提取核酸序列

根据每个fq 文件比对到基因集的统计其丰度（相对丰度）

再根据丰度（相对丰度） 从基因集里提取序列

getDataFromList.pl
#!/usr/bin/perl -w
use strict;
use Getopt::Long;
my $usage = <<_USAGE_;
usage : 
version 1.0
getDataFromList.pl -i inputList -l log -td TMP_DONE -d target -p perl dir -q query column -t target column -o output dir -m mark
_USAGE_

my ($inputList, $totalRunLog, $TMP_DONE, $target, $queryColumn, $targetColumn, $perl_dir, $outputDir, $mark);
GetOptions(
	"i=s" => \$inputList,
	"d=s" => \$target,
	"l=s" => \$totalRunLog,
	"td=s" => \$TMP_DONE,
	"q=s" => \$queryColumn,
	"t=s" => \$targetColumn,
	"o=s" => \$outputDir,
	"p=s" => \$perl_dir,
	"m=s" => \$mark
);
die $usage if (!$inputList || !$totalRunLog || !$TMP_DONE || !$target || !$queryColumn || !$targetColumn || !$outputDir|| !$perl_dir);

$queryColumn--;
$targetColumn--;
#my @targets = split/\s+/, $targetLine;
#foreach my $target (@targets){
#	$target =~ /.+\/(.+)\./;
#	my $mark = $1;
	my %target;
	open  (my $t, "$target") || die "$!:$target\n";
	while (<$t>){
		chomp;next if ($_ eq '');s/\r//g;
		my @entries = split/\t/;
		if ($target{$entries[$targetColumn]}){
			push (@{$target{$entries[$targetColumn]}}, $_);
		}else{
			$target{$entries[$targetColumn]}->[0] = $_;
		}
	}
	close $t;

	$inputList =~ /.+\/(.+?)\./;
	my $sample = $1;
	open (my $in, "$inputList" ) || die "$!:$inputList\n";
	open (my $out, ">$outputDir/$sample.$mark.output") || die "$!:$outputDir/$sample.$mark.output\n";
	while (<$in>){
		chomp;next if ($_ eq '');s/\r//g;
		my @entries = split/\t/;
		my $key = $entries[$queryColumn];
		if ($target{$key}){
			foreach my $annot ( @{$target{$key}}){
				print $out "$annot\n";
			}
		}
	}
	close $in;
	close $out;
#}