--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PGAP-1.2.1/Converter_draft.pl	Thu Jun 24 13:51:52 2021 +0000
@@ -0,0 +1,245 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use Getopt::Std;
+
+my %opt;
+getopts('N:I:O:',\%opt);
+
+my @usage=qq(
+Version: 2016042201
+Usage:   perl Converter_draft.pl [options]
+
+Options: 
+
+  -N String    Input the strain nickname
+  -I String    Input file directory
+  -O String    Output file directory
+);
+
+if (!scalar(keys %opt)) 
+	{
+		print join("\n",@usage)."\n";
+		exit;
+	}
+
+my $prefix;
+if (exists($opt{"N"})) 
+	{
+		$prefix=$opt{"N"}
+	}else
+		{
+			print "-N 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;
+my $list;
+my @list;
+my $pttlost;
+my $gi;
+
+if ((-e $output) and ((-d $output))) 
+	{
+	}else
+	{
+		mkdir($output);
+	}
+
+if ($input!~/\/$/) 
+	{
+		$input=$input."/";
+	}
+
+if ($output!~/\/$/) 
+	{
+		$output=$output."/";
+	}
+
+opendir(DIR,"$input") || die "The input directory ( $input ) is not exists!\n";
+@list=grep(/faa$/,readdir(DIR));
+closedir(DIR);
+$_=join("\t",@list);
+s/.faa//g;
+@list=split(/\t/,$_);
+
+open(PEP,">$output$prefix.pep");
+open(NUC,">$output$prefix.nuc");
+open(FUN,">$output$prefix.function");
+
+foreach $list (@list) 
+	{
+		%hash=();
+		if (!(-e $input.$list.".faa")) 
+			{
+				print $input.$list.".faa is not exists!\n$list.faa, $list.ffn and $list.ptt are skipped!\n";
+				next;
+			}
+
+		if (!(-e $input.$list.".ffn")) 
+			{
+				print $input.$list.".ffn is not exists!\n$list.faa, $list.ffn and $list.ptt are skipped!\n";
+				next;
+			}
+
+		if (!(-e $input.$list.".ptt")) 
+			{
+				open(F,$input.$list.".faa");
+				@_=<F>;
+				close(F);
+				@_=grep(/^>/,@_);
+				if (scalar(@_)>1) 
+					{
+					print $input.$list.".ptt is not exists!\n";
+					print "There are more than 1 sequence in $list.faa and $list.ffn, So $list.faa, $list.ffn and $list.ptt are skipped!\n";
+					next;
+					}
+				$pttlost=1;
+			}else
+				{
+					$pttlost=0;
+				}
+
+		$file=$input.$list.".faa";
+		open(F,$file) or die "could not open $file";
+		while ($line=<F>) 
+			{
+				if ($line=~/^>/) 
+					{
+						@row=split(/\|/,$line);
+						print PEP ">$row[1]\n";
+						if ($pttlost ==1) 
+							{
+								$gi=$row[1];
+							}
+					}else
+						{
+							print PEP $line;
+						}
+			}
+		close(F);
+
+		if ($pttlost ==1) 
+			{
+				print FUN "$gi\t-\thypothetical protein\n";
+			}else
+				{
+				$file=$input.$list.".ptt";
+				open(F,"$file") or die "could not open $file";
+				$_=<F>;
+				$_=<F>;
+				$_=<F>;
+				while ($line=<F>) 
+					{
+						chomp($line);
+						@row=split(/\t/,$line);
+						print FUN $row[3]."\t".$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(F);
+				}
+
+
+
+		$file=$input.$list.".ffn";
+		open(F,"$file") or die "could not open $file";;
+		while ($line=<F>) 
+			{
+				if ($line=~/^>/) 
+					{
+						if ($pttlost==1) 
+							{
+								print NUC ">$gi\n";
+								$flag=1;
+							}else
+								{
+									my $key=&getKey($line);
+									if (exists($hash{$key})) 
+										{
+											$flag=1;
+											print NUC ">$hash{$key}\n";
+										}else
+											{
+												$flag=0;
+											}
+								}
+					}else
+						{
+							if ($flag) 
+								{
+									print NUC $line;
+								}
+						}
+			}
+		close(F);
+	}
+
+close(PEP);
+close(NUC);
+close(FUN);
+
+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];
+	}
+}
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