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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PanExplorer_workflow/Perl/GetCogOfCluster.pl	Thu May 30 11:16:08 2024 +0000
@@ -0,0 +1,297 @@
+#!/usr/bin/perl
+
+use strict;
+use File::Basename;
+my $dirname = dirname(__FILE__);
+
+my $pav_matrix = $ARGV[0];
+my $prot_dir = $ARGV[1];
+my $cog_outfile = $ARGV[2];
+my $cog_stats = $ARGV[3];
+my $cog_stats2 = $ARGV[4];
+my $cog_clusters = $ARGV[5];
+my $strain_info_file = $ARGV[6];
+
+
+
+my %cogs_categories = (
+        "J"=>"INFORMATION STORAGE AND PROCESSING",
+        "A"=>"INFORMATION STORAGE AND PROCESSING",
+        "K"=>"INFORMATION STORAGE AND PROCESSING",
+        "L"=>"INFORMATION STORAGE AND PROCESSING",
+        "B"=>"INFORMATION STORAGE AND PROCESSING",
+        "D"=>"CELLULAR PROCESSES AND SIGNALING",
+        "Y"=>"CELLULAR PROCESSES AND SIGNALING",
+        "V"=>"CELLULAR PROCESSES AND SIGNALING",
+        "T"=>"CELLULAR PROCESSES AND SIGNALING",
+        "M"=>"CELLULAR PROCESSES AND SIGNALING",
+        "N"=>"CELLULAR PROCESSES AND SIGNALING",
+        "Z"=>"CELLULAR PROCESSES AND SIGNALING",
+        "W"=>"CELLULAR PROCESSES AND SIGNALING",
+        "U"=>"CELLULAR PROCESSES AND SIGNALING",
+        "O"=>"CELLULAR PROCESSES AND SIGNALING",
+        "C"=>"METABOLISM",
+        "G"=>"METABOLISM",
+        "E"=>"METABOLISM",
+        "F"=>"METABOLISM",
+        "H"=>"METABOLISM",
+        "I"=>"METABOLISM",
+        "P"=>"METABOLISM",
+        "Q"=>"METABOLISM",
+        "R"=>"POORLY CHARACTERIZED",
+        "S"=>"POORLY CHARACTERIZED"
+);
+
+my %strain_names;
+open(S,$strain_info_file);
+while(<S>){
+	my $line = $_;
+	$line =~s/\n//g;$line =~s/\r//g;
+	my ($id,$strain_name) = split(/\t/,$line);
+	$strain_names{$id} = $strain_name;
+}
+close(S);
+
+my %strain_of_prot;
+my %proteins;
+open( DIR, "ls $prot_dir/*pep |" );
+while(<DIR>) {
+	my $filename = $_;
+	my $strain;
+	my $id;
+	if ($filename =~/\/([^\/]*).pep/){
+		$strain = $1;
+	}
+	#open(F,"zcat $filename|" );
+	open(F,"$filename" );
+	while(<F>){
+		if (/>(.*)/){
+			$id = $1;
+			$strain_of_prot{$id} = $strain;
+		}
+		else{
+			$proteins{$id}.= $_;
+		}
+	}
+	close(F);
+}
+closedir(DIR);
+
+my %functions;
+my %accessory_clusters;
+my %genes_of_cluster;
+my %cluster_of_gene;
+open(S,">$pav_matrix.selection_prot.fa");
+open(O,$pav_matrix);
+<O>;
+while(<O>){
+        my $line = $_;
+        $line =~s/\n//g;$line =~s/\r//g;
+        my @infos = split(/\t/,$line);
+        my $cluster = $infos[0];
+        print S ">$cluster\n";
+	for (my $i=1; $i <= $#infos; $i++){
+		my @genenames = split(/,/,$infos[$i]);
+		foreach my $genename(@genenames){
+                	if ($genename=~/\w+/){
+                        	$genes_of_cluster{$cluster} .= "$genename,";
+			}
+		}
+	}
+	for (my $i=1; $i <= $#infos; $i++){
+                if ($infos[$i] =~/-/){$accessory_clusters{$cluster} = 1;}
+        }
+        LINE: for (my $i=1; $i <= $#infos; $i++){
+		my @genenames = split(/,/,$infos[$i]);
+		foreach my $genename(@genenames){
+			if ($genename=~/\w+/){
