在FASTA文件中删除换行符 [英] Remove line breaks in a FASTA file

问题描述

我有一个FASTA文件，其中的序列被打破了换行。我想删除的换行符。这是我的文件的例子：

I have a fasta file where the sequences are broken up with newlines. I'd like to remove the newlines. Here's an example of my file:

>accession1
ATGGCCCATG
GGATCCTAGC
>accession2
GATATCCATG
AAACGGCTTA

我想它转换成这样：

I'd like to convert it into this:

>accession1
ATGGCCCATGGGATCCTAGC
>accession2
GATATCCATGAAACGGCTTA

我发现在这个网站，它看起来像这样一个潜在的解决方案：

I found a potential solution on this site, which looks like this:

cat input.fasta | awk '{if (substr($0,1,1)==">"){if (p){print "\n";} print $0} else printf("%s",$0);p++;}END{print "\n"}' > joinedlineoutput.fasta

不过，这个地方每个条目之间的一个额外的换行符，所以文件看起来是这样的：

However, this places an extra line break between each entry, so file looks like this:

>accession1
ATGGCCCATGGGATCCTAGC

>accession2
GATATCCATGAAACGGCTTA

我是一个awk小白，但我还是把射击在修改命令。我的猜测是如果（P）{打印\\ n;} 是罪魁祸首...潜在打印\\ n是增加了两个换行符。我无法弄清楚如何添加一个换行......这可能是一些容易，但就像我说的，我是一个菜鸟。这里是我的（失败）解决方案：

I'm an awk noob, but I took a shot at modifying the command. My guess was the if (p){print "\n";} was the culprit...potentially print "\n" is adding two line breaks. I couldn't figure out how to add just one newline...this is probably something easy, but like I said, I'm a noob. Here was my (unsuccessful) solution:

awk '{if (substr($0,1,1)==">"){print "\n"$0} else printf("%s",$0);p++;}END{print "\n"}' input.fasta > joinedoutput.fasta

然而，这增加了在文件开头的空行，因为它总是打印新的生产线将打印的第一个加入号码前：

However, this adds an empty line at the beginning of the file because it's always printing a new line before it prints the first accession number:

{empty line} 
>accession1
ATGGCCCATGGGATCCTAGC
>accession2
GATATCCATGAAACGGCTTA

任何人都有一个解决方案，使我的文件格式是否正确？谢谢！

Anyone have a solution to get my file in the correct format? Thanks!

推荐答案

本 AWK 程序：

% awk '!/^>/ { printf "%s", $0; n = "\n" } 
/^>/ { print n $0; n = "" }
END { printf "%s", n }
' input.fasta

将产生：

>accession1
ATGGCCCATGGGATCCTAGC
>accession2
GATATCCATGAAACGGCTTA

说明：

在不以＆GT开头的行; ，打印时不用换行和存储换行符（变量ñ ），供以后使用。

Explanation:

On lines that don't start with a >, print the line without a line break and store a newline character (in variable n) for later.

在那些开始与＆GT线; ，打印存储的换行符（如果有的话）而行。重置 N ，如果这是最后一道防线。

On lines that do start with a >, print the stored newline character (if any) and the line. Reset n, in case this is the last line.

用新行结束，如果需要的话。

End with a newline, if required.

在默认情况下，变量被初始化为空字符串。没有必要明确初始化，在 AWK ，这是你会在ç和其他大多数传统语言。

By default, variables are initialized to the empty string. There is no need to explicitly "initialize" a variable in awk, which is what you would do in c and in most other traditional languages.

- 6.1.3.1在程序使用变量，<一个HREF =htt​​p://www.gnu.org/software/gawk/manual/gawk.html>的GNUAwk用户指南

--6.1.3.1 Using Variables in a Program, The GNU Awk User's Guide

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