txtToFastq.pl

#!/usr/bin/perl -sw

# sample inputs:
#ILLUMINA-A93428   66    1     1     7848  1267  CGATGT      1      ATGTTGGCTGGCGGTGAAATAAATCTCAAACGTACCTGTTACAAAATTGTGTTAATCCTTTCAGATTCGCAG      ggggggggggggggcfdffdgggfefffffcfcffcccacBeddddded_cffefgggggBBBBBBBBBBBB      chrX.fa           122287709   R     40C21GAC7   269                                 Y

# output for sample input:
#@ILLUMINA-A93428:66:1:1:7848:1267:#CGATGT/1
#ATGTTGGCTGGCGGTGAAATAAATCTCAAACGTACCTGTTACAAAATTGTGTTAATCCTTTCAGATTCGCAG
#+ILLUMINA-A93428:66:1:1:7848:1267:#CGATGT/1
#ggggggggggggggcfdffdgggfefffffcfcffcccacBeddddded_cffefgggggBBBBBBBBBBBB

# command line:
# perl txtToFastq.pl < sampleInput.txt > output.fastq


while (<>){
    chomp;
    my @parts = split (/\s+/, $_);
    print "@","$parts[0]:$parts[1]:$parts[2]:$parts[3]:$parts[4]:$parts[5]:#$parts[6]/$parts[7]\n";
    print "$parts[8]\n";
    print "+","$parts[0]:$parts[1]:$parts[2]:$parts[3]:$parts[4]:$parts[5]:#$parts[6]/$parts[7]\n";
    print "$parts[9]\n";
}