使用.fasta文件计算序列的相对内容 [英] Using a .fasta file to compute relative content of sequences

问题描述

所以我是我的菜鸟"，最近才通过Perl被引入编程领域，但我仍然对所有这些都已经习惯了.我有一个必须使用的.fasta文件，尽管不确定我是否能够打开它，或者不确定是否必须盲目"使用它.

无论如何，我拥有的文件包含以.fasta格式编写的三个基因的DNA序列.

显然是这样的:

>label
sequence
>label
sequence
>label
sequence

我的目标是编写一个脚本来打开和读取文件，这是我现在所掌握的，但是我必须读取每个序列，计算每个序列中'G'和'C'的相对数量，并然后将基因名称以及它们各自的'G'和'C'内容写到TAB分隔文件中.

任何人都可以提供一些指导吗?我不确定TAB分隔的文件是什么，并且我仍在尝试找出如何打开.fasta文件以实际查看内容的方法.到目前为止，我已经处理过可以轻松打开的.txt文件，但是无法打开.fasta.

我很抱歉听起来很困惑.多谢您的耐心配合.我不像你这样的专业人士！

解决方案

我建议您检查以下链接:

fasta perl on stackoverflow

BioPerl HowTo

在perl和dna中崩溃了我们

So me being the 'noob' that I am, being introduced to programming via Perl just recently, I'm still getting used to all of this. I have a .fasta file which I have to use, although I'm unsure if I'm able to open it, or if I have to work with it 'blindly', so to speak.

Anyway, the file that I have contains DNA sequences for three genes, written in this .fasta format.

Apparently it's something like this:

>label
sequence
>label
sequence
>label
sequence

My goal is to write a script to open and read the file, which I have gotten the hang of now, but I have to read each sequence, compute relative amounts of 'G' and 'C' within each sequence, and then I'm to write it to a TAB-delimited file the names of the genes, and their respective 'G' and 'C' content.

Would anyone be able to provide some guidance? I'm unsure what a TAB-delimited file is, and I'm still trying to figure out how to open a .fasta file to actually see the content. So far I've worked with .txt files which I can easily open, but not .fasta.

I apologise for sounding completely bewildered. I'd appreciate your patience. I'm not like you pros out there!!

解决方案

I advice you check links below:

fasta perl on stackoverflow

BioPerl HowTo

A crash ourse in perl and dna

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