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analytical_code/hmmfetch_toxic.sh

+#! /bin/bash -l
+
+hmmfetch="/work/projects/ecosystem_biology/local_tools/hmmer-3.1b1-linux-intel-x86_64/binaries/hmmfetch"
+
+#KEGG
+db=KEGG
+hmm_file=/work/projects/ecosystem_biology/data/hmm/KEGG/KO.hmm
+IDs=ID_mini_KEGG_newest_2.txt
+keggout_file=$db.hmm
+$hmmfetch -f $hmm_file $IDs >>$keggout_file
+
+#META-cyc
+#db=metacyc
+#hmm_file=/work/projects/ecosystem_biology/data/hmm/$db/$db.hmm
+#metacycout_file=$db.hmm
+#IDs=ID_mini_MetaCyc.txt
+#$hmmfetch -f $hmm_file $IDs >>$metacycout_file
+
+#Pfam
+db=Pfam-A
+hmm_file=/work/projects/ecosystem_biology/data/hmm/$db/$db.hmm
+pfamout_file=$db.hmm
+IDs=ID_mini_Pfam_newest_2.txt
+$hmmfetch -f $hmm_file $IDs >>$pfamout_file
+
+#TIGR
+db=tigrpfam
+hmm_file=/work/projects/ecosystem_biology/data/hmm/TIGRPFAM/$db.hmm
+tigrpfamout_file=$db.hmm
+IDs=ID_mini_TIGR_newest_2.txt
+$hmmfetch -f $hmm_file $IDs >>$tigrpfamout_file
+
+#swissprot
+db=swissprot
+hmm_file=/work/projects/ecosystem_biology/data/hmm/SwissProt/$db.hmm
+swissprotout_file=$db.hmm
+IDs=ID_mini_Swiss_newest_2.txt
+$hmmfetch -f $hmm_file $IDs >>$swissprotout_file