Mercurial > repos > vipints > qseq2fastq

comparison qseq2fastq/qseq2fastq.pl @ 0:6682236a1432 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author vipints
date Tue, 07 Jun 2011 17:42:46 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:6682236a1432
1 #!/usr/bin/perl -w
2 use strict;
3 use Carp;
4
5 my $usage = q(
6 qseq2fastq.pl - a script to convert all qseq files in a directory into a single fastq file with sanger-style ASCII q-score encoding
7 USAGE: qseq2fastq.pl <qseq.txt file> <output file>
8 );
9
10 if (scalar(@ARGV) != 2) {
11 print $usage;
12 exit;
13 }
14
15 my $in_file = $ARGV[0];
16 my $output_fastq_file = $ARGV[1];
17
18 my $qfilter = "";
19 open(OUTFASTAQFILE, "> $output_fastq_file");
20
21 open INFILE, "< $in_file" || die "Error: Couldn't open $in_file\n";
22 while(<INFILE>)
23 {
24 chomp;
25 my @this_line = split/\t/, $_;
26 croak("Error: invalid column number in $in_file\n") unless(scalar(@this_line) == 11);
27 if($this_line[10] == 1) {
28 $qfilter = "Y";
29 } else {
30 $qfilter = "N";
31 }
32 # Convert quality scores
33 my @quality_array = split(//, $this_line[9]);
34 my $phred_quality_string = "";
35 # convert each char to Phred quality score
36 foreach my $this_char (@quality_array){
37 my $phred_quality = ord($this_char) - 64; # convert illumina scaled phred char to phred quality score
38 my $phred_char = chr($phred_quality + 33); # convert phred quality score into phred char (sanger style)
39 $phred_quality_string = $phred_quality_string . $phred_char;
40 }
41 # replace "." gaps with N
42 $this_line[8] =~ s/\./N/g;
43 # output line
44 print OUTFASTAQFILE "@" . $this_line[2] . ":" . $this_line[3] . ":" . $this_line[4] . ":" . $this_line[5] . ":" . $qfilter . "\n" . #header line
45 $this_line[8] . "\n" . # output sequence
46 "+" . $this_line[2] . ":" . $this_line[3] . ":" . $this_line[4] . ":" . $this_line[5] . ":" . $qfilter . "\n" . # header line
47 $phred_quality_string . "\n"; # output quality string
48 }
49 close INFILE;
50 close OUTFASTAQFILE;
51 exit;