This is my bed file for all the exon coordinates ..small subset so i want to take out all the exons that of a given gene let say i have gene in chr 1 which starts from
chr1 11868 12227 so i want to parse out all the exons that comes in between
this is my small subset
cat exon.bed | head -10 chr1 11868 12227 + exon chr1 11871 12227 + exon chr1 11873 12227 + exon chr1 12009 12057 + exon chr1 12178 12227 + exon chr1 12594 12721 + exon chr1 12612 12697 + exon chr1 12612 12721 + exon chr1 12612 12721 + exon chr1 12974 13052 + exon
How do i parse out , i use mostly R and bit of shell script but I m not sure if i can use R , may a few lines of perl or shell script can help me solve my problem.
Any help or suggestion would be highly appreciated