+				#$genename =~s/\|/_/g;
+				print S $proteins{$genename};
+				$cluster_of_gene{$genename} = $cluster;
+				my $function = `grep '$genename' $prot_dir/*func`;
+                                $function =~s/\n//g;$function =~s/\r//g;
+                                my @t = split(/$genename/,$function);
+                                if ($t[1] =~/-\s+(.*)/){
+                                        $function = $1;
+                                        $function =~s/'//g;
+                                }
+                                $functions{$cluster} = $function;
+				last LINE;
+			}
+		}
+        }
+}
+close(O);
+close(S);
+
+
+#########################################################################################################################################
+# Test if COG are already provided in Genbank files. If provided, rpsblast is not launched, we get the COG information from Genbank files
+#########################################################################################################################################
+my %cog_of_genes;
+open(LS,"ls $prot_dir/*gb |");
+while(my $gb_file = <LS>){
+	chomp($gb_file);
+	open(GB,$gb_file);
+	my $current_cog;
+	my $current_gene;
+	while(my $l=<GB>){
+		if ($l=~/(COG\d+)/){
+			$current_cog = $1;
+		}
+		if ($l =~/protein_id=\"(.*)\"/ && $current_cog){
+			$current_gene = $1;
+			$cog_of_genes{$current_gene} .= ",$current_cog";
+		}
+		if ($l =~/locus_tag=\"(.*)\"/ && $current_cog){
+                        $current_gene = $1;
+			$cog_of_genes{$current_gene} .= ",$current_cog";
+                }
+	}
+	close(GB);
+}
+close(LS);
+
+my %count_letter;
+if (scalar keys(%cog_of_genes) > 1){
+	open(WHOG,"$dirname/../COG/whog");
+	my %letters_of_cog;
+	while(my $l=<WHOG>){
+		if ($l=~/\[(\w+)\] (COG\d+) /){
+			my $letter = $1;
+			my $cogid = $2;
+			$letters_of_cog{$cogid} = $letter;
+		}
+	}
+	close(WHOG);
+
+	my %cogs_of_cluster;
+	foreach my $gene(keys(%cog_of_genes)){
+		my $cluster = $cluster_of_gene{$gene};
+		my $cogs = $cog_of_genes{$gene};
+		$cogs_of_cluster{$cluster} = $cogs;	
+	}
+	open(COG_CLUST,">$cog_clusters");	
+	foreach my $cluster(sort {$a<=>$b} keys(%cogs_of_cluster)){
+		my $cogids = $cogs_of_cluster{$cluster};
+		my @ids = split(/,/,$cogids);
+		foreach my $id(@ids){
+			if ($id =~/\w+/ && $cluster){
+				my $letter = $letters_of_cog{$id};
+				my @letters = split(//,$letter);
+				my $letters_string = join("\t",@letters);
+				#$letter =~s//\t/g;
+				print COG_CLUST "$cluster	$id	$letters_string\n";
+			}
+		}
+	}
+	close(COG_CLUST);
+}
+else{
+
+	my $is_plus = `which rpsblast+`;
+	my $is_not_plus = `which rpsblast`;
+	my $software = "rpsblast";
+	if ($is_plus){$software = "rpsblast+";}
+	system("$software -query $pav_matrix.selection_prot.fa -db $dirname/../COG/Cog -out $pav_matrix.selection.rps-blast.out -evalue 1e-2 -outfmt '7 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovs'");
+
+	system("perl $dirname/../COG/bac-genomics-scripts/cdd2cog/cdd2cog.pl -r $pav_matrix.selection.rps-blast.out -c $dirname/../COG/cddid.tbl -f $dirname/../COG/fun.txt -w $dirname/../COG/whog -a");
