Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff orthologs/ucsb_hamster/ucsb_galaxy_hamster.sh @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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--- /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