Mercurial > repos > petr-novak > re_utils
diff paired_fastq_filtering_wrapper.sh @ 0:a4cd8608ef6b draft
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author | petr-novak |
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date | Mon, 01 Apr 2019 07:56:36 -0400 |
parents | |
children | 628b235d76c7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paired_fastq_filtering_wrapper.sh Mon Apr 01 07:56:36 2019 -0400 @@ -0,0 +1,66 @@ +#!/bin/bash +set -euo pipefail +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="" +RENAME="" +FILTER_SEQ="" +while getopts "a:b:o:n:c:p:e:s:N:C:G:F:R" OPTION +do + case $OPTION in + a) + FASTAA=$OPTARG;; + b) + FASTAB=$OPTARG;; + o) + PAIRED_OUTPUT=$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};; + R) + RENAME="-R";; + F) + FILTER_SEQ=( -F ${OPTARG} );; + + esac +done +fasta_tmp_fileX=$(mktemp) +fasta_tmp_fileY=$(mktemp) + +if [ -z "$CUTADAPT" ] # test if$CUTADAPT is empty +then + ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ + -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N $RENAME ${FILTER_SEQ[@]} +else + ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ + -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" $RENAME ${FILTER_SEQ[@]} +fi + +${WD}/fasta_interlacer.py -a $fasta_tmp_fileX -b $fasta_tmp_fileY -p $PAIRED_OUTPUT -x fasta_tmp_single + + +rm $fasta_tmp_fileX +rm $fasta_tmp_fileY