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1 #!/usr/bin/perl -w
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2
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3 # Author: lh3
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4 # Note: Ideally, this script should be written in C. It is a bit slow at present.
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5 # Also note that this script is different from the one contained in MAQ.
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6
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7 use strict;
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8 use warnings;
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9 use Getopt::Std;
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10
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11 my %opts;
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12 my $version = '0.1.3';
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13 my $usage = qq{
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14 Usage: solid2fastq.pl <in.title> <out.prefix>
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15
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16 Note: <in.title> is the string showed in the `# Title:' line of a
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17 ".csfasta" read file. Then <in.title>F3.csfasta is read sequence
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18 file and <in.title>F3_QV.qual is the quality file. If
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19 <in.title>R3.csfasta is present, this script assumes reads are
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20 paired; otherwise reads will be regarded as single-end.
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21
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22 The read name will be <out.prefix>:panel_x_y/[12] with `1' for R3
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23 tag and `2' for F3. Usually you may want to use short <out.prefix>
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24 to save diskspace. Long <out.prefix> also causes troubles to maq.
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25
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26 };
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27
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28 getopts('', \%opts);
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29 die($usage) if (@ARGV != 2);
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30 my ($title, $pre) = @ARGV;
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31 my (@fhr, @fhw);
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32 my @fn_suff = ('F3.csfasta', 'F3_QV.qual', 'R3.csfasta', 'R3_QV.qual');
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33 my $is_paired = (-f "$title$fn_suff[2]" || -f "$title$fn_suff[2].gz")? 1 : 0;
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34 if ($is_paired) { # paired end
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35 for (0 .. 3) {
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36 my $fn = "$title$fn_suff[$_]";
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37 $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
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38 open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
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39 }
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40 open($fhw[0], "|gzip >$pre.read2.fastq.gz") || die; # this is NOT a typo
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41 open($fhw[1], "|gzip >$pre.read1.fastq.gz") || die;
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42 open($fhw[2], "|gzip >$pre.single.fastq.gz") || die;
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43 my (@df, @dr);
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44 @df = &read1(1); @dr = &read1(2);
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45 while (@df && @dr) {
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46 if ($df[0] eq $dr[0]) { # mate pair
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47 print {$fhw[0]} $df[1]; print {$fhw[1]} $dr[1];
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48 @df = &read1(1); @dr = &read1(2);
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49 } else {
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50 if ($df[0] le $dr[0]) {
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51 print {$fhw[2]} $df[1];
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52 @df = &read1(1);
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53 } else {
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54 print {$fhw[2]} $dr[1];
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55 @dr = &read1(2);
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56 }
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57 }
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58 }
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59 if (@df) {
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60 print {$fhw[2]} $df[1];
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61 while (@df = &read1(1, $fhr[0], $fhr[1])) {
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62 print {$fhw[2]} $df[1];
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63 }
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64 }
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65 if (@dr) {
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66 print {$fhw[2]} $dr[1];
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67 while (@dr = &read1(2, $fhr[2], $fhr[3])) {
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68 print {$fhw[2]} $dr[1];
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69 }
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70 }
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71 close($fhr[$_]) for (0 .. $#fhr);
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72 close($fhw[$_]) for (0 .. $#fhw);
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73 } else { # single end
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74 for (0 .. 1) {
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75 my $fn = "$title$fn_suff[$_]";
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76 $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
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77 open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
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78 }
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79 open($fhw[2], "|gzip >$pre.single.fastq.gz") || die;
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80 my @df;
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81 while (@df = &read1(1, $fhr[0], $fhr[1])) {
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82 print {$fhw[2]} $df[1];
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83 }
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84 close($fhr[$_]) for (0 .. $#fhr);
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85 close($fhw[2]);
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86 }
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87
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88 sub read1 {
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89 my $i = shift(@_);
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90 my $j = ($i-1)<<1;
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91 my ($key, $seq);
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92 my ($fhs, $fhq) = ($fhr[$j], $fhr[$j|1]);
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93 while (<$fhs>) {
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94 my $t = <$fhq>;
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95 if (/^>(\d+)_(\d+)_(\d+)_[FR]3/) {
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96 $key = sprintf("%.4d_%.4d_%.4d", $1, $2, $3); # this line could be improved on 64-bit machines
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97 die(qq/** unmatched read name: '$_' != '$_'\n/) unless ($_ eq $t);
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98 my $name = "$pre:$1_$2_$3/$i";
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99 $_ = substr(<$fhs>, 2);
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100 tr/0123./ACGTN/;
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101 my $s = $_;
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102 $_ = <$fhq>;
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103 s/^(\d+)\s*//;
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104 s/-1\b/0/eg;
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105 s/(\d+)\s*/chr($1+33)/eg;
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106 $seq = qq/\@$name\n$s+\n$_\n/;
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107 last;
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108 }
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109 }
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110 return defined($seq)? ($key, $seq) : ();
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111 }
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