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Replace BED intervals

Hi!

I want to make all the intervals in a series of BED files equal to 1bp by taking the middle position of each interval.

Any suggestion about how to do it (possibly also with GNU Parallel?)

Example:

chr1   150   170   +

I'd like to replace it as:

chr1   160   161   +

Thank you in advance!

script bed
• 3,470 views • link
updated by Ram Ram • written by mujupas mujupas

Ok, thanks a lot, I'll give it a try!

• 1 views • link
written by mujupas mujupas

Thanks, it worked.

The only problem is that now the new 1bp BED files are using spaces as separators and not TAB.

I've tried the following command but it doesn't work in replacing spaces with tabs:

awk=$'\'{OFS="\\t"}{print $1"\t"int(($3-$2)/2)+$2"\t"int(($3-$2)/2)+$2+1}\''
[me@me]$ echo $awk
'{OFS="\t"}{print $1" "int(($3-$2)/2)+$2" "int(($3-$2)/2)+$2+1}'
parallel 'cat {} | awk '$awk' {} > {.}.output' ::: *.input

Any idea?

Thanks in advance!

• 1 views • link
updated by Ram Ram • written by mujupas mujupas

2 answers 

midbed() { 
  perl -ane '$F[1]=int(($F[1]+$F[2])/2);$F[2]=$F[1]+1;print join("\t",@F)."\n"' $1;
}
export -f midbed
parallel midbed {} '>' {.}.mbed ::: *.bed
• 1 views • link
updated by Ram Ram • written by ole.tange ole.tange

Worked like a charm, thank you so much!

• 0 views • link
written by mujupas mujupas

Consider using awk; generally:

$ awk '{print $1"\t"int(($3-$2)/2)+$2"\t"int(($3-$2)/2)+$2+1}' foo.bed > bar.bed
• 1 views • link
updated by Ram Ram • written by Alex Reynolds Alex Reynolds

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