bed file in bad format

Question

[biostarsb]

Hi,

i have a bed file, when i use cat -e

chr4     177604691   177713895 $
chr1     223967595   224033674 $
chr1     43766566    43788781 $
chr16    11361714    11363160 $
chr11    120973375   121061515 $
chr4     70706930    70725870 $
chr9     108424738   108425385 $

can any one help me to delete the "" at the end of lines ?

Thank you.

Answer 1

[Alex Reynolds]

The awk command can be used to strip off trailing whitespace.

Compare:

$ echo -e "chrN\t100\t200\tfoo " | cat -e
chrN    100 200 foo $

with:

$ echo -e "chrN\t100\t200\tfoo " | awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$4}' | cat -e
chrN    100 200 foo$

For a three-column file:

$ awk 'BEGIN{OFS="\t"}{print $1,$2,$3}' bad.bed3 | sort-bed - > good.sorted.bed3

Answer 2

[d-cameron]

If you just want to remove columns, the cut command is the simplest approach:

echo -e "chrN\t100\t200\tfoo " | cut -f 1-3

Answer 3

[GenoMax]

sed 's/\ $//g' your_file > new_file should also work.