Mercurial > repos > hogart > unafold
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author | hogart |
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date | Tue, 10 Mar 2015 05:54:18 -0400 |
parents | 51baa0ab6def |
children |
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#!/bin/bash set -e #arguments are -i input sequence file in fasta # -o output zip arhive # -t temp directory with results # -a DNA|RNA # -c tempreature (C) # -s [Na+] in M # -m [Mg++] in M # -b maxbp #-n, --NA=(RNA | DNA) (defaults to RNA) #-t, --temp=<temperature> (defaults to 37) #-N, --sodium=<[Na+] in M> (defaults to 1) #-M, --magnesium=<[Mg++] in M> (defaults to 0) #-p, --polymer #-C, --Ct=<total strand concentration> #-I, --noisolate #-m, --maxbp=<maximum basepair distance> #-c, --constraints=<name of constraints file> (defaults to prefix.aux) #-P, --percent=<energy increment percent> (defaults to 5) #-W, --window=<window size> (default set by sequence length) #-X, --max=<maximum number of foldings> (defaults to 100) # --ann=(none | p-num | ss-count) (defaults to none) # --mode=(auto | bases | lines) (defaults to auto) # --label=<base numbering frequency> # --rotate=<structure rotation angle> # --run-type=(text | html) (defaults to text) # --model=(EM | PF) (defaults to EM) # --circular #Obscure options: # --allpairs # --maxloop=<maximum bulge/interior loop size> (defaults to 30) # --nodangle # --simple # --prefilter=<filter value> NA=RNA TM=37 NAT=1 MG=0 while getopts ":i:o:t:a:c:s:m:" OPTION; do case $OPTION in i) INPUT="$OPTARG";; o) ZIP_ARHIVE="$OPTARG";; t) TEMP_DIR="$OPTARG";; a) NA="$OPTARG";; c) TM="$OPTARG";; s) NAT="$OPTARG";; m) MG="$OPTARG";; esac done mkdir -p ${TEMP_DIR}/unafold cd ${TEMP_DIR}/unafold NA=$(echo $NA | tr '[:lower:]' '[:upper:]') # calucalation of RNA don't need the concentraion of salts if [[ ${NA} == 'DNA' ]]; then UNAFold.pl -n ${NA} -t ${TM} -N ${NAT} -M ${MG} ${INPUT} else UNAFold.pl -n ${NA} -t ${TM} ${INPUT} fi echo "" echo "Parametres of UNAFold run:" cat *run cd ../ zip -r -q unafold.zip unafold mv unafold.zip ${ZIP_ARHIVE}