Mercurial > repos > vipints > qseq2fastq

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