FluxToTab.pl

#!/usr/bin/perl
use strict;
use warnings;

my $credits = "Written by Miente Martijn Terpstra from UMCG Department of Genetics subgroup oncogentics last modified [Thu Jul  4 16:35:29 CEST 2013]";


my $exampleGTF = <<"END";
chr1	HAVANA	transcript	12010	13670	.	+	.	transcript_id "ENST00000450305.2"; locus_id "chr1:11869-14412W"; gene_id "ENSG00000223972.4"; reads 0.000000; length 632; RPKM 0.000000
chr1	HAVANA	transcript	11869	14409	.	+	.	transcript_id "ENST00000456328.2"; locus_id "chr1:11869-14412W"; gene_id "ENSG00000223972.4"; reads 232.000000; length 1657; RPKM 6.344208
chr1	ENSEMBL	transcript	11872	14412	.	+	.	transcript_id "ENST00000515242.2"; locus_id "chr1:11869-14412W"; gene_id "ENSG00000223972.4"; reads 0.000000; length 1653; RPKM 0.000000
chr1	ENSEMBL	transcript	11874	14409	.	+	.	transcript_id "ENST00000518655.2"; locus_id "chr1:11869-14412W"; gene_id "ENSG00000223972.4"; reads 0.000000; length 1483; RPKM 0.000000
chr1	ENSEMBL	transcript	30366	30503	.	+	.	transcript_id "ENST00000408384.1"; locus_id "chr1:29554-31109W"; gene_id "ENSG00000221311.1"; reads 0.000000; length 138; RPKM 0.000000
chr1	HAVANA	transcript	30267	31109	.	+	.	transcript_id "ENST00000469289.1"; locus_id "chr1:29554-31109W"; gene_id "ENSG00000243485.1"; reads 0.000000; length 535; RPKM 0.000000
chr1	HAVANA	transcript	29554	31097	.	+	.	transcript_id "ENST00000473358.1"; locus_id "chr1:29554-31109W"; gene_id "ENSG00000243485.1"; reads 56.000000; length 712; RPKM 3.563855
chr1	HAVANA	transcript	62948	63887	.	+	.	transcript_id "ENST00000492842.1"; locus_id "chr1:62948-63887W"; gene_id "ENSG00000240361.1"; reads 0.000000; length 940; RPKM 0.000000
chr1	HAVANA	transcript	69091	70008	.	+	.	transcript_id "ENST00000335137.3"; locus_id "chr1:69091-70008W"; gene_id "ENSG00000186092.4"; reads 36.000000; length 918; RPKM 1.776936
chr1	HAVANA	transcript	131104	133923	.	+	.	transcript_id "ENST00000442987.2"; locus_id "chr1:131104-133923W"; gene_id "ENSG00000233750.2"; reads 522.000000; length 2820; RPKM 8.387516
END

my $use = <<"END";
	simple fluxCapacitor.txt to tab reader
	use:
	$0 fluxCapacitor.gff > fluxCapacitor.table
	this should be flexable and is tested with flux-capacitor version 1.2.2 + the gencode.v13.annotation_corrected_statuses.gff + ucsc hg19
	input should look like:'
	$exampleGTF'
	
	$credits
	
END

my $script;
################################################################################
#no arg cathching
if (scalar(@ARGV)==0){
print $use;
exit(0);
}
#file input#####################################################
my $file = shift(@ARGV);
#my $basename = $file
#$basename =~ s/.fluxCapacitor.txt//;
#check max amount of fields#####################################################
open(my $in,'<', $file)or die "$0: failed to open script:'$file'!!!!\n$!\n";
my $fieldIndex = 0;
my %fields;
while(<$in>){
	my %gtfline = &readFlux($_);
	for my $key (keys(%gtfline)){
		if( not($fields{$key}) ){
		 $fields{$key} = $fieldIndex;
		 $fieldIndex++;
		}
	}	
}
close $in or die "write error cannot close $file\n";
	my @sortedkeyFields = sort(keys(%fields));
#reformat to tab################################################################



open(my $in2,'<', $file)or die "$0: failed to open script:'$file'!!!!\n$!\n";
my $first = 0;

for my $key (@sortedkeyFields){
		if($first == 0){
			if($key){
				print $key;
			}
		}else{
			if($key){
				print "\t".$key;
			}
		} 
		$first++;
}
print "\n";

while(<$in2>){
	my %gtfline = &readFlux($_);
	$first = 0;

	for my $key (@sortedkeyFields){
		if($first == 0){
			if($gtfline{$key}){
				print $gtfline{$key};
			}else{
				print "\t";
			}
		}else{
			if($gtfline{$key}){
				print "\t".$gtfline{$key};
			}else{
				print "\t";
			}
		} 
		$first++;
	}
	print "\n";
	
#	exit();
}
close $in2 or die "write error cannot close $file\n";

################################################################################

sub readFlux {
	my $inputline = shift @_;
	chomp $inputline;
	
	my @tabdelim;
	@tabdelim = split("\t",$inputline);
	
	my %gtfParsed;
	$gtfParsed{"CHROM"} = $tabdelim[0];
	$gtfParsed{"ANNOTATIONSCOURCE"} = $tabdelim[1];
	$gtfParsed{"ANNOTATIONTYPE"} = $tabdelim[2];
	$gtfParsed{"START"} = $tabdelim[3];
	$gtfParsed{"END"} = $tabdelim[4];
	$gtfParsed{"COL6"} = $tabdelim[5];
	$gtfParsed{"STRAND"} = $tabdelim[6];
	$gtfParsed{"COL8"} = $tabdelim[7];
	$gtfParsed{"INFO"} = $tabdelim[8];
	
	my @semicolomndelimINFO;
	@semicolomndelimINFO = split(';',$gtfParsed{"INFO"});
	
	for my $element (@semicolomndelimINFO){
		my @spacedelim = split(' ',$element);
		if($spacedelim[0] ne "" && $spacedelim[1] ne "" && not($spacedelim[2]) ){
			$gtfParsed{$spacedelim[0]} = $spacedelim[1];
		}elsif($spacedelim[0] eq "" && $spacedelim[1] ne "" && $spacedelim[2] ne "" ){
			$gtfParsed{$spacedelim[1]} = $spacedelim[2];
		}elsif($spacedelim[0] eq "" && $spacedelim[1] ne "" && $spacedelim[2] ne "" ){
			$gtfParsed{$spacedelim[1]} = $spacedelim[2];
		}else{
			die "incomplete datapairs in the INFO column!!!!on line: '$.'\non infotag:'".$gtfParsed{"INFO"}."'\n$!";
		}	
	}
	return %gtfParsed;
}