phasiHunter

#!/bin/bash
# ----------> declaration variables <------------
tmp=`which phasiHunter`
wd=${tmp%/*}

# ----------> parameter capture start <------------
if [ "$#" -eq 0 ] ; then echo -e "type ${0##*/} -h for help message"
    exit 1
fi
if [ $1 = '-h' ]
then
echo "Usage:
    phasiHunter subcommand options 

subcommand:
    run:            one command executing mode, config.yaml file required
    preprocess:     generating map file for phasiRNA cluster prediction
    phase:          predicting phasiRNA cluster based on multiple reference sequences
    integration:    integrating phase module output
    visulization:   for phasiRNA cluster visulization
    target:         for sRNA target gene prediction
    initiator:      for phasiRNA initiator prediction
    deg:            for phasiRNA initiator or phasiRNA target gene verrification based on degradome verrification

type phasiHunter subcommad -h for more subcommad detail"
exit 1
fi

if [ "$#" -gt 0 ]
    then
    for (( i=1; i<="$#"; i++ )) ; do
        case ${!i} in
            -v)
                echo "phasiHunter version 1.0"
                exit 1
                ;;
        esac
    done
fi
# ----------> parameter capture end<------------

tmp=(`echo $@`)
parameter=${tmp[@]:1:$#}

[ $1 != 'preprocess' ] || bash $wd/bin/preprocess.sh $parameter
[ $1 != 'phase' ] || python3 $wd/bin/phase.py $parameter
[ $1 != 'integration' ] || python3 $wd/bin/integration.py $parameter
[ $1 != 'visulization' ] || python3 $wd/bin/visualization.py $parameter
[ $1 != 'initiator' ] || python3 $wd/bin/initiator.py $parameter
if [ $1 = 'target' ]; then
    if [[ $parameter == *-t* ]]; then
        perl $wd/bin/TarHunterL_Modified.pl $parameter
    else
        perl $wd/bin/TarHunterL_Modified.pl $parameter "-t"
    fi
fi
[ $1 != 'deg' ] || python3 $wd/bin/deg.py $parameter
[ $1 != 'read' ] || python3 $wd/bin/readstdin.py $parameter
[ $1 != 'run' ] || python3 $wd/bin/run.py $parameter