Modify BED with poliregions [closed] - r

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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 canonical 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 maintaining chromosome number and strand.

Answer 1

Could you please try following.
awk '
{
num=split($2,array1,";")
num1=split($3,array2,";")
}
num>1 || num1>1{
for(i=1;i<=num;i++){
print $1,array1[i],array2[i],$NF
}
next
}
1' Input_file | column -t
Output will be as follows.
1 12349 12398 +
1 23523 23578 -
1 23550 23640 +
1 23570 23689 +
1 23590 23652 +
1 43533 43569 +
1 56021 56099 +
1 56078 56155 +

Answer 2

#!/usr/bin/env bash
# ^^^^-- NOT /bin/sh
while read -r a b c d; do
if [[ $b = *';'* ]]; then # if b contains any ';'s
IFS=';' read -r -a ba <<<"$b" # read string b into array ba
IFS=';' read -r -a ca <<<"$c" # read string c into array ca
for idx in "${!ba[#]}"; do # iterate over the indices of array ba
# print a and d with the values for a given index for both ba and ca
printf '%s\t%s\t%s\t%s\n' "$a" "${ba[idx]}" "${ca[idx]}" "$d"
done
else
printf '%s\t%s\t%s\t%s\n' "$a" "$b" "$c" "$d"
fi
done
This combines the answers to existing StackOverflow questions:
bash script loop through two variables in lock step
Reading a delimited string into an array in Bash
...and guidance in the BashFAQ:
How can I read a file (data stream, variable) line-by-line (and/or field-by-field)?
See this running at https://ideone.com/wmrXPE

Answer 3

$ cat tst.awk
BEGIN { FS="[[:space:];]+" }
{
n = (NF - 2) / 2
for (i=1; i<=n; i++) {
print $1, $(i+1), $(i+n), $NF
}
}
$ awk -f tst.awk file
1 12349 12349 +
1 23523 23523 -
1 23550 23590 +
1 23570 23640 +
1 23590 23689 +
1 43533 43533 +
1 56021 56078 +
1 56078 56099 +

Answer 4

Try Perl solution
perl -lane ' if( /;/ and /(\S{2,})\s+(\S{2,})/ ) {
$i=0;#x=split(";",$1);#y=split(";",$2); while($i++<scalar(#x))
{ print join(" ",$F[0],$x[$i-1],$y[$i-1],$F[-1]) }} else { print } ' emilio.txt| column -t
with the given inputs
$ cat emilio.txt
1 12349 12398 +
1 23523 23578 -
1 23550;23570;23590 23640;23689;23652 +
1 43533 43569 +
1 56021;56078 56099;56155 +
$ perl -lane ' if( /;/ and /(\S{2,})\s+(\S{2,})/ ) {
$i=0;#x=split(";",$1);#y=split(";",$2); while($i++<scalar(#x))
{ print join(" ",$F[0],$x[$i-1],$y[$i-1],$F[-1]) }} else { print } ' emilio.txt| column -t
1 12349 12398 +
1 23523 23578 -
1 23550 23640 +
1 23570 23689 +
1 23590 23652 +
1 43533 43569 +
1 56021 56099 +
1 56078 56155 +
$