+	system("cp -rf results/protein-id_cog.txt $cog_clusters");
+	system("rm -rf results");
+}
+
+open(COG,">$cog_outfile");
+my %cogs;
+open(C,$cog_clusters);
+while(<C>){
+	my $line = $_;
+	$line =~s/\n//g;$line =~s/\r//g;
+	my @infos = split(/\t/,$line);
+	my $coginfo = "";
+	my $cluster = $infos[0];
+	for (my $i = 1; $i <= $#infos; $i++){
+		$coginfo .= "\t".$infos[$i];
+	}
+	my $gene_list = $genes_of_cluster{$cluster};
+	chop($gene_list);
+	my @genes = split(",",$gene_list);
+	foreach my $gene(@genes){
+		my @letters = split(/\t/,$coginfo);
+		my $strain = $strain_of_prot{$gene};
+		for (my $i = 2; $i <= $#letters; $i++){
+			my $letter = $letters[$i];
+			my $cat = $cogs_categories{$letter};
+			$count_letter{$strain}{$letter}++;
+			$count_letter{$strain}{$cat}++;
+		}
+		print COG $gene.$coginfo."\n";
+	}
+}
+close(C);
+close(COG);
+
+
+
+my %cogs_of_clusters;
+my %cogcats_of_clusters;
+open(C,$cog_clusters);
+while(<C>){
+        my $line = $_;
+        $line =~s/\n//g;$line =~s/\r//g;
+        my @infos = split(/\t/,$line);
+        my $cluster = $infos[0];
+        my $cog = $infos[1];
+        my $cog_category = $infos[2];
+        $cogs_of_clusters{$cluster}{$cog} = 1;
+        $cogcats_of_clusters{$cluster} = $cog_category;
+}
+close(C);
+
+open(CC,">$cog_clusters.2");
+foreach my $cluster(sort{$a<=>$b} keys(%genes_of_cluster)){
+        my $cog_category = "Unknown";
+        my $cog_list = "Unknown";
+        if ($cogcats_of_clusters{$cluster}){
+                $cog_category = $cogcats_of_clusters{$cluster};
+                my $ref_cogs_of_clusters = $cogs_of_clusters{$cluster};
+                $cog_list = join(",",keys(%$ref_cogs_of_clusters));
+        }
+	my $function = "Unknown";
+	if ($functions{$cluster}){
+		$function = $functions{$cluster};
+	}
+        if ($accessory_clusters{$cluster}){
+                print CC "$cluster\t$cog_list\t$cog_category\t$function\n";
+        }
+}
+close(CC);
+
+my @cat_of_cat = ("INFORMATION STORAGE AND PROCESSING","METABOLISM","CELLULAR PROCESSES AND SIGNALING","POORLY CHARACTERIZED");
+my @cog_categories = ("D","M","N","O","T","U","V","W","Y","Z","A","B","J","K","L","C","E","F","G","H","I","P","Q","R","S");
+open(COG_STAT,">$cog_stats");
+open(COG_STAT2,">$cog_stats2");
+print COG_STAT "COG\t".join("\t",@cog_categories)."\n";
+print COG_STAT2 "COG\t".join("\t",@cat_of_cat)."\n";
+foreach my $strain(keys(%count_letter)){
+	my $strain_name = $strain_names{$strain};
+	print COG_STAT "$strain_name";
+	print COG_STAT2 "$strain_name";
+	my $ref_subhash = $count_letter{$strain};
+	my %subhash = %$ref_subhash;
+	foreach my $letter(@cog_categories){
+		my $n = 0;
+		if ($count_letter{$strain}{$letter}){$n = $count_letter{$strain}{$letter};}
+		print COG_STAT "\t".$n;
+	}
+	print COG_STAT "\n";
+
+	foreach my $cat(@cat_of_cat){
+		my $n = 0;
+		if ($count_letter{$strain}{$cat}){$n = $count_letter{$strain}{$cat};}			
+		print COG_STAT2 "\t".$n;
+	}
+	print COG_STAT2 "\n";
+}
+close(COG_STAT);
+close(COG_STAT2);
+