diff orthologs/ucsb_hamster/ucsb_galaxy_hamster.sh @ 0:5b9a38ec4a39 draft default tip

First commit of old repositories

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orthologs/ucsb_hamster/ucsb_galaxy_hamster.sh	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,87 @@
+#!/bin/sh
+# set -x
+# Uncomment 'set -x' for debug information
+
+#############################################
+# 		UCSB HAMSTER - GALAXY HISTORY 		#
+# 											#
+# Executed when user chooses Galaxy history #
+#############################################
+
+# Set your hamster script location here. The directory containing these scripts should be in 
+#your path
+script="hamstrsearch_local-hmmer3.pl"
+# Set your unbuild.py script location here
+unbuild="unbuild.py"
+# Set your emap2fasta.pl script location here
+emap2fasta="emap2fasta.pl"
+
+
+# 1 - Sequence input file
+# 2 - Proteins results output file
+# 3 - CDS results output file
+# 4 - Screen log
+# 5 - Species name
+# 6 -  whether to use EST flag D=DNA so use -est flag P=Protein so do not use -est flag in hmmstr call
+# 7 - HMM Input from UCSB HMMBUILD
+# 8 - MUSCLE data from UCSB MUSCLE
+# 9 - Reference Species File
+# 10 - Reference Species Name
+
+input=$1
+proteins=$2
+cdsfile=$3
+screenlog=$4
+speciesName=$5
+datatype=$6
+hmm_data=$7
+muscle_data=$8
+filepath=`pwd`
+tail="_prot"
+tail2="_temp"
+
+# set flag based on input
+if [ $datatype = "P" ];
+        then
+            	estflag="-protein"
+        else
+            	estflag="-est"
+fi
+
+refspfile=${9}
+refsphist=${10}
+
+
+
+echo "Protein or EST? : $estflag" >> $screenlog
+echo "Reference genome file from galaxy history: $refspfile" >> $screenlog
+echo "Reference species genome name: $refsphist" >> $screenlog
+
+# unbuild.py here on $hmm_data
+mkdir core
+mkdir core/hmm_dir
+cp $hmm_data core/core.fa
+
+$unbuild core/hmm_dir core/core.fa
+cp core/hmm_dir/hmmlist.txt core/hmmlist.txt
+
+# use formatdb to generate new blastdb from this input file
+refsphistGALAXY=$refsphist
+mkdir $refsphistGALAXY
+
+cp $muscle_data $refsphistGALAXY/$refsphist$tail2
+$emap2fasta $refsphistGALAXY/$refsphist$tail2 $refsphist
+cp full.fasta core/core.fa
+
+cp $refspfile $refsphistGALAXY/$refsphist$tail
+cd $refsphistGALAXY
+formatdb -t $refsphist -i $refsphist$tail -n $refsphist$tail
+
+echo "*** Direcotry Structure of Ref. Genome ***" >> $screenlog
+ls -l >> $screenlog
+echo >> $screenlog
+
+cd $filepath
+
+# script execution
+$script -sequence_file=$1 $estflag -taxon=$5 -hmmset=core -refspec=$refsphistGALAXY -galaxyout=$2 -2galaxyout=$cdsfile 2>log.txt >> $screenlog