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1 #!/usr/bin/perl
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2
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3 #-------------------------------------------------------------------------------
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4 #
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5 # Read a VCF file (via STDIN), split EFF fields from INFO column into many lines
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6 # leaving one line per effect.
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7 #
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8 # Note: In lines having multiple effects, all other information will be
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9 # repeated. Only the 'EFF' field will change.
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10 #
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11 # Pablo Cingolani 2012
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12 #-------------------------------------------------------------------------------
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13
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14 $INFO_FIELD_NUM = 7;
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15
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16 while( $l = <STDIN> ) {
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17 # Show header lines
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18 if( $l =~ /^#/ ) { print $l; }
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19 else {
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20 chomp $l;
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21
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22 @t = @infos = @effs = (); # Clear arrays
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23
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24 # Non-header lines: Parse fields
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25 @t = split /\t/, $l;
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26
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27 # Get INFO column
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28 $info = $t[ $INFO_FIELD_NUM ];
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29
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30 # Parse INFO column
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31 @infos = split /;/, $info;
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32
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33 # Find EFF field
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34 $infStr = "";
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35 foreach $inf ( @infos ) {
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36 # Is this the EFF field? => Find it and split it
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37 if( $inf =~/^EFF=(.*)/ ) { @effs = split /,/, $1; }
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38 else { $infStr .= ( $infStr eq '' ? '' : ';' ) . $inf; }
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39 }
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40
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41 # Print VCF line
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42 if( $#effs <= 0 ) { print "$l\n"; } # No EFF found, just show line
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43 else {
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44 $pre = "";
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45 for( $i=0 ; $i < $INFO_FIELD_NUM ; $i++ ) { $pre .= ( $i > 0 ? "\t" : "" ) . "$t[$i]"; }
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46
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47 $post = "";
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48 for( $i=$INFO_FIELD_NUM+1 ; $i <= $#t ; $i++ ) { $post .= "\t$t[$i]"; }
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49
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50 foreach $eff ( @effs ) { print $pre . "\t" . $infStr . ( $infStr eq '' ? '' : ';' ) . "EFF=$eff" . $post . "\n" ; }
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51 }
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52 }
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53 }
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