change ".." to tab or change a string of characters into different column

Question

[Ming Lu]

I want to change a CTCF CHIA-PET bed file data to its two end bed file. how can I change

       chrX:154145949..154146870-chrX:154314445..154315402,2
       chrX:154208778..154209800-chrX:154376894..154377812,3
       chrX:154208831..154209797-chrX:154285357..154286294,4

into

      chrX 154145949 154146870
      chrX 154314445 154315402
      chrX 154208778 154209800
      chrX 154376894 154377812
      chrX 154208831 154209797
      chrX 154285357 154286294

Answer 1

[Puli Chandramouli Reddy]

Hi,

Use this

sed 's/-/\n/g;s/:/\t/g;s/\.\./\t/g;s/,[0-9]//g' ./your_file > ./your_file_mod

Answer 2

[Alex Reynolds]

To create an unsorted BED file:

$ awk -v OFS="\t" '{n=split($0, a, /[:.\-,]/); printf("%s\t%s\t%s\n%s\t%s\t%s\n", a[1],a[2],a[4],a[5],a[6],a[8]);}' chia-pet.txt > chia-pet.unsorted.bed

To create a sorted BED file:

$ awk -v OFS="\t" '{n=split($0, a, /[:.\-,]/); printf("%s\t%s\t%s\n%s\t%s\t%s\n", a[1],a[2],a[4],a[5],a[6],a[8]);}' chia-pet.txt | sort-bed - > chia-pet.bed

Sorted BED files allow BEDOPS binaries to do set operations on BED files correctly and efficiently.

Answer 3

[cpad0112]

output:

$ awk -v OFS="\t" '{gsub("-","\n"); gsub(/:|\../," ")}1' test.txt | sed 's/,.*//g' or $ sed 's/,.*//g' test.txt | tr ":" " " | tr ".." " " | tr "-" "\n"

chrX 154145949 154146870
chrX 154314445 154315402
chrX 154208778 154209800
chrX 154376894 154377812
chrX 154208831 154209797
chrX 154285357 154286294

input:

$ cat test.txt 
chrX:154145949..154146870-chrX:154314445..154315402,2
chrX:154208778..154209800-chrX:154376894..154377812,3
chrX:154208831..154209797-chrX:154285357..154286294,4