shell实现从gff文件的第9列提取基因名称

 

001、sed

[root@PC1 test]# ls
a.txt
[root@PC1 test]# cat a.txt     ## 测试数据
ID=gene-LOC124418406;Dbxref=GeneID:124418406;Name=LOC124418406;gbkey=Gene;gene=LOC124418406;gene_biotype=lncRNA
ID=gene-LOC121106832;Dbxref=CGNC:86713,GeneID:121106832;Name=LOC121106832;gbkey=Gene;gene=LOC121106832;gene_biotype=lncRNA
ID=gene-LOC107049418;Dbxref=CGNC:72437,GeneID:107049418;Name=LOC107049418;gbkey=Gene;gene=LOC107049418;gene_biotype=lncRNA
ID=gene-LOC124417607;Dbxref=GeneID:124417607;Name=LOC124417607;gbkey=Gene;gene=LOC124417607;gene_biotype=lncRNA
ID=gene-RNF212B;Dbxref=CGNC:55930,GeneID:770305;Name=RNF212B;gbkey=Gene;gene=RNF212B;gene_biotype=lncRNA
[root@PC1 test]# sed 's/\(^.*\+\)\(gene=\S\+\)\(;.*\)/\2/' a.txt    ## 提取命令
gene=LOC124418406
gene=LOC121106832
gene=LOC107049418
gene=LOC124417607
gene=RNF212B

 

 

002、awk

[root@PC1 test2]# ls
a.txt
[root@PC1 test2]# cat a.txt
ID=gene-LOC124418406;Dbxref=GeneID:124418406;Name=LOC124418406;gbkey=Gene;gene=LOC124418406;gene_biotype=lncRNA
ID=gene-LOC121106832;Dbxref=CGNC:86713,GeneID:121106832;Name=LOC121106832;gbkey=Gene;gene=LOC121106832;gene_biotype=lncRNA
ID=gene-LOC107049418;Dbxref=CGNC:72437,GeneID:107049418;Name=LOC107049418;gbkey=Gene;gene=LOC107049418;gene_biotype=lncRNA
ID=gene-LOC124417607;Dbxref=GeneID:124417607;Name=LOC124417607;gbkey=Gene;gene=LOC124417607;gene_biotype=lncRNA
ID=gene-RNF212B;Dbxref=CGNC:55930,GeneID:770305;Name=RNF212B;gbkey=Gene;gene=RNF212B;gene_biotype=lncRNA
[root@PC1 test2]# awk -F "gene=" '{print $2}' a.txt | cut -d ";" -f 1
LOC124418406
LOC121106832
LOC107049418
LOC124417607
RNF212B