Mercurial > repos > petr-novak > re_utils
view paired_fastq_filtering_wrapper.sh @ 32:628b235d76c7 draft
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
author | petr-novak |
---|---|
date | Fri, 04 Aug 2023 07:37:49 +0000 |
parents | a4cd8608ef6b |
children |
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#!/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 Rscript ${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 Rscript ${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 python ${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