forgot to download

test/unpack.sh

@@ -2,7 +2,79 @@ set -xeu
 
 cd data
 
-tar axvf datafa.tar.xz
+function get {
+    SPP=$1
+    PREFIX=$2
 
-find . -name *.fasta | xargs -I{} bash -c 'f={}; bn=`basename $f`; ap=`echo $f | sed "s/\.fasta//"`; echo $f $bn $ap; mkdir $ap; mv $f ap'
+    if [[ ! -f "$SPP/$SPP.fasta" ]]; then
+        mkdir -p $SPP
+        cd $SPP
+        wget --no-clobber --continue --timeout=60 --tries=2 --random-wait ${PREFIX}*.fna
+        cat *.fna > ../$SPP.fasta
+        cd ..
+    fi
+}
+
+SPP=Aspergillus_fumigatus_uid14003
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Aspergillus_fumigatus_uid14003/
+get $SPP $PREFIX
+
+SPP=Aspergillus_nidulans_FGSC_A4_uid13961
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Aspergillus_nidulans_FGSC_A4_uid13961/
+get $SPP $PREFIX
+
+SPP=Aspergillus_niger_CBS_513_88_uid19263
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Aspergillus_niger_CBS_513_88_uid19263/
+get $SPP $PREFIX
+
+SPP=Aspergillus_oryzae_RIB40_uid28175
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Aspergillus_oryzae_RIB40_uid28175/
+get $SPP $PREFIX
+
+SPP=Candida_dubliniensis_CD36_uid38659
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Candida_dubliniensis_CD36_uid38659/
+get $SPP $PREFIX
+
+SPP=Candida_glabrata
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Candida_glabrata/
+get $SPP $PREFIX
+
+SPP=Candida_glabrata_CBS138_uid12376
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Candida_glabrata_CBS138_uid12376/
+get $SPP $PREFIX
+
+SPP=Cryptococcus_gattii_WM276
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Cryptococcus_gattii_WM276/
+get $SPP $PREFIX
+
+SPP=Cryptococcus_neoformans_var_JEC21_uid10698
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Cryptococcus_neoformans_var_JEC21_uid10698/
+get $SPP $PREFIX
+
+SPP=Kluyveromyces_lactis_NRRL_Y-1140_uid12377
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Kluyveromyces_lactis_NRRL_Y-1140_uid12377/
+get $SPP $PREFIX
+
+SPP=Neurospora_crassa_uid132
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Neurospora_crassa_uid132/
+get $SPP $PREFIX
+
+SPP=Saccharomyces_cerevisiae_uid128
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Saccharomyces_cerevisiae_uid128/
+get $SPP $PREFIX
+
+SPP=Schizosaccharomyces_pombe_uid127
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Schizosaccharomyces_pombe_uid127/
+get $SPP $PREFIX
+
+SPP=Yarrowia_lipolytica_CLIB122_uid12414
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Yarrowia_lipolytica_CLIB122_uid12414/
+get $SPP $PREFIX
+
+SPP=Zygosaccharomyces_rouxii_CBS_732_uid39573
+PREFIX=ftp://ftp.ncbi.nih.gov/genomes/Fungi/Zygosaccharomyces_rouxii_CBS_732_uid39573/
+get $SPP $PREFIX
+
+
+#find . -name *.fasta | xargs -I{} bash -c 'f={}; bn=`basename $f`; ap=`echo $f | sed "s/\.fasta//"`; echo $f $bn $ap; mkdir $ap; mv $f ap'