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1 #!/usr/bin/env perl
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2
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3 use warnings;
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4 use strict;
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5 use Getopt::Long;
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6 use File::Basename;
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7
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8 # VALIDATE INPUT
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9 die("Expected 3 args") unless @ARGV == 3;
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10 my ($sff, $extra_files_path, $fastq) = @ARGV;
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11
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12 # DEFINE PATHS
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13 mkdir($extra_files_path) unless -d $extra_files_path;
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14 my $base = basename($sff);
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15 my $fasta = "$extra_files_path/$base.fasta";
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16 my $qual = "$extra_files_path/$base.qual";
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17
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18 # GENERATE FASTA, QUAL, FASTQ
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19 my $outf;
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20 my $out;
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21 eval { $out=`sffinfo -seq $sff > $fasta` };
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22 die("ERROR: $out") if $@;
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23 print $out;
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24 eval { $out=`sffinfo -qual $sff > $qual` };
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25 die("ERROR: $out") if $@;
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26 print $out;
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27 eval { $out=`fasta_qual_to_fastq $fasta $qual $fastq` };
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28 die("ERROR: $out") if $@;
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29 print $out;
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30 unlink($fasta, $qual);
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31 exit 0;
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