Open BennyHz opened 6 months ago
Hi!
I can't reproduce this issue. A stack trace leading up to the error, and a minimal reproducible example could be helpful to further diagnose.
Also, which python version are you using?
My python version:
python -V
Python 3.11.6
What I've done to verify this issue:
# Create some temp dir:
# cd /tmp/
# mkdir 2024.scDamAndTools.issue_3
# Create a venv for this issue
python -m venv .venv
source .venv/bin/activate
# Install the packages as per the instructions for scDamAndTools
pip install --upgrade pip wheel setuptools
pip install -I cython
pip install git+https://github.com/KindLab/scDamAndTools.git
# Create some example data
# mkdir data/
# vim data/reference.fa
cat data/reference.fa
>chr1
AGAAGATGACGAGACAGTGATGCA
TGAGAGACTGGAGATGATGGGAGA
TCACACAAACAAACAGTAAAAAAA
Generate the bed file:
find_motif_occurrences.py ./data/reference.fa GATC | gzip > data/motif_GATC.bed.gz
zcat data/motif_GATC.bed.gz
chr1 46 50
Run fetch_regions.py
:
fetch_regions.py -l 10 ./data/motif_GATC.bed.gz ./data/reference.fa
>chr1_46_50_plus
GATCACACAA
>chr1_46_50_minus
GATCTCCCAT
Thanks a lot! I have fixed the problem by using a new virtual environment.
Hello! I was trying to use
fetch_region.py
to conduct in silico digest. I trusted that we dowloaded the input genome.fa file correctly from Ensembl and used it to generate the GATC.position.bed.gz correctly viafind_motif_occurrences.py
. But when thefetch_region.py
was carried out like this:fetch_region.py -q -l 150 ./refarrays/genome.GATC.positions.bed.gz $FASTAFN
, an error occurred:TypeError: a bytes-like object is required, not 'dict'
. We find it trouble to understand why this error happened, cause there's not many space for customized operation in this code. It would be appreciated for any help!