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1 #!/usr/bin/perl -w
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2
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3 use strict;
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4 use warnings;
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5
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6 die("Usage: qualfa2fq.pl <in.fasta> <in.qual>\n") if (@ARGV != 2);
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7
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8 my ($fhs, $fhq, $q);
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9 open($fhs, ($ARGV[0] =~ /\.gz$/)? "gzip -dc $ARGV[0] |" : $ARGV[0]) || die;
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10 open($fhq, ($ARGV[1] =~ /\.gz$/)? "gzip -dc $ARGV[1] |" : $ARGV[1]) || die;
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11
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12 $/ = ">"; <$fhs>; <$fhq>; $/ = "\n";
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13 while (<$fhs>) {
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14 $q = <$fhq>;
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15 print "\@$_";
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16 $/ = ">";
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17 $_ = <$fhs>; $q = <$fhq>;
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18 chomp; chomp($q);
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19 $q =~ s/\s*(\d+)\s*/chr($1+33)/eg;
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20 print $_, "+\n";
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21 for (my $i = 0; $i < length($q); $i += 60) {
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22 print substr($q, $i, 60), "\n";
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23 }
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24 $/ = "\n";
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25 }
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26
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27 close($fhs); close($fhq);
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