Linux 中sed命令实现从gff文件中仅仅提取基因名称

 

001、

(base) [b20223040323@admin1 x_test]$ ls                                 ## 测试gff文件
GCF_000001405.40_GRCh38.p14_genomic.fna.gz  GCF_000001405.40_GRCh38.p14_genomic.gff
(base) [b20223040323@admin1 x_test]$ grep -v "^#" GCF_000001405.40_GRCh38.p14_genomic.gff | awk -F "\t" '$3 == "gene"' | sed 's/\(.*\)\(gene=[^;]\+\)\(.*\)/\2/' | head      ## 仅仅提取基因名称，并保留前10行
gene=MIR6859-1
gene=MIR1302-2HG
gene=MIR1302-2
gene=FAM138A
gene=OR4F5
gene=LOC124903816
gene=LOC124900384
gene=LOC729737
gene=LOC124903814
gene=MIR6859-2
(base) [b20223040323@admin1 x_test]$ grep -v "^#" GCF_000001405.40_GRCh38.p14_genomic.gff | awk -F "\t" '$3 == "gene"' | sed 's/\(.*\)\(gene=[^;]\+\)\(.*\)/\2/' | tail     ## 仅仅提取基因名称，并保留后10行
gene=ND4
gene=TRNH
gene=TRNS2
gene=TRNL2
gene=ND5
gene=ND6
gene=TRNE
gene=CYTB
gene=TRNT
gene=TRNP

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