diff PanExplorer_workflow/Perl/CreateGenePathsFromGFA.pl @ 1:032f6b3806a3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PanExplorer_workflow/Perl/CreateGenePathsFromGFA.pl	Thu May 30 11:16:08 2024 +0000
@@ -0,0 +1,180 @@
+#!/usr/bin/perl
+
+use strict;
+
+
+
+my $gfa = $ARGV[0];
+my $gff3 = $ARGV[1];
+my $out = $ARGV[2];
+
+my %segment_is_covered_by_genes;
+my %coordinates;
+my %store_gene_paths;
+
+my %allgenes;
+my %coding_positions;
+open(LENGTH,">$out.gene_length.txt");
+open(F,$gff3);
+while(my $line = <F>){
+		chomp($line);
+		my @infos = split(/\t/,$line);
+		#if ($infos[2] eq "gene" && /CITME_006g014440/){
+		if ($infos[2] eq "CDS"){
+			my $chr;
+			# case eukaryotes
+			if ($line =~/Parent=([^;]+);*/){
+				$chr = $infos[0];
+			}
+			# case prokaryotes/prokka
+			elsif ($line =~/ID=([^;]+);*/){
+				$chr = $infos[0];
+			}
+			my $start = $infos[3];
+			my $end = $infos[4];
+			my $gene = $1;
+			$gene =~s/\n//g;$gene =~s/\r//g;
+			if ($line =~/protein_id=([^;]+);/){
+				$gene = $1;
+			}
+			$coordinates{$chr}.= "$gene:$start-$end|";
+			for (my $i = $start; $i <= $end; $i++){
+				$allgenes{$gene}=1;
+				$coding_positions{$chr}{$i} = "$gene,";
+			}
+			my $genelength = $end-$start;
+			print LENGTH "$gene	$genelength\n";
+		}
+}
+close(F);
+close(LENGTH);
+
+print "Start GFA parsing ($gfa)...\n";
+
+my %segments_chr;
+my %segments_of_gene;
+my %segments;
+#open(ZCAT,"zcat $gfa |");
+open(GFA,$gfa);
+while(my $line = <GFA>){
+	chomp($line);
+	if ($line =~/^S/){
+		my ($type,$segment,$segment_sequence,$SN,$tag) = split(/\t/,$line);
+		$segments{$segment} = $segment_sequence;
+	}
+	elsif ($line =~/^P/ or $line =~/^W/){
+
+		my $path;
+		my $chrom;
+		my @segments;
+		if ($line =~/^W/){
+	                my ($type,$sample,$strand,$chromW,$start,$length,$pathW) = split(/\t/,$line);
+			$path = $pathW;
+			$chrom = $chromW;
+			@segments = split(/[\>\<]/,$path);
+		}
+		elsif ($line =~/^P/){
+			my ($type,$strain_chrom,$pathP) = split(/\t/,$line);
+			my ($stra,$chromP) = split(/#/,$strain_chrom);
+			$path = $pathP;
+			$chrom = $chromP;
+			@segments = split(/,/,$path);
+		}
+		$chrom =~s/\.\d+$//g;
+		my @genes = split(/\|/,$coordinates{$chrom});
+		if ($coordinates{$chrom}){
+			my $end_segment = 0;
+			my $start_segment = 0;
+			my $nb_gene = 0;
+			
+			my %genes_located;
+			my %first_segment_of_gene;
+			print "$chrom: ". scalar @segments."\n";
+			my $cumul = 0;
+			LOOP_SEGMENT: foreach my $segment(@segments){
+				if ($segment eq ""){next;}
+				my $segment_including_strand = $segment;
+				$segment =~s/\+//g;
+				$segment =~s/\-//g;
+				my $size = length($segments{$segment});
+				$start_segment = $end_segment+1;
+				$end_segment = $start_segment+$size-1;
+				$cumul+=$size;
+				my $current_gene;
+
+				if ($segment_including_strand =~/\+/){
+					my $pos_in_segment = 0;
+					for (my $k = $start_segment; $k <= $end_segment; $k++){
+						$pos_in_segment++;
+						#print "$k\n";
+					
+						if ($coding_positions{$chrom}{$k}){
+							my $info_gene = $coding_positions{$chrom}{$k};
+							chop($info_gene);
+							my @genes = split(/,/,$info_gene);
+							foreach my $gene(@genes){
+								$segments_of_gene{$gene} .= "s$segment:$pos_in_segment|";
+							}
+						}				
+					}
+				}
+				elsif ($segment_including_strand =~/\-/){
+					my $pos_in_segment = $size+1;
+					for (my $k = $start_segment; $k <= $end_segment; $k++){
+						$pos_in_segment--;
+						if ($coding_positions{$chrom}{$k}){
+							my $info_gene = $coding_positions{$chrom}{$k};
+							chop($info_gene);
+							my @genes = split(/,/,$info_gene);
+							foreach my $gene(@genes){
+								$segments_of_gene{$gene} .= "s$segment:$pos_in_segment|";
+							}
+						}
+					}
+				}
+			
+			}
+			print "$chrom $cumul $end_segment\n";
+		}
+	}
+}
+close(GFA);
+
+open(O,">$out");
+open(BED,">$out.bed");
+foreach my $gene(keys(%segments_of_gene)){
+	my $segments = $segments_of_gene{$gene};
+	my @positions = split(/\|/,$segments);
+	my $previous_segment;
+	
+	#print O "$gene	$segments\n";
+	print O "$gene\t";
+	
+	my $concat = "";
+	foreach my $pos(@positions){
+		
+		my ($segment,$pos_in_segment) = split(/:/,$pos);
+		if ($segment ne $previous_segment){
+			$concat .= ">$segment:$pos_in_segment";
+		}
+		$concat .= "-$pos_in_segment";
+		$previous_segment = $segment;
+	}
+	my @segments = split(/>/,$concat);
+	foreach my $segment(@segments){
+		if (!$segment){next;}
+		my ($segmentname,$pos) = split(/:/,$segment);
+		my @positions = split(/-/,$pos);
+		my $start = $positions[0];
+		my $end = $positions[$#positions];
+		if ($start > $end){
+			$start = $positions[$#positions];
+			$end = $positions[0];
+		}
+		print O ">$segmentname:$start-$end";
+		print BED "$segmentname	$start	$end	$gene\n";
+	}
+	print O "\n";
+}
+close(O);
+close(BED);