统计fasta格式数据数量

最新推荐文章于 2024-10-10 07:35:12 发布

最新推荐文章于 2024-10-10 07:35:12 发布 · 607 阅读

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#Perl #Gmail #F# #C #C++

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作者使用Perl编写了一个简单的脚本来统计FASTA格式文件中的序列数量，并对比了一种更简洁的方法：使用grep命令行工具。

今天很2b地用perl自己写了个统计fasta格式数据量的script

#!/usr/bin/perl -w
# Program name: detectDataNum.pl
# Author      : SunChen
# Contact     : bbsunchen@gmail.com
# Date        : 04/21/2011
# Last Update : 04/21/2011
# Reference   : Please cite our following papers when you are using this script.
#				None
#
# Description : connect 2 meta-pair files to 1 file for the PE assembler.

#===========================================================================
use warnings;
use strict;
use Getopt::Long;

my %opts;
GetOptions(\%opts,"f:s");
my $usage= <<"USAGE";
	Program	: $0
	INPUT:
	-f	blabla...
USAGE
die $usage unless $opts{f};

open DATA, "< $opts{f}" or die "Can't open file ".$!;
my $lines = 0;
while(<DATA>)
{
	my $data = $_;

	chomp($data);#deal with \n
	$data=~s/\r//g;#deal with \r
	next unless($data=~/\S+/); #deal with blank line here.
	if($data =~ m/^>/)
	{
		$lines++;	
	}
}
close DATA;

print "data num is $lines /n";

实际上只要用一句话就行...