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 (executable)
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 10716bcb01c5eef47d85610080ebd7b0a7e2312b..f7ff44271641eef16b4b17a8d3c8e73242274fc8 100755 (executable)
--- 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;
 }