index.pl

#!/bin/bash
for genome

in Trichomonas_vaginalis Trypanosoma_brucei Plasmodium_yoelii Plasmodium_vivax Paramecium_tetraurelia Plasmodium_knowlesi Phytophthora_infestans Plasmodium_gallinaceum Plasmodium_falciparum Leishmania_major Leishmania_infantum Cryptosporidium_hominis Babesia_bigemina Toxoplasma_gondii_GT1 Perkinsus_marinus Plasmodium_chabaudi Plasmodium_berghei Neospora_caninum Leishmania_mexicana Leishmania_braziliensis Eimeria_tenella Entamoeba_invadens Emiliania_huxleyi Entamoeba_dispar Dictyostelium_purpureum Acanthamoeba_castellanii Aureococcus_anophagefferens Thalassiosira_pseudonana Theileria_parva Trypanosoma_cruzi Theileria_annulata Phytophthora_sojae Phytophthora_ramorum Monosiga_brevicollis Giardia_intestinalis Entamoeba_terrapinae Entamoeba_histolytica Babesia_bovis;

do {

blastdb=`grep $genome /cursos/BI/genomes/protists/genomes_list_and_info.tab | cut -f 4`
fastaindex $blastdb ~/novell/home/treball/eEFsec/$genome.index
fastaindex $blastdb ~/novell/home/treball/Fep15/$genome.index
fastaindex $blastdb ~/novell/home/treball/Lmsel1/$genome.index
fastaindex $blastdb ~/novell/home/treball/SBP2/$genome.index
fastaindex $blastdb ~/novell/home/treball/Sel3/$genome.index
fastaindex $blastdb ~/novell/home/treball/Sel15/$genome.index
fastaindex $blastdb ~/novell/home/treball/SelM/$genome.index
fastaindex $blastdb ~/novell/home/treball/SelP/$genome.index
fastaindex $blastdb ~/novell/home/treball/SelU/$genome.index
fastaindex $blastdb ~/novell/home/treball/Sps2/$genome.index

} done