I have a somewhat tricky BED file format, which I should convert to a classic BED format so as I can properly use it for further steps:
I have this unconventional BED format:
1 12349 12398 +
1 23523 23578 -
1 23550;23570;23590 23640;23689;23652 +
1 43533 43569 +
1 56021;56078 56099;56155 +
Say that those multiple position rows are representing non-coding fragmented regions.
What I would like to get is a cannonical BED file such as:
1 12349 12398 +
1 23523 23578 -
1 23550 23640 +
1 23570 23689 +
1 23590 23652 +
1 43533 43569 +
1 56021 56099 +
1 56078 56155 +
where the poliregions that were mixed in one row, are put in other rows, while mantaining chromosome number and strand.
I have been struggling with a proper way to do this for a while...
Could anyone help?
Thanks
•
written
by
Emilio Marmol
2 answers
awk '{N=split($2,a,/[;]/);split($3,b,/[;]/);for(i=1;i<=N;i++) printf("%s\t%s\t%s\t%s\n",$1,a[i],b[i],$4);}' input.bed
1 12349 12398 +
1 23523 23578 -
1 23550 23640 +
1 23570 23689 +
1 23590 23652 +
1 43533 43569 +
1 56021 56099 +
1 56078 56155 +
Good luck. In the last line test.pseudobed is the input file. I called it pseudobed because your input is not in BED format. Column 4 in BED is a name, the strand is in column 6. The code snippet will take care of it, producing a standard BED with 6 columns, leaving the 4th and 5th with a . as spaceholder. If you do not want that, simply remove the ".", "." part from the awk commands.
while read i; do
if [[ $(echo $i | tr " " "\t" | grep -c ';' /dev/stdin) > 0 ]]; then
CHR="$(echo $i | tr " " "\t" | cut -f1)"
STR="$(echo $i | tr " " "\t" | cut -f4)"
paste \
<(echo $i | tr " " "\t" | cut -f2 | tr ";" "\n") \
<(echo $i | tr " " "\t" | cut -f3 | tr ";" "\n") | \
awk -v chr=$CHR -v str=$STR 'OFS="\t" {print chr, $1, $2, ".", ".", str}'
else
echo $i | tr " " "\t" | awk 'OFS="\t" {print $1, $2, $3, ".", ".", $4}'
fi
done < test.pseudobed
1 12349 12398 . . +
1 23523 23578 . . -
1 23550 23640 . . +
1 23570 23689 . . +
1 23590 23652 . . +
1 43533 43569 . . +
1 56021 56099 . . +
1 56078 56155 . . +
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