Mercurial > repos > greg > snpeff_v2_from_pablo
comparison snpEff_2_1a/scripts/vcfEffOnePerLine.pl @ 0:f8eaa3f8194b default tip
Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
| author | greg |
|---|---|
| date | Fri, 20 Apr 2012 14:47:09 -0400 |
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| children |
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| -1:000000000000 | 0:f8eaa3f8194b |
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| 1 #!/usr/bin/perl | |
| 2 | |
| 3 #------------------------------------------------------------------------------- | |
| 4 # | |
| 5 # Read a VCF file (via STDIN), split EFF fields from INFO column into many lines | |
| 6 # leaving one line per effect. | |
| 7 # | |
| 8 # Note: In lines having multiple effects, all other information will be | |
| 9 # repeated. Only the 'EFF' field will change. | |
| 10 # | |
| 11 # Pablo Cingolani 2012 | |
| 12 #------------------------------------------------------------------------------- | |
| 13 | |
| 14 $INFO_FIELD_NUM = 7; | |
| 15 | |
| 16 while( $l = <STDIN> ) { | |
| 17 # Show header lines | |
| 18 if( $l =~ /^#/ ) { print $l; } | |
| 19 else { | |
| 20 chomp $l; | |
| 21 | |
| 22 @t = @infos = @effs = (); # Clear arrays | |
| 23 | |
| 24 # Non-header lines: Parse fields | |
| 25 @t = split /\t/, $l; | |
| 26 | |
| 27 # Get INFO column | |
| 28 $info = $t[ $INFO_FIELD_NUM ]; | |
| 29 | |
| 30 # Parse INFO column | |
| 31 @infos = split /;/, $info; | |
| 32 | |
| 33 # Find EFF field | |
| 34 $infStr = ""; | |
| 35 foreach $inf ( @infos ) { | |
| 36 # Is this the EFF field? => Find it and split it | |
| 37 if( $inf =~/^EFF=(.*)/ ) { @effs = split /,/, $1; } | |
| 38 else { $infStr .= ( $infStr eq '' ? '' : ';' ) . $inf; } | |
| 39 } | |
| 40 | |
| 41 # Print VCF line | |
| 42 if( $#effs <= 0 ) { print "$l\n"; } # No EFF found, just show line | |
| 43 else { | |
| 44 $pre = ""; | |
| 45 for( $i=0 ; $i < $INFO_FIELD_NUM ; $i++ ) { $pre .= ( $i > 0 ? "\t" : "" ) . "$t[$i]"; } | |
| 46 | |
| 47 $post = ""; | |
| 48 for( $i=$INFO_FIELD_NUM+1 ; $i <= $#t ; $i++ ) { $post .= "\t$t[$i]"; } | |
| 49 | |
| 50 foreach $eff ( @effs ) { print $pre . "\t" . $infStr . ( $infStr eq '' ? '' : ';' ) . "EFF=$eff" . $post . "\n" ; } | |
| 51 } | |
| 52 } | |
| 53 } |