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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PanExplorer_workflow/Perl/get_data.pl	Thu May 30 11:16:08 2024 +0000
@@ -0,0 +1,316 @@
+#!/usr/bin/perl
+
+use strict;
+
+use YAML qw(LoadFile);
+use Data::Dumper qw(Dumper);
+use File::Basename;
+my $dirname = dirname(__FILE__);
+
+
+my %continents;
+open(F,"countries.txt");
+<F>;
+while(my $line =<F>){
+        chomp($line);
+        my ($continent,$country) = split(/,/,$line);
+        $continents{$country} = $continent;
+}
+close(F);
+
+my $input_yml = $ARGV[0];
+my $outdir = $ARGV[1];
+ 
+open(LIST,">$outdir/list.txt"); 
+my $data = LoadFile($input_yml);
+my %hashtable = %$data;
+
+if ($hashtable{"ids"}){
+	my $ref_ids = $hashtable{"ids"};
+	my @ids = @$ref_ids;
+	foreach my $id(@ids){
+		print LIST "$id\n";
+	}
+}
+if ($hashtable{"input_genbanks"}){
+	my $ref_gbs = $hashtable{"input_genbanks"};
+	my @gbs = @$ref_gbs;
+	foreach my $gb(@gbs){
+        	print LIST "$gb\n";
+	}
+}
+close(LIST);
+
+
+
+my $concat = "";
+open(O2,">$outdir/genbanks.txt");
+open(O,">$outdir/strains.txt");
+open(GENES,">$outdir/genes.txt");
+open(L,">$outdir/list_genomes.txt");
+open(L2,">$outdir/list_genomes2.txt");
+open(L3,">$outdir/genomes.txt");
+open(L4,">$outdir/genomes2.txt");
+open(SEQFILE,">$outdir/seqfile");
+open(PanSN,">$outdir/all_genomes.fa");
+open(METADATA,">$outdir/metadata_strains.txt");
+
+open(F,"$outdir/list.txt");
+#open(TEST,">$outdir/test");
+while(my $line =<F>){
+	chomp($line);
+	my $genbank = $line;
+	if (!-e "$genbank"){
+
+		my $assembly_accession = $genbank;
+		system("datasets download genome accession --include-gbff --filename $outdir/$assembly_accession.zip $assembly_accession");
+		system("unzip -o $outdir/$assembly_accession.zip");
+		system("cp -rf ncbi_dataset/data/$assembly_accession/$assembly_accession*genomic.fna $outdir/$genbank.fasta");
+		system("cp -rf ncbi_dataset/data/$assembly_accession/genomic.gbff $outdir/$genbank.gb");
+
+		
+	}
+	else{
+		my $genbank_file = $genbank;
+		my $grep = `grep 'LOCUS' $genbank_file`;
+		$genbank = "unknown";
+		if ($grep =~/LOCUS\s+([\-\:\w]+)/){$genbank = $1;}
+
+		#$genbank =~s/\:/_/g;	
+
+		my $cmd = "cp -rf $genbank_file $outdir/$genbank.gb";
+		system($cmd);
+
+		my %genome_seqs;
+		my $current_chr;
+		my $go = 0;
+		open(G,"$outdir/$genbank.gb");
+		while(<G>){
+			if ($go == 1 && /(\d+) (.*)$/){
+				my $line = $2;
+				$line =~s/ //g;
+				$genome_seqs{$current_chr}.=$line;
+			}
+			if (/LOCUS       ([^\s]+)/){
+				$current_chr = $1;
+			}
+			if (/ORIGIN/){$go = 1;}
+			if (/^\/\//){$go = 0;}
+		}
+		close(G);
+
+		open(FASTA,">$outdir/$genbank.fasta");
+		foreach my $ch(keys(%genome_seqs)){
+			print FASTA ">$ch\n";
+			my $seq = $genome_seqs{$ch};
+			print FASTA "$seq\n";
+		}
+		close(FASTA);
+	}
+	#my $get_organism_line = `head -10 $outdir/$genbank.gb | grep DEFINITION `;
+	
+	# remove single quote in genbank file
+	`sed -i "s/'//g" $outdir/$genbank.gb`;
+	my $get_organism_line = `head -10 $outdir/$genbank.gb | grep -A 1 DEFINITION `;
+
+	# if several lines for DEFINITION, concatenate the lines
+	my @lines_organism = split(/\n/,$get_organism_line);
+	my $first_line = $lines_organism[0];
+	my $second_line = $lines_organism[1];
+	if ($second_line =~/^            (.*)/){
+		$get_organism_line = $first_line. " ".$1;
+	}
+	else{
+		$get_organism_line = $first_line;
+	}
+
+        my $strain;
+	my $genus;
+        if ($get_organism_line =~/DEFINITION  (.*)$/){
+                $strain = $1;
+		($genus) = split(/\s/,$strain);
+        }
+	my $country = `head -100 $outdir/$genbank.gb | grep country `;
+        $country =~s/^\s+//g;
+        $country =~s/\/country=//g;
+        $country =~s/\"//g;
+        $country =~s/\n//g;$country =~s/\r//g;
+        if ($country =~/:/){
+                my $city;
+                ($country,$city) = split(/:/,$country);
+        }
+        if ($country eq ""){$country = "unresolved";}
+        my $continent = "unresolved";
+        if ($continents{$country}){
+                $continent = $continents{$country};
+        }
+	$strain =~s/\.//g;
+	my ($info1,$info2 ) = split(",",$strain);
+        $strain = $info1;
+        $strain =~s/ /_/g;
+        $strain =~s/strain_//g;
+        $strain =~s/_chromosome//g;
+        $strain =~s/_genome//g;
+        $strain =~s/_str_/_/g;
+	$strain =~s/[^\w\-\_]//g;
+	$strain =~s/\-/_/g;
+
+	print O "$genbank	$strain\n";	
+	$concat .= "$genbank,";
+	print L "$genbank	$outdir/$genbank.gb\n";
+	print L2 "$genbank\n";
+	print L3 "$outdir/$genbank.fasta\n";
+	print L4 "$outdir/$genbank.fasta	$strain\n";
+	print SEQFILE "$genbank	$outdir/$genbank.fasta\n";
+	print METADATA "$strain\t$genus\t$country\t$continent\n";
