Create fqtk.sh

Author: Raymond Kiu

src/fqtk.sh

@@ -0,0 +1,146 @@
+#!/bin/bash
+#print the options
+usage () {
+  echo ""
+  echo "This program provides several scripts to perform common tasks on sequences in standard FASTQ format"
+  echo ""
+  echo "For user manual please go to: https://github.com/raymondkiu/fqtk"
+  echo ""
+  echo "Usage: fqtk [options] FASTQ"
+  echo ""
+  echo "Options:"
+  echo " -a Rename FASTQ identifier for FASTQ reads. Optionally with /1 or /2. Usage: ./fqtk -a R1.FASTQ NEWIDENTIFIER /1"
+  echo " -q Print FASTQ stats"
+  echo " -t Convert FASTQ to FASTA. Usage: ./fqtk -t FASTQ > NEWFILENAME"
+  echo " -r Print FASTQ stats in tabular format"
+  echo " -h Print usage and exit"
+  echo " -v Print version and exit"
+  echo ""
+  echo "Version 1.0 (2022)"
+  echo "Author: Raymond Kiu [email protected]"
+  echo "";
+}
+
+version (){
+echo "fqtk v1.0"
+}
+
+
+FILE=$2
+name=$3
+sequence=$4
+
+rename1(){
+if [ -e "$FILE" ];then
+:
+else
+    echo "$FILE file does not seem to exist. Program will now exit."
+    exit 1
+fi
+
+cat $FILE | awk '{print (NR%4 == 1) ? "@'$name'" ++i "'$sequence'": $0}' 
+}
+
+
+fastqstats () {
+if [ -e "$FILE" ];then
+:
+else
+    echo "$FILE file does not seem to exist. Program will now exit."
+    exit 1
+fi
+COUNT=$(cat $FILE|echo $((`wc -l`/4)))
+READ=$(awk 'NR % 4 == 2 { s += length($1); t++} END {print s/t}' $FILE)
+SIZE=$(awk 'BEGIN{sum=0;}{if(NR%4==2){sum+=length($0);}}END{print sum;}' $FILE)
+filesize=$(du -sh $FILE|awk '{print $1}')
+MaxRead=$(awk 'NR%4==2{print length($0)}' $FILE|sort -n|tail -n 1)
+MinRead=$(awk 'NR%4==2{print length($0)}' $FILE|sort -n|head -n 1)
+
+echo "Sample: $FILE"
+echo "File size: $filesize"
+echo "Total bases: $SIZE"
+echo "Reads: $COUNT"
+echo "Max read length: $MaxRead"
+echo "Min read length: $MinRead"
+echo "Mean read length: $READ"
+exit 0
+}
+fastq2fasta (){
+if [ -e "$FILE" ];then
+:
+else
+    echo "$FILE file does not seem to exist. Program will now exit."
+    exit 1
+fi
+
+sed -n '1~4s/^@/>/p;2~4p' $FILE
+}
+
+fastqtabular () {
+if [ -e "$FILE" ];then
+:
+else
+    echo "$FILE file does not seem to exist. Program will now exit."
+    exit 1
+fi
+COUNT=$(cat $FILE|echo $((`wc -l`/4)))
+READ=$(awk 'NR % 4 == 2 { s += length($1); t++} END {print s/t}' $FILE)
+SIZE=$(awk 'BEGIN{sum=0;}{if(NR%4==2){sum+=length($0);}}END{print sum;}' $FILE)
+filesize=$(du -sh $FILE|awk '{print $1}')
+MaxRead=$(awk 'NR%4==2{print length($0)}' $FILE|sort -n|tail -n 1)
+MinRead=$(awk 'NR%4==2{print length($0)}' $FILE|sort -n|head -n 1)
+
+# Print info in tabular format, -e is for backslash, -n for new line:
+echo -n -e "SampleID\t";
+echo -n -e "Size\t";
+echo -n -e "Total_bases\t";
+echo -n -e "Reads\t";
+echo -n -e "MaxRL\t";
+echo -n -e "MinRL\t";
+echo -e "MeanRL\t";
+
+echo -n -e "$FILE\t"
+echo -n -e "$filesize\t"
+echo -n -e "$SIZE\t"
+echo -n -e "$COUNT\t"
+echo -n -e "$MaxRead\t"
+echo -n -e "$MinRead\t"
+echo -e "$READ"
+exit 0
+}
+
+# Skip over processed options
+shift $((OPTIND-1))
+# check for mandatory positional parameters, only 1 positional argument will be checked
+if [ $# -lt 1 ]; then
+   echo "Missing optional argument or positional argument, please supply your fastq reads"
+   echo ""
+   echo "Options: ./fqtk -h"
+   echo ""
+   echo ""
+   exit 1
+fi
+
+# Call options
+while getopts ':aqtrhv' opt;do
+  case $opt in
+    a) rename1; exit;;
+    q) fastqstats; exit;;
+    t) fastq2fasta; exit;;
+    r) fastqtabular; exit;;
+    h) usage; exit;;
+    v) version; exit;;
+    \?) echo "Invalid option: -$OPTARG" >&2; exit 1;;
+    :) echo "Missing option argument for -$OPTARG" >&2; exit 1;;
+    *) echo "Unimplemented option: -$OPTARG" >&2; exit 1;;
+   esac
+done
+
+shift $((OPTIND-1))
+if [ $OPTIND -eq 1 ];then
+   echo "Missing optional argument"
+   echo ""
+   echo "Options: ./fqtk -h"
+   echo ""
+   exit 1
+fi