Bioinformatics Asked by Libby Kosolapov on January 25, 2021
I want to create custom tracks from these files
I can add the line : track type=narrowPeak name=“narrowPeak” manually by opening it with text editor:
track type=narrowPeak name=“narrowPeak”
but I wonder if there is no simple way to do it with code- to open all files that end with bed and add them this line.
Didnt find this option in bed tools, If it is possible to add the name extracting it from the file name it would be amazing.
Many thanks
I don't think you need to go to R or Python to do that. In bash
set -euxo pipefail
for f in *.bed
do
bn="$(basename ${f})"
on="${bn%%.bed}_with_header.bed"
echo 'track type=narrowPeak name="narrowPeak"' > "${on}"
cat "${f}" >> "${on}"
done
EDIT: I just read you want to set the name based on the filename.
EDIT2: And also to add an arbitrary directory
set -euxo pipefail
INDIR="/path/to/bedfiles"
for f in $(find "${INDIR}" -name "*.bed")
do
bn=$(basename "${f}")
on="${bn%%.bed}_with_header.bed"
dn=$(dirname "${f}")
echo "track type=narrowPeak name="${bn}"" > "${dn}"/"${on}"
cat "${f}" >> "${dn}"/"${on}"
done
Answered by Bastian Schiffthaler on January 25, 2021
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