+
+
+	my %genome_sequences;
+	my $genome = "";
+	my $seqid = "";
+        open(GENOME,"$outdir/$genbank.fasta");
+        while(<GENOME>){
+                if (!/^>/){
+                        my $line = $_;
+                        $line =~s/\n//g;$line =~s/\r//g;
+			$genome_sequences{$seqid} .= $line;
+                        $genome .= $line;
+			print PanSN $_;
+                }
+		elsif (/>([^\s]+)/){
+			$seqid = $1;
+			$seqid =~s/\.\d+$//g;
+			print PanSN ">$strain#$seqid\n";
+		}
+        }
+        close(GENOME);
+
+
+	open(N,">$outdir/$genbank.nuc");
+        open(P,">$outdir/$genbank.pep");
+        open(FUNC,">$outdir/$genbank.func");
+        my $go = 0;
+        my $start;
+        my $end;
+        my $product;
+        my $complement = 0;
+        my $end_gene = "no";
+        my $protein = "";
+	my $has_translation = `grep -c 'translation=' $outdir/$genbank.gb`;
+	$has_translation =~s/\n//g;$has_translation =~s/\r//g;
+        open(G,"$outdir/$genbank.gb");
+        my $current_gene;
+	my $current_chrom;
+        while(<G>){
+                if (/^\s+ORGANISM\s+(.*)$/){
+                }
+		if (/protein_id=\"(.*)\"/){
+			$current_gene = $1;
+		}
+		if (/LOCUS       ([^\s]+)/){
+			$current_chrom = $1;
+		}        
+                if (/locus_tag=\"(.*)\"/){
+                        $current_gene = $1;
+		}
+                if ($go == 1){
+                        my $line = $_;
+                        $line =~s/ //g;
+                        $line =~s/\n//g;$line =~s/\r//g;
+                        $protein .= $line;
+                        if (/\"$/){
+                                $protein =~s/\"//g;
+                                $end_gene = "yes";
+
+                        }
+                }
+                if (/\/translation=\"(.*)/ or ($has_translation == 0 && /protein_id=/)){
+                        $go = 1;
+                        $protein .= $1;
+			print P ">$current_gene\n";
+			print N ">$current_gene\n";
+			print GENES "$current_gene $product [$strain]\n";
+
+                        if ($protein =~/\"$/){
+                                $end_gene = "yes";
+                        }
+			if ($has_translation == 0){$end_gene = "yes";}
+                }
+                if ($end_gene eq "yes"){
+                        $protein =~s/\"//g;
+                        print P "$protein\n";
+                        $protein = "";
+                                my $length = $end - $start + 1;
+
+				#print "okkkk $current_chrom\n";
+                                #my $geneseq = substr($genome,$start-1,$length);
+                                my $geneseq = substr($genome_sequences{$current_chrom},$start-1,$length);
+
+
+                                if ($complement){
+                                        my $revcomp = reverse $geneseq;
+                                        $revcomp =~ tr/ATGCatgc/TACGtacg/;
+                                        $geneseq = $revcomp;
+                                }
+                                print N "$geneseq\n";
+                                print FUNC "$current_gene  -       $product\n";
+                                $go = 0;
+                        $end_gene = "no";
+                }
+                if (/\/product=\"(.*)\"/){
+                        $product = $1;
+                }
+                if (/^\s+CDS\s+(\d+)\.\.(\d+)\s*$/){
+                        $start = $1;
+                        $end = $2;
+                        $complement = 0;
+                }
+                if (/^\s+CDS\s+complement\((\d+)\.\.(\d+)\)\s*$/){
+                        $start = $1;
+                        $end = $2;
+                        $complement = 1;
+                }
+        }
+        close(G);
+        close(P);
+        close(N);
+        close(FUNC);
+
+	if ($has_translation == 0){
+		system("perl $dirname/translate.pl $outdir/$genbank.nuc $outdir/$genbank.pep");
+	}
+	
+	my $prot_num = 0;
+        open(PRT,">$outdir/$genbank.prt");
+        open(P,"$outdir/$genbank.pep");
+        while(<P>){
+                if (/>(.*)/){
+                        my $prot_id = $1;
+                        $prot_num++;
+                        my $new_id = "$strain"."_".$prot_num;
+                        print PRT ">$new_id\n";
+                }
+                else{
+                        print PRT $_;
+                }
+        }
+        close(P);
+        close(PRT);
+}
+close(F);
+close(O);
+close(METADATA);
+chop($concat);
+print O2 $concat;
+close(O2);
+close(L);
+close(L2);
+close(L3);
+close(L4);
+close(GENES);
+close(SEQFILE);
+close(PanSN);
+#close(TEST);
+
+unlink("prokaryotes.txt");
+unlink("eukaryotes.txt");