--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PGAP-1.2.1/Converter_NCBINewFormatData.pl	Thu Jun 24 13:51:52 2021 +0000
@@ -0,0 +1,300 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use Getopt::Long;
+
+
+
+my %optionHash=qw();
+my $inprefix="";
+my $outprefix="";
+my $indir="";
+my $outdir="";
+my @inList;
+my @outList;
+
+GetOptions(\%optionHash,"inprefix:s","outprefix:s","indir:s","outdir:s","help|h!");
+
+
+if(scalar(keys %optionHash)==0){
+	&print_usage("");
+}
+
+if(exists($optionHash{"h"}) or exists($optionHash{"help"}) ){
+	&print_usage("");
+}
+
+if( exists($optionHash{"inprefix"} ) ){
+	$inprefix = $optionHash{"inprefix"};
+	@inList=split(/\+/,$inprefix);
+}else{
+	&print_usage("--inprefix should be provided!");
+}
+
+if( exists($optionHash{"outprefix"} ) ){
+	$outprefix = $optionHash{"outprefix"};
+	@outList=split(/\+/,$outprefix);
+}
+
+if( exists($optionHash{"indir"} ) ){
+	$indir = $optionHash{"indir"};
+}else{
+	&print_usage("--indir should be provided!");
+}
+
+if( exists($optionHash{"outdir"} ) ){
+	$outdir = $optionHash{"outdir"};
+}else{
+	&print_usage("--outdir should be provided!");
+}
+
+
+if( $inprefix eq "" or $indir eq "" or $outdir eq "" ){
+	&print_usage("");
+}
+
+if( scalar(@outList) >0 and scalar(@outList) != scalar(@inList) ){
+	&print_usage("If outprefix was provided, the name number should be identical with inprefix");
+}
+
+
+system("mkdir -p $outdir");
+
+foreach my $idx (0 .. (scalar(@inList) -1)  ){
+	my $inname = $inList[$idx];
+	my $feature_table = $indir."/".$inname."_feature_table.txt";
+	my $faa           = $indir."/".$inname."_protein.faa";
+	my $fna           = $indir."/".$inname."_genomic.fna";
+
+	my %genePositionHash;
+	my %genomeSequenceHash;
+	my %geneAnnotationHash;
+	my %gene2genomeHash;
+	my %genefaaHash;
+	my $count=0;
+
+	my $outname;
+
+	if($outprefix eq ""){
+		my @tmp=split(/\./,$inname);
+		$outname = $tmp[0];
+	}else{
+		$outname = $outList[$idx];
+	}
+
+	# check file
+	if( ! -e $feature_table){
+		print "$feature_table was not found!\n";
+		print "$inname was skipped!\n";
+		next;
+	}
+
+	if( ! -e $faa){
+		print "$faa was not found!\n";
+		print "$inname was skipped!\n";
+		next;
+	}
+
+	if( ! -e $fna){
+		print "$fna was not found!\n";
+		print "$inname was skipped!\n";
+		next;
+	}
+
+	# read feature
+	&read_feature($feature_table,\%geneAnnotationHash,\%genePositionHash,\%gene2genomeHash);
+
+	# get genome sequence
+	&read_genomeSequence($fna,\%genomeSequenceHash);
+
+	# get faa
+	&read_faa($faa,\%genefaaHash);
+
+	# extract nuc and output
+
+	open(PEP,">$outdir/$outname.pep");
+	open(NUC,">$outdir/$outname.nuc");
+	open(FUN,">$outdir/$outname.function");
+
+	foreach my $mygene (keys %genePositionHash){
+		if( (!exists( $geneAnnotationHash{$mygene}))  or (!exists($gene2genomeHash{$mygene})) or (!exists($genefaaHash{$mygene})) or (!exists($genomeSequenceHash{$gene2genomeHash{$mygene}})) ){
+			print $inname . "\t" . $mygene . "\t" . "skipped for insufficient data!\n";
+			next;
+		}
+
+		my $nuc = &getSeq($genePositionHash{$mygene}, $genomeSequenceHash{$gene2genomeHash{$mygene}} );
+
+		if( $nuc eq ""){
+			print $inname . "\t" . $mygene . "\t" . "skipped for insufficient data!\n";
+			next;
+		}
+
+		print PEP ">$mygene\n$genefaaHash{$mygene}\n";
+		print NUC ">$mygene\n$nuc\n";
+		print FUN "$mygene\t-\t$geneAnnotationHash{$mygene}\n";
+		$count++;
+	}
+	close(PEP);
+	close(NUC);
+	close(FUN);
+
+	print $inname . " -> $outname: $count genes were extracted in total.\n";
+}
+
+
+sub getSeq(){
+	(my $pos,my $genomeSeq)=@_;
