Mercurial > repos > petr-novak > re_utils
view single_fastq_filtering_wrapper.sh @ 11:16150c85fb3a draft
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author | petr-novak |
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date | Tue, 04 Feb 2020 07:39:32 -0500 |
parents | a4cd8608ef6b |
children | 628b235d76c7 |
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#!/bin/bash #set -euo pipefail # this is something like string in perl IFS=$'\n\t' # run filtering WD="`dirname $0`" ORIDIR=$PWD cd $WD WD=$PWD # absolute path to this script cd $ORIDIR SAMPLING="" TRIM_END="" TRIM_START="" PERCENT_ABOVE="95" CUTADAPT="" FILTER_SEQ="" while getopts "a:o:n:c:p:e:s:N:C:G:F:" OPTION do case $OPTION in a) FASTAA=$OPTARG;; o) OUTPUT=$OPTARG;; n) SAMPLING=( -n ${OPTARG} );; c) CUT_OFF=$OPTARG;; p) PERCENT_ABOVE=$OPTARG;; e) TRIM_END=( -e ${OPTARG} );; s) TRIM_START=( -s ${OPTARG} );; N) MAX_N=${OPTARG};; C) CUTADAPT=(-C " "${OPTARG}" " );; G) PNG_OUTPUT=${OPTARG};; F) FILTER_SEQ=( -F ${OPTARG} );; esac done if [ -z "$CUTADAPT" ] # test if $CUTADAPT is empty then ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF\ -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N -G $PNG_OUTPUT ${FILTER_SEQ[@]} else ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" ${FILTER_SEQ[@]} fi