Updated the species detection for new species, still need to do gene headers

svn path=/; revision=24

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 1e6c16ed760aa23786d6fbb6dbe24851cccec97a..eaf444dc47f903abe6a36c4d19aa46725114d237 100755 (executable)
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -2,58 +2,92 @@
 #  Common subroutines to find the species from the        #
 #    string (filename) and the gene from the gene header  #
 #                                                         #
+#   Written by Justin Elser                               #
+#     Updated 9/2/10 for new species                      #
 ###########################################################
 
 sub find_species {
        my $temp = $_[0];
-       if ($temp =~ /Arabidopsis/) {
-               $temp = "Ath";
-       }elsif ($temp =~ /brachypodium/) {
-               $temp = "Brachy";
+       if ($temp =~ /Arabidopsis\_lyrata/) {
+               $temp = "Arabidopsis_lyrata";
+       }elsif ($temp =~ /Arabidopsis\_thaliana/) {
+               $temp = "Arabidopsis_thaliana";
+       }elsif ($temp =~ /Batrachochytrium/) {
+               $temp = "Batrachochytrium_distachyon";
+       }elsif ($temp =~ /Brachypodium/) {
+               $temp = "Brachypodium_distachyon";
        }elsif ($temp =~ /elegans/) {
-               $temp = "C_elegans";
+               $temp = "Caenorhabditis_elegans";
+       }elsif ($temp =~ /Carica\_papaya/) {
+               $temp = "Carica_papaya";
        }elsif ($temp =~ /Chlamy/) {
-               $temp = "Chlamy";
+               $temp = "Chlamydomonas_reinhardtii";
+       }elsif ($temp =~ /Cucumis\_sativus/) {
+               $temp = "Cucumis_sativus";
        }elsif ($temp =~ /Danio/) {
-               $temp = "Danio";
-       }elsif ($temp =~ /E\_coli/) {
-               $temp = "E_coli";
+               $temp = "Danio_rerio";
+       }elsif ($temp =~ /Drosophila/) {
+               $temp = "Drosophila_melanogaster";
+       }elsif ($temp =~ /Ectocarpus/) {
+               $temp = "Ectocarpus_siliculosus";
+       }elsif ($temp =~ /Escherichia\_coli/) {
+               $temp = "Escherichia_coli";
        }elsif ($temp =~ /Fragaria/) {
-               $temp = "Fragaria";
+               $temp = "Fragaria_vesca";
        }elsif ($temp =~ /Glycine/) {
-               $temp = "Glycine";
+               $temp = "Glycine_max";
        }elsif ($temp =~ /Homo\_sapiens/) {
-               $temp = "Human";
-       }elsif ($temp =~ /Maize/) {
-               $temp = "Maize";
-       }elsif ($temp =~ /musculus/) {
-               $temp = "Mouse";
-       }elsif ($temp =~ /neurospora/) {
-               $temp = "Neurospora";
+               $temp = "Homo_sapiens";
+       }elsif ($temp =~ /Laccaria/) {
+               $temp = "Laccaria_bicolor";
+       }elsif ($temp =~ /Magnaporthe/) {
+               $temp = "Magnaporthe_grissa";
+       }elsif ($temp =~ /Manihot/) {
+               $temp = "Manihot_esculenta";
+       }elsif ($temp =~ /Medicago/) {
+               $temp = "Medicago_truncatula";
+       }elsif ($temp =~ /Mimulus/) {
+               $temp = "Mimulus_guttatus";
+       }elsif ($temp =~ /Mus\_musculus/) {
+               $temp = "Mus_musculus";
+       }elsif ($temp =~ /Neurospora/) {
+               $temp = "Neurospora_crassa";
+       }elsif ($temp =~ /Nostoc/) {
+               $temp = "Nostoc_punctiforme";
        }elsif ($temp =~ /Oryza\_sativa/) {
                $temp = "Oryza_sativa";
-       }elsif ($temp =~ /Cpapaya/) {
-               $temp = "Carica_papaya";
+       }elsif ($temp =~ /Pediculus/) {
+               $temp = "Pediculus_humanus";
        }elsif ($temp =~ /Physcomit/) {
-               $temp = "Physcomitrella";
+               $temp = "Physcomitrella_patens";
        }elsif ($temp =~ /Populus/) {
-               $temp = "Poplar";
-       }elsif ($temp =~ /Ppersica/) {
-               $temp = "P_persica";
+               $temp = "Populus_trichocarpa";
+       }elsif ($temp =~ /Prunus/) {
+               $temp = "Prunus_persica";
+       }elsif ($temp =~ /Rattus/) {
+               $temp = "Rattus_norvegicus";
+       }elsif ($temp =~ /Rhizopus/) {
+               $temp = "Rhizopus_oryzae";
+       }elsif ($temp =~ /Ricinus/) {
+               $temp = "Ricinus_communis";
        }elsif ($temp =~ /cerevisiae/) {
-               $temp = "Sacc_cerevisiae";
+               $temp = "Saccharomyces_cerevisiae";
        }elsif ($temp =~ /pombe/) {
-               $temp = "Schizo_pombe";
+               $temp = "Schizosaccharomyces_pombe";
        }elsif ($temp =~ /Selaginella/) {
-               $temp = "Selaginella";
+               $temp = "Selaginella_moellendorffii";
        }elsif ($temp =~ /Sorghum/) {
-               $temp = "Sorghum";
+               $temp = "Sorghum_bicolor";
        }elsif ($temp =~ /Synechocystis/) {
-               $temp = "Synechocystis";
+               $temp = "Synechocystis_pcc6803";
+       }elsif ($temp =~ /Trichodesmium/) {
+               $temp = "Trichodesmium_erythraeum";
        }elsif ($temp =~ /Vitis\_vinifera/) {
-               $temp = "Vitis";
+               $temp = "Vitis_vinifera";
+       }elsif ($temp =~ /Zea\_mays/) {
+               $temp = "Zea_mays";
        }else {
-               die "Error: Species can not be found from file name!";
+               die "Error: Species can not be found from file name $temp!";
        }
        return $temp;
 }
@@ -130,7 +164,7 @@ sub find_gene {
                my ($name,$gene_id,$chrom_id,$id) = split(/\|/,$gene_header);
                $gene = $gene_id; #???
        }else {
-               die "Error: Gene id can not be found!";
+               die "Error: Gene id can not be found for species $species!";
        }
        return $gene;
 }