生信数据格式转换汇总（一）

zhendehaibucuo

已于 2024-07-08 09:45:53 修改

阅读量1.9k

点赞数 15

CC 4.0 BY-SA版权

文章标签： linux

于 2024-07-05 16:47:18 首次发布

本文链接：https://blog.youkuaiyun.com/zhendehaibucuo/article/details/140211006

fasta格式转换

由于一些软件对输入的fasta文件格式具有要求有时需要将其从一行转化为多行，有事需要将其从多行转化成一行。这时候我们就需要用到FASTX-Toolkit工具将其进行转化。

FASTX-Toolkit下载

wget http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
tar xjvf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2

主要参数

(haphic) [liyanchun@login1 00.data]$ fasta_formatter -h
usage: fasta_formatter [-h] [-i INFILE] [-o OUTFILE] [-w N] [-t] [-e]
Part of FASTX Toolkit 0.0.14 by assafgordon@gmail.com

   [-h]         = This helpful help screen.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.
   [-w N]       = max. sequence line width for output FASTA file.
                  When ZERO (the default), sequence lines will NOT be wrapped -
                  all nucleotides of each sequences will appear on a single 
                  line (good for scripting).
   [-t]         = Output tabulated fo