachis_ipaensis', '130454',
+		'Asparagus_officinalis', '4686',
+		'Azolla_filiculoides', '84609',
 		'Batrachochytrium_dendrobatidis', '109871',
 		'Brachypodium_distachyon', '15368',
 		'Brachypodium_sylvaticum.Corv', '29664',
@@ -1317,19 +1320,24 @@ sub find_taxon {
 		'Capsicum_annuum', '4072',
 		'Carica_papaya', '3649',
 		'Chlamydomonas_reinhardtii', '3055',
+		'Chondrus_crispus', '2769',
 		'Cicer_arietinum', '3827',
 		'Citrullus_lanatus', '3654',
 		'Citrus_clementina', '85681',
 		'Citrus_sinensis', '2711',
 		'Coffea_canephora', '49390',
+		'Corchorus_capsularis', '210143',
+		'Corchorus_olitorius', '93759',
 		'Cucumis_sativus', '3659',
 		'Danio_rerio', '7955',
 		'Drosophila_melanogaster', '7227',
+		'Durio_zibethinus', '66656',
 		'Ectocarpus_siliculosus', '2880',
 		'Elaphocordyceps_capitata', '45325',
 		'Elaphocordyceps_ophioglossoides', '71617',
 		'Elaphocordyceps_paradoxa', '94208',
 		'Epichloe_festucae', '35717',
+		'Erythranthe_guttata', '4155',
 		'Escherichia_coli', '562',
 		'Eucalyptus_grandis', '71139',
 		'Fragaria_vesca', '57918',
@@ -1343,6 +1351,8 @@ sub find_taxon {
 		'Gossypium_hirsutum', '3635',
 		'Homo_sapiens', '9606',
 		'Hordeum_vulgare', '4513',
+		'Humulus_lupulus.haplotig', '3486',
+		'Humulus_lupulus.primary', '3486',
 		'Jatropha_curcas', '180498',
 		'Kalanchoe_laxiflora', '1670617',
 		'Laccaria_bicolor', '29883',
@@ -1352,13 +1362,16 @@ sub find_taxon {
 		'Malus_domestica', '3750',
 		'Manihot_esculenta', '3983',
 		'Medicago_truncatula', '3880',
+		'Mentha_longifolia', '38859',
 		'Mimulus_guttatus', '4155',
 		'Mus_musculus', '10090',
 		'Musa_acuminata', '4641',
 		'Nectria_haematococca', '140110',
 		'Nelumbo_nucifera', '4432',
 		'Neurospora_crassa', '5141',
+		'Nicotiana_attenuata', '49451',
 		'Nostoc_punctiforme', '272131',
+		'Ocimum_tenuiflorum', '204149',
 		'Oncorhynchus_mykiss', '8022',
 		'Oryza_australiensis', '4532',
 		'Oryza_barthii', '65489',
@@ -1374,6 +1387,10 @@ sub find_taxon {
 		'Oryza_officinalis', '4535',
 		'Oryza_punctata', '4537',
 		'Oryza_rufipogon', '4529',
+		'Oryza_sativa.AUS.kasalath', '1736659',
+		'Oryza_sativa.AUS.N22', '1736659',
+		'Oryza_sativa.indica', '39946',
+		'Oryza_sativa.indica.9311.OGE', '39946',
 		'Oryza_sativa.indica.gramene', '39946',
 		'Oryza_sativa.indica.iplant', '39946',
 		'Oryza_sativa.indica.IR29', '39946',
@@ -1381,6 +1398,7 @@ sub find_taxon {
 		'Oryza_sativa.japonica.iplant', '39947',
 		'Oryza_sativa.japonica.IRGSP', '39947',
 		'Oryza_sativa.japonica.MSU', '39947',
+		'Oryza_sativa.japonica.OGE', '39947',
 		'Oryzias_latipes', '8090',
 		'Pediculus_humanus', '121225',
 		'Phaseolus_vulgaris', '3885',
@@ -1397,27 +1415,35 @@ sub find_taxon {
 		'Rhizopus_oryzae', '64495',
 		'Ricinus_communis', '3988',
 		'Saccharomyces_cerevisiae', '4932',
+		'Salvia_hispanica', '49212',
 		'Salvia_hispancia.salba', '49212',
 		'Salvia_splendens', '180675',
+		'Salvinia_cucullata', '32188',
 		'Schizosaccharomyces_pombe', '4896',
 		'Selaginella_moellendorffii', '88036',
 		'Setaria_italica', '4555',
 		'Solanum_lycopersicum', '4081',
 		'Solanum_tuberosum', '4113',
 		'Sorghum_bicolor', '4558',
-		'Synechocystis_pcc6803', '1148',
+		'Synechocystis_sp.pcc.6803', '1148',
 		'Takifugu_rubripes', '31033',
 		'Tetraodon_nigroviridis', '99883',
 		'Theobroma_cacao', '3641',
 		'Tolypocladium_inflatum', '29910',
 		'Trichodesmium_erythraeum', '1206',
 		'Triticum_aestivum', '4565',
+		'Triticum_dicoccoides', '85692',
 		'Triticum_monococcum.DV92', '4568',
 		'Triticum_monococcum.G3116', '4568',
 		'Triticum_turgidum', '4571',
 		'Triticum_urartu', '4572',
+		'Utricularia_gibba', '13748',
+		'Vigna_radiata', '157791',
 		'Vitis_vinifera', '29760',
 		'Zea_mays', '4577',
+		'Zoysia_japonica.Nagirizaki', '309978',
+		'Zoysia_matrella.Wakaba', '38722',
+		'Zoysia_pacifica.Zanpa', '1070856',
 		);
 	my $taxon = $taxon_hash{$species};
 	return $taxon;
@@ -1426,7 +1452,7 @@ sub find_taxon {
 sub ensembl_gene {
 		my $gene_header = $_[0];
 		my ($gene, $type, $contig, $gene_alias, $transcript, $biotype, $description) = split(/\s/, $gene_header);
-		$transcipt =~ s/transcript\://;
+		$transcript =~ s/transcript\://;
 		return $transcript;
 }