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1 #!/bin/perl
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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: a.pl a.raw_splice trusted.plisce > filtered.splice\n" if ( @ARGV == 0 ) ;
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7
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8 my %trustedSplices ;
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9
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10 open FP1, $ARGV[1] ;
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11 while ( <FP1> )
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12 {
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13 chomp ;
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14 my @cols = split /\s+/, $_ ;
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15 my $key = $cols[0]." ".$cols[1]." ".$cols[2] ;
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16 $trustedSplices{ $key } = $cols[4] ;
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17 }
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18 close FP1 ;
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19
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20 open FP1, $ARGV[0] ;
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21 while ( <FP1> )
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22 {
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23 chomp ;
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24 my @cols = split /\s+/, $_ ;
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25 my $key = $cols[0]." ".$cols[1]." ".$cols[2] ;
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26 next if ( !defined $trustedSplices{ $key } ) ;
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27
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28 my $trustedStrand = $trustedSplices{ $key } ;
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29 if ( $cols[3] <= 0 )
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30 {
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31 print $cols[0], " ", $cols[1], " ", $cols[2], " 1 ", $trustedStrand, " 1 0 0 0\n" ;
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32 }
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33 else
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34 {
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35 if ( $cols[4] eq $trustedStrand )
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36 {
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37 print $_, "\n" ;
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38 }
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39 else
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40 {
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41 $cols[4] = $trustedStrand ;
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42 print join( " ", @cols ), "\n" ;
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43 }
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44 }
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45
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46 }
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47 close FP1 ;
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48
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