diff paired_fastq_filtering_wrapper.sh @ 0:a4cd8608ef6b draft

Uploaded

--- /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