Replace BED intervals
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7.8 years ago
mujupas ▴ 70

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 • 2.1k views
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Ok, thanks a lot, I'll give it a try!

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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!

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2
Entering edit mode
7.8 years ago
ole.tange ★ 4.3k
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
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Worked like a charm, thank you so much!

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1
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7.8 years ago

Consider using awk; generally:

$ awk '{print $1"\t"int(($3-$2)/2)+$2"\t"int(($3-$2)/2)+$2+1}' foo.bed > bar.bed
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