Modify BED with poliregions

Question

[Emilio Marmol]

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

Answer 1

[Pierre Lindenbaum]

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   +

Answer 2

[ATpoint]

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   .   .   +