根据taxid获取名称的方法

最新推荐文章于 2024-01-03 07:01:34 发布

youyouJaney

最新推荐文章于 2024-01-03 07:01:34 发布

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文章标签： bash

本文链接：https://blog.csdn.net/youyouJaney/article/details/125363186

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head virus_taxid

28883
28883
10662
28883
...

`
1.#get the lineage 
taxonkit lineage virus_taxid > virus_line

28883	Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales
10662	Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales;Myoviridae
28883	Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales
28883	Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales

2.#获取最后的一个名字

awk '{$1="";print $0}' virus_line|awk -F ";" '{print $NF}' > virus_name

3.#删除行首空格及tab键
sed -i 's/^[ \t]*//g' virus_name
`

Caudovirales
Caudovirales
Caudovirales
Myoviridae
Caudovirales
Caudovirales

这种同样适用于

1.没有分支的，只是virus：

10239	Viruses
10239	Viruses

会变成：（前面会有一个小空格）

 Viruses
 Viruses
 Viruses
 Viruses

2.名字很长，其中有空格

1173749	Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;Guernseyvirinae;Cornellvirus;Salmonella virus SP31;Salmonella phage FSL SP-031
1173749	Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;Guernseyvirinae;Cornellvirus;Salmonella virus SP31;Salmonella phage FSL SP-031
1173749	Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;Guernseyvirinae;Cornellvirus;Salmonella virus SP31;Salmonella phage FSL SP-031

会变成：

Salmonella phage FSL SP-031
Salmonella phage FSL SP-031
Salmonella phage FSL SP-031
Salmonella phage FSL SP-031
Salmonella phage FSL SP-031
Salmonella phage FSL SP-031

正是想要的格式

#删除行首空格及tab键
sed -i 's/^[ \t]*//g' virus_name