--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PGAP-1.2.1/Converter_finished.pl	Thu Jun 24 13:51:52 2021 +0000
@@ -0,0 +1,188 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use Getopt::Std;
+
+my %opt;
+getopts('S:I:O:',\%opt);
+
+my @usage=qq(
+Version: 2016042201
+Usage:   perl Converter_finished.pl [options]
+
+Options: 
+
+  -S String    Input the strains nickname, 
+               If 2 or more, join them with '+', 
+               For example: CT18+NC_011834+SPA
+  -I String    Input file directory
+  -O String    Output file directory
+);
+
+if (!scalar(keys %opt)) 
+	{
+		print join("\n",@usage)."\n";
+		exit;
+	}
+
+my @sp;
+if (exists($opt{"S"})) 
+	{
+		@sp=split(/\+/,$opt{"S"});
+	}else
+		{
+			print "-S could not be empty!";
+			print join("\n",@usage)."\n";
+			exit;
+		}
+
+my $output;
+if (exists($opt{"O"})) 
+	{
+		$output=$opt{"O"};
+	}else
+		{
+			print "-O could not be empty!";
+			print join("\n",@usage)."\n";
+			exit;
+		}
+
+my $input;
+if (exists($opt{"I"})) 
+	{
+		$input=$opt{"I"};
+	}else
+		{
+			print "-I could not be empty!";
+			print join("\n",@usage)."\n";
+			exit;
+		}
+
+my $sp;
+my $line;
+my @row;
+my @tmp;
+my %hash;
+my $flag;
+my $file;
+
+
+if ((-e $output) and ((-d $output))) 
+	{
+	}else
+	{
+		mkdir($output);
+	}
+
+if ($input!~/\/$/) 
+	{
+		$input=$input."/";
+	}
+
+
+if ($output!~/\/$/) 
+	{
+		$output=$output."/";
+	}
+
+
+foreach $sp (@sp) 
+	{
+		%hash=();
+		$file=$input.$sp.".faa";
+		open(F,$file) or die "could not open $file";
+		open(R,">$output$sp.pep");
+		while ($line=<F>) 
+			{
+				if ($line=~/^>/) 
+					{
+						@row=split(/\|/,$line);
+						print R ">$row[1]\n";
+					}else
+						{
+							print R $line;
+						}
+			}
+		close(F);
+		close(R);
+
+		$file=$input.$sp.".ptt";
+		open(F,"$file") or die "could not open $file";
+		open(R,">$output$sp.function");
+		$_=<F>;
+		$_=<F>;
+		$_=<F>;
+		while ($line=<F>) 
+			{
+				chomp($line);
+				@row=split(/\t/,$line);
+				print R $row[3]."\t".$row[7]."\t".$row[8]."\n";
+				@tmp=split(/\.\./,$row[0]);
+				if ($row[1] eq "+") 
+					{
+						$hash{$tmp[0]."-".$tmp[@tmp-1]}=$row[3];
+					}else
+						{
+							$hash{"c".$tmp[@tmp-1]."-".$tmp[0]}=$row[3];
+						}
+			}
+		close(R);
+		close(F);
+
+		$file=$input.$sp.".ffn";
+		open(F,"$file") or die "could not open $file";;
+		open(R,">$output/$sp.nuc");
+		while ($line=<F>) 
+			{
+				if ($line=~/^>/) 
+					{
+						my $key=&getKey($line);
+						if (exists($hash{$key})) 
+							{
+								$flag=1;
+								print R ">$hash{$key}\n";
+							}else
+								{
+									$flag=0;
+								}
+					}else
+						{
+							if ($flag) 
+								{
+									print R $line;
+								}
+						}
+			}
+		close(R);
+		close(F);
+	}
+
+sub getKey()
+{
+	(my $line)=@_;
+	my @tmp;
+	my $strand;
+	chomp($line);
+	@tmp=split(/ /,$line);
+	@tmp=split(/\:/,$tmp[0]);
+
+	if($tmp[@tmp-1]=~/c/)
+	{
+		$strand="-";
+	}else
+	{
+		$strand="+";
+	}
+	$_=$tmp[@tmp-1];
+	s/c//g;
+	s/ //g;
+	@tmp=split(/\,|-/,$_);
+	@tmp=sort{$a<=>$b} @tmp;
+	if($strand eq "-")
+	{
+		return "c".$tmp[@tmp-1]."-".$tmp[0];
+	}else
+	{
+		return $tmp[0]."-".$tmp[@tmp-1];
+	}
+}