Update SeqFromRef Version1.0

.BinList.xls

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+Reference	DEFAULTDIR/DB/Reference/hg38/ucsc.hg38.fasta

.Modules/Parameter/BinList.pm

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+# Package Name
+package Parameter::BinList;
+
+# Exported name
+require Exporter;
+@ISA = qw(Exporter);
+@EXPORT = qw(BinListGet BinSearch DayStamp TimeStamp DayTimeStamp ScriptBegin TimeString IfFileExist Chr2Num Num2Chr);
+
+use FindBin qw($Bin);
+use File::Basename;
+
+sub BinListGet
+{
+	my $BinList = $Bin . "/.BinList.xls";
+	return $BinList if(-s $BinList);
+
+	$BinList = "/biobiggen/data/headQuarter/user/xiezhangdong/Scripts/.BinList.xls";
+	die "[ Error ] File not exist ($BinList).\n" unless(-s $BinList);
+
+	return $BinList;
+}
+
+sub BinSearch
+{
+	my ($BinName,$BinList,$JumpConfirmFlag) = @_;
+
+	die "[ Error ] File not exist ($BinList).\n" unless(-s $BinList);
+	my $Return = `grep '^$BinName'\$'\\t' $BinList`;
+	chomp $Return;
+
+	die "Name ($BinName) not unique.\n($Return)\n" if($Return =~ /\n/);
+	#print "[ Info ] $Return\n";
+	my @Cols = split /\t/, $Return;
+	# 替换成Bin目录
+	if($Cols[1] =~ s/^BINDIR//)
+	{
+		$Cols[1] = $Bin . $Cols[1];
+	}
+	# 替换成Scripts目录
+	elsif($Cols[1] =~ s/^DEFAULTDIR//)
+	{
+		my @Items = split /\//, $Bin;
+		my $LastId = -1;
+		for($i = $#Items;$i >= 0;$i --)
+		{
+			if($Items[$i] eq "Scripts")
+			{
+				$LastId = $i - 1;
+				last;
+			}
+			elsif($Items[$i] eq "xiezhangdong")
+			{
+				$LastId = $i;
+				last;
+			}
+		}
+
+		if($LastId >= 0)
+		{
+			my $RDir = join("/",@Items[0 .. $LastId]);
+			$Cols[1] = $RDir . $Cols[1];
+		}
+	}
+	die "[ Error ] $Cols[1] for $BinName not exist!\n" unless($Cols[1] && (-e $Cols[1] || $JumpConfirmFlag ));
+
+	return $Cols[1];
+}
+
+sub DayStamp
+{
+	my @temp_time = localtime();
+	my $localtime_year = $temp_time[5] + 1900;
+	my $localtime_month = $temp_time[4] + 1;
+	my $DayStamp = $localtime_year . "/" . $localtime_month . "/" . $temp_time[3];
+
+	return $DayStamp;
+}
+
+sub TimeStamp
+{
+	my @temp_time = localtime();
+	my $TimeStamp = $temp_time[2] . ":" . $temp_time[1] . ":" . $temp_time[0];
+
+	return $TimeStamp;
+}
+
+sub DayTimeStamp
+{
+	my $DayStamp = &DayStamp();
+	my $TimeStamp = &TimeStamp();
+	my $Stamp = $DayStamp . " " . $TimeStamp;
+
+	return $Stamp;
+}
+
+sub ScriptBegin
+{
+	my ($MuteFlag,$Name) = @_;
+
+	$BeginTime = time;
+	if($BeginTime && !$MuteFlag)
+	{
+		my $Stamp = &DayTimeStamp();
+		print "[ $Stamp ] This script begins.\n" unless($Name);
+		print "[ $Stamp ] This script ($Name) begins.\n" if($Name);
+	}
+	elsif(!$BeginTime)
+	{
+		die "[ Error ] Fail to get system time with 'time'.\n";
+	}
+
+	return $BeginTime;
+}
+
+sub TimeString
+{
+	my ($TimeCurrent,$TimeBegin) = @_;
+	my $TimeString = "";
+
+	my $Sec = $TimeCurrent - $TimeBegin;
+
+	my $Day = int($Sec / 86400);
+	$TimeString .= $Day . "d" if($Day);
+
+	my $Tail = $Sec % 86400;
+	my $Hour = int($Tail / 3600);
+	$TimeString .= $Hour . "h" if($Hour);
+
+	$Tail = $Tail % 3600;
+	my $Min = int($Tail / 60);
+	$TimeString .= $Min . "min" if($Min);
+
+	$Sec = $Tail % 60;
+	$TimeString .= $Sec . "s" if($Sec);
+
+	$TimeString = "0s" unless($TimeString);
+
+	return $TimeString;
+}
+
+sub IfFileExist
+{
+	my @File = @_;
+
+	for my $i (0 .. $#File)
+	{
+		die "[ Error ] File ($File[$i]) not exist.\n" unless($File[$i] && -e $File[$i]);
+	}
+
+	return 1;
+}
+
+sub Chr2Num
+{
+	my $Chr = $_[0];
+	my $Num;
+
+	if($Chr =~ /X/i)
+	{
+		$Num = 23;
+	}
+	elsif($Chr =~ /Y/i)
+	{
+		$Num = 24;
+	}
+	elsif($Chr =~ /M/i)
+	{
+		$Num = 25;
+	}
+	else
+	{
+		$Chr =~ s/chr//i;
+		$Num = $Chr;
+	}
+
+	return $Num;
+}
+
+sub Num2Chr
+{
+	my $Num = $_[0];
+	my $Chr = "chr";
+
+	if($Num <= 22)
+	{
+		$Chr .= $Num;
+	}
+	elsif($Num == 23)
+	{
+		$Chr .= "X";
+	}
+	elsif($Num == 24)
+	{
+		$Chr .= "Y";
+	}
+	elsif($Num == 25)
+	{
+		$Chr .= "M";
+	}
+
+	return $Chr;
+}
+
+1;