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1 #!/usr/bin/perl
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2
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3 #-------------------------------------------------------------------------------
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4 # Add 'Parent' option in mRNA lines
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5 #
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6 # Pablo Cingolani
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7 #-------------------------------------------------------------------------------
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8
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9 while( $l = <STDIN> ) {
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10 chomp $l;
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11 @t = split /\t/,$l;
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12
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13 $type = $t[2];
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14
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15 # Is it an mRNA?
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16 if( $type eq 'mRNA' ) {
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17 # Parse ID in options
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18 $opts = $t[8];
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19 if( $opts =~ /ID=(.*?)-\d+;/ ) {
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20 $pid = $1;
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21 $pid =~ tr/t/g/;
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22 # Add 'Parent' option
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23 $l .= ";Parent=$pid";
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24 }
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25 }
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26
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27 print "$l\n";
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28 }
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