使用awk来提取内容

1.提取gff文件中的HLA基因的相关bed文件。

gff的格式:

zcat *gz|gawk 'BGIN{FS="\t";OFS="\t"}$3=="gene"{match($9,/gene_name([^;]+)/,a);if(a[1]~/HLA-/){print $1,$4,$5,a[1]}}' 
chr6 29722775 29738528 "HLA-F"
chr6	29726601	29749049	"HLA-F-AS1"
chr6	29790954	29797811	"HLA-V"
chr6	29800415	29802425	"HLA-P"
chr6	29826967	29831125	"HLA-G"
chr6	29887752	29890482	"HLA-H"
chr6	29896654	29897786	"HLA-T"
chr6	29926459	29929232	"HLA-K"
chr6	29934101	29934286	"HLA-U"
chr6	29941260	29945884	"HLA-A"
chr6	29956596	29958570	"HLA-W"
chr6	30005971	30009956	"HLA-J"
chr6	30259584	30293014	"HLA-L"
chr6	30351416	30351550	"HLA-N"
chr6	30489467	30494205	"HLA-E"
chr6	31268749	31272130	"HLA-C"
chr6	31269491	31357188	"HLA-B"

  

 

 

 

 

 

 

posted on 2017-12-18 15:40  青萍,你好  阅读(679)  评论(0编辑  收藏  举报

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