+	my @tmp=split(/\|/,$pos);
+	if( $tmp[1]> length($genomeSeq) ){
+		return "";
+	}
+	my $seq = substr($genomeSeq,$tmp[0]-1,$tmp[1]-$tmp[0]+1);
+	if($tmp[2] eq "-"){
+		$seq = &rcseq($seq);
+	}
+	return $seq;
+}
+
+
+
+sub rcseq(){
+	(my $seq)=@_;
+	$seq=uc($seq);
+
+	$_=$seq;
+	tr/ACGT/TGCA/;
+	$seq = $_;
+	return reverse($_);
+}
+
+
+
+sub read_faa(){
+	(my $infile, my $seqHash)=@_;
+	my $seq="";
+	my $name="";
+	my @content;
+	open(F,$infile);
+	@content=<F>;
+	close(F);
+	chomp(@content);
+
+	for (my $line = 0; $line < @content; $line++) {
+		if($content[$line] =~/^>/ ){
+			if($name ne ""){
+				$$seqHash{$name}=$seq;
+			}
+			my @tmp=split(/\s+/,$content[$line]);
+			@tmp=split(/\./,$tmp[0]);
+
+			$name=substr($tmp[0], 1, length($tmp[0])-1);
+			$seq="";
+		}else{
+			$seq = $seq . $content[$line];
+		}
+	}
+	$$seqHash{$name}=$seq;
+}
+
+
+
+
+
+
+sub read_genomeSequence(){
+	(my $infile,my $seqHash)=@_;
+	my $seq="";
+	my $name="";
+	my @content;
+	open(F,$infile);
+	@content=<F>;
+	close(F);
+	chomp(@content);
+
+	for (my $line = 0; $line < @content; $line++) {
+		if($content[$line] =~/^>/ ){
+			if($name ne ""){
+				$$seqHash{$name}=$seq;
+			}
+			my @tmp=split(/\s+/,$content[$line]);
+			$name=substr($tmp[0], 1, length($tmp[0])-1);
+			$seq="";
+		}else{
+			$seq = $seq . $content[$line];
+		}
+	}
+	$$seqHash{$name}=$seq;
+}
+
+
+
+sub read_feature(){
+	(my $infile, my $annHash,my $posHash,my $gene2genomeHash)=@_;
+	my @content;
+	open(F,$infile);
+	@content=<F>;
+	close(F);
+	chomp(@content);
+
+	for (my $line = 1; $line < @content - 1; $line=$line+1) {
+		my @row=split(/\t/,$content[$line]);
+		my @nextrow=split(/\t/,$content[$line+1]);
+
+		if($row[1] ne "protein_coding"){
+			next;
+		}
+
+		# in case
+		if( $row[7]."|".$row[8]."|".$row[9] ne $nextrow[7]."|".$nextrow[8]."|".$nextrow[9]){
+			next;
+		}
+
+		# print $nextrow[10]."\n";
+		# print $row[7]."|".$row[8]."|".$row[9]."\n";
+
+		my @tmp=split(/\./,$nextrow[10]);
+		my $geneName = $tmp[0];
+
+		$$annHash{$geneName}=$nextrow[13];
+		$$posHash{$geneName}=$row[7]."|".$row[8]."|".$row[9];
+		$$gene2genomeHash{$geneName}=$row[6];
+	}
+}
+
+
+sub print_usage(){
+	my $message=shift;
+my @usage=qq(
+Version: 2016042201
+Usage:   perl Converter_NCBINewFormatData.pl [options]
+
+
+Options: 
+
+   --inprefix   String     The prefix of the input files, such as GCF_000007545.1_ASM754v1
+                           If two or more strains were provided, please join their prefixs with "+"
+                           Such as GCF_000007545.1_ASM754v1+GCF_000008105.1_ASM810v1+GCF_000711315.1_ASM71131v1
+
+   --indir      String     The directory of those input files
+
+   --outprefix  String     The prefix for the output files.
+                           If a value "ty2" was provided, the output files would be: ty2.nuc, ty2.pep, and ty2.function
+                           If two or more strains were provided, please join their prefixs with "+"
+                           If the prefix was not provided, the assembly value would be used as the prefix, such as GCF_000007545
+
+   --outdir     String     The directory for the output files
+
+Note:
+   1. Before converting data with this script, please prepare *feature_table.txt, *genomic.fna and *protein.faa files for each strain.
+   
+   2. This script was designed for NCBI new format data only. If part of your data is in the old format, please use the Converter_finished.pl or Converter_draft.pl script to convert the data. 
+
+
+);
+
+	print join("\n",@usage)."\n";
+	print $message."\n";
+	exit;
+}
+
+