linux 中shell 脚本将 gff文件转换为bed文件

 

001、

[b20223040323@admin1 test]$ ls    ## 测试gff文件
exons_only.gff
[b20223040323@admin1 test]$ gff2bed <exons_only.gff > exons_only.bed  ##  gff2bed模块转换
Warning: If your Wiggle data is a significant portion of available system memory, use the --max-mem and --sort-tmpdir options, or use --do-not-sort to disable post-conversion sorting. See --help for more information.
[b20223040323@admin1 test]$ ls    ## 转换结果
exons_only.bed  exons_only.gff
[b20223040323@admin1 test]$ awk -F "\t" '{OFS = "\t"; print $1, $4 - 1, $5, $6, $8, $7, $2, $3, ".", $NF}' exons_only.gff > tem.gff  ## 列的重排，
[b20223040323@admin1 test]$ cut -f 1 tem.gff | sort | uniq | while read i; do grep $i tem.gff | sort -k 2n -k 3n >> result.bed; done   ## 排序
[b20223040323@admin1 test]$ ls   ## 结果文件
exons_only.bed  exons_only.gff  result.bed  tem.gff
[b20223040323@admin1 test]$ diff exons_only.bed result.bed   ## 比较gff2bed模块和shell脚本的结果， 有一行差异？？
54392c54392
< NC_052532.1   67271350        67271351        .       .       -       Gnomon  exon   .ID=exon-XM_015290272.4-6;Parent=rna-XM_015290272.4;Dbxref=GeneID:418207,Genbank:XM_015290272.4,CGNC:10484;experiment=COORDINATES: cap analysis [ECO:0007248] and polyA evidence [ECO:0006239];gbkey=mRNA;gene=KRAS;product=KRAS proto-oncogene%2C GTPase%2C transcript variant X3;transcript_id=XM_015290272.4;zero_length_insertion=True
---
> NC_052532.1   67271350        67271351        .       .       -       Gnomon  exon   .ID=exon-XM_015290272.4-6;Parent=rna-XM_015290272.4;Dbxref=GeneID:418207,Genbank:XM_015290272.4,CGNC:10484;experiment=COORDINATES: cap analysis [ECO:0007248] and polyA evidence [ECO:0006239];gbkey=mRNA;gene=KRAS;product=KRAS proto-oncogene%2C GTPase%2C transcript variant X3;transcript_id=XM_015290272.4