code snip to decide Phred encoding of FASTQ file

It's a common task to check the Phred quality score encoding of fastq file. Sure, it's fairly easy to check this by eyes (according to the rul below), and also there might be already some tools for that purpose.  The task is essentially a problem of converting ASCII character into its decimal format.

  SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS.....................................................
  ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......................
  ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII......................
  .................................JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ......................
  LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL....................................................
  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
  |                         |    |        |                              |                     |
 33                        59   64       73                            104                   126

 S - Sanger        Phred+33,  raw reads typically (0, 40)
 X - Solexa        Solexa+64, raw reads typically (-5, 40)
 I - Illumina 1.3+ Phred+64,  raw reads typically (0, 40)
 J - Illumina 1.5+ Phred+64,  raw reads typically (3, 40)
    with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold) 
    (Note: See discussion above).
 L - Illumina 1.8+ Phred+33,  raw reads typically (0, 41)

To be simple, I just wrote a line of code for that, by only looking the first lines of reads. Here it is:

head input.fastq | 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!";}'

To use it, you can also save it into a bash, like

#!/bin/sh

inputfile=$1

# Update: The following part for checking the file extension can be simplified (Thanks to the comment from Unknown) 
[[ "$inputfile" =~ ".*\.(fq\.gz$|fastq\.gz$)" ]] && zcat $inputfile | head -n40 ...
[[ "$inputfile" =~ ".*\.(fq$|fastq$)" ]] && head -n40 $inputfile | ...

less $inputfile | head -n40 | 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!";}'

The only trick is the command od, which is to display/convert file content in a specific format. Here is the more detail for od (http://publib.boulder.ibm.com/infocenter/pseries/v5r3/index.jsp?topic=/com.ibm.aix.cmds/doc/aixcmds4/od.htm).