check Fastq ( Phred+33 or Phred+64 ) ( shell script )

checkFastq.sh

#!/bin/sh

inputfile=$1

# you can add friendly code to check the extension and use zcat if it's *.fastq.gz or *.fq.gz...

[[ "$inputfile" =~ ".*\.(fq\.gz$|fastq\.gz$)" ]] && zcat $inputfile | head -n400 | awk '{if(NR%4==0) printf("%s",$0);}' |  od -A n -t u1 | awk 'BEGIN{min=100;max=0;}{for(i=1;i<=NF;i++) {if($i>max) max=$i; if($i<min) min=$i;}}END{if(max<=74 && min<59) print "Phred+33"; else if(max>73 && min>=64) print "Phred+64"; else if(min>=59 && min<64 && max>73) print "Solexa+64"; else print "Unknown score encoding!";}'


[[ "$inputfile" =~ ".*\.(fq$|fastq$)" ]] && head -n400 $inputfile | awk '{if(NR%4==0) printf("%s",$0);}' |  od -A n -t u1 | awk 'BEGIN{min=100;max=0;}{for(i=1;i<=NF;i++) {if($i>max) max=$i; if($i<min) min=$i;}}END{if(max<=74 && min<59) print "Phred+33"; else if(max>73 && min>=64) print "Phred+64"; else if(min>=59 && min<64 && max>73) print "Solexa+64"; else print "Unknown score encoding!";}'

ls_fastq.sh

#/usr/bin/env sh

if [ $# -ge 1 ]
    then
      dir=$1
    else
      dir="./"
fi

for i0 in $dir/*.fastq
    do
       # dir=${i0%/*.fastq}
        i=${i0##*/}
        if [ "$i" == "*.fastq" ]
            then
              echo "no fastq in this directory"
              break
        fi
        j2=${i%_1.fastq}
        mate2="${j2}_2.fastq"
        j1=${i%_2.fastq}
        mate1="${j1}_1.fastq"
       if [ ! -f "$dir/$mate1" ]
       then
        if [ -f "$dir/$mate2" ]
            then
               echo "paired end $i $mate2"
            else
              echo "single end $i"
        fi
       fi 
    done

ls_fq.sh

#/usr/bin/env sh

if [ $# -ge 1 ]
    then
      dir=$1
    else
      dir="./"
fi
for i0 in $dir/*.fq
    do
       # dir=${i0%/*.fq}
        
        i=${i0##*/}
        if [ "$i" == "*.fq" ]
            then
              echo "no fq in this directory"
              break
        fi
        j2=${i%_1.fq}
        mate2="${j2}_2.fq"
        j1=${i%_2.fq}
        mate1="${j1}_1.fq"
       if [ ! -f "$dir/$mate1" ]
       then
        if [ -f "$dir/$mate2" ]
            then
               echo "paired end $i $mate2"
            else
              echo "single end $i"
        fi
       fi 
    done