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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} | +
| + | + | +