Activity-normalized variant effect size estimation from pooled CRISPR screens
Home Page: https://pinellolab.github.io/crispr-bean/
License: GNU Affero General Public License v3.0
Concat gives KeyError when uns keys are not exactly the same
Hi,
Congrats on the release of this package. It seems that this tool will be quite useful for the CRISPR community. I especially like the functionality for accounting for heterogeneity in editing efficiency across gRNAs.
I am trying to work through the tutorials but am having a bit of difficulty. In particular, the variant sorting screen tutorial uses an example "test file", but I am unable to locate this test file. Is the idea that I should download the test directory from here and then update the file paths on my machine?
Thanks,
Tim
Currently not clear when guide column has numeric index or name as index. Clear up so that you won't get errors from calling methods that use self.guides['name'].
Copying error report from Elijah Login Mena @bwh
just want to let you know I had a minor issues installing bean on my computer yesterday. What worked for me was adding the following two lines to the beginning of the
CRISPResso2Align.pyx
file:
from numpy cimport import_array
import_array()
Otherwise I got the following error message:
>>>
import bean Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/emena/Dropbox .../crispr-bean/bean/__init__.py", line 3, in <module> from . import mapping as mp File "/Users/emena/Dropbox
.../crispr-bean/bean/mapping/__init__.py", line 1, in <module> from .GuideEditCounter import GuideEditCounter File "/Users/user/Dropbox .../crispr-bean/bean/mapping/GuideEditCounter.py",
line 16, in <module> from ._supporting_fn import ( File "/Users/user/Dropbox .../crispr-bean/bean/mapping/_supporting_fn.py", line 9, in <module> from bean.mapping.CRISPResso2Align import read_matrix, global_align_base_editor
File "bean/mapping/CRISPResso2Align.pyx", line 1, in init bean.mapping.CRISPResso2Align # Copied & modified from CRISPResso2 https://github.com/pinellolab/CRISPResso2/blob/master/CRISPResso2/CRISPResso2Align.pyx ImportError: numpy.core.multiarray failed to
import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use '<void>numpy._import_array' to disable if you are certain you don't need it).
Example file required for bean-create-screen as it's not clear
Suggestion by @TYTYBU
Report by Lukas Edward Dow ([email protected])
Using cached [email protected]_2_17_x86_64.manylinux2014_x86_64.whl (385 kB)
Using cached numba-0.59.1-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.7 MB)
Using cached nvidia_nvjitlink_cu12-12.4.127-py3—none-manylinux2014_x86_64.whl (21.1 MB)
Using cached [email protected]—none-any.whl (11 kB)
Using cached [email protected] (38 kB)
Using cached toposort-1.10-py3—-none-any.whl (8.5 kB)
Using cached [email protected]—none-any.whl (34 kB)
Building wheels for collected packages: sharedarray
Building wheel for sharedarray (pyproject.toml) ... error
: subprocess-exited-with-error
Building wheel for sharedarray (pyproject.toml) did not run successfully.
exit code: 1
running bdist_wheel
running build
running build_ext
building 'SharedArray' extension
creating build
creating build/temp.linux-x86_64-—cpython-39
creating build/temp.1linux-x86_64-cpython-39/src
gcc -pthread -B /home/1ud200@5/.conda/envs/crispr—bean/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -02 -Wall
-fPIC -02 -isystem /home/1ud2005/.conda/envs/crispr—bean/include -I/home/1ud20@5/.conda/envs/crispr—bean/include -fPIC -02 -isyst
em /home/1ud2005/.conda/envs/crispr—bean/include -fPIC -I/scratch/1ud2005_11425453/pip—build—env-i7eammi4/overlay/lib/python3.9/s
ite-packages/numpy/core/include —I/home/1ud2005/.conda/envs/crispr—bean/include/python3.9 -c ./src/map_owner.c -o build/temp.linu
x-x86_64-cpython-39/./src/map_owner.o
gcc -pthread -B /home/1ud200@5/.conda/envs/crispr—bean/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -02 -Wall
-fPIC -02 -isystem /home/1ud2005/.conda/envs/crispr—bean/include -I/home/1ud20@5/.conda/envs/crispr—bean/include -fPIC -02 -isyst
em /home/1ud2005/.conda/envs/crispr—bean/include -fPIC -I/scratch/1ud2005_11425453/pip—build—env-i7eammi4/overlay/lib/python3.9/s
ite-packages/numpy/core/include —I/home/1ud2005/.conda/envs/crispr—bean/include/python3.9 -c ./src/map_owner_mlock.c -o build/tem
p. linux-x86_64-cpython-39/./src/map_owner_mlock.o
gcc -pthread -B /home/1ud200@5/.conda/envs/crispr—bean/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -02 -Wall
-fPIC -02 -isystem /home/1ud2005/.conda/envs/crispr—bean/include -I/home/1ud20@5/.conda/envs/crispr—bean/include -fPIC -02 -isyst
em /home/1ud2005/.conda/envs/crispr—bean/include -fPIC -I/scratch/1ud2005_11425453/pip—build—env-i7eammi4/overlay/lib/python3.9/s
ite-packages/numpy/core/include —I/home/1ud2005/.conda/envs/crispr—bean/include/python3.9 -c ./src/map_owner_msync.c -o build/tem
p. linux-x86_64-cpython-39/./src/map_owner_msync.o
gcc -pthread -B /home/1ud200@5/.conda/envs/crispr—bean/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -02 -Wall
-fPIC -02 -isystem /home/1ud2005/.conda/envs/crispr—bean/include -I/home/1ud20@5/.conda/envs/crispr—bean/include -fPIC -02 -isyst
em /home/1ud2005/.conda/envs/crispr—bean/include -fPIC -I/scratch/1ud2005_11425453/pip—build—env-i7eammi4/overlay/lib/python3.9/s
ite-packages/numpy/core/include —I/home/1ud2005/.conda/envs/crispr—bean/include/python3.9 -c ./src/map_owner_munlock.c -o build/t
emp. linux-x86_64-cpython-39/./src/map_owner_munlock.o
gcc -pthread -B /home/1ud200@5/.conda/envs/crispr—bean/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -02 -Wall
-fPIC -02 -isystem /home/1ud2005/.conda/envs/crispr—bean/include -I/home/1ud20@5/.conda/envs/crispr—bean/include -fPIC -02 -isyst
em /home/1ud2005/.conda/envs/crispr—bean/include -fPIC -I/scratch/1ud2005_11425453/pip—build—env-i7eammi4/overlay/lib/python3.9/s
ite-packages/numpy/core/include —I/home/1ud2005/.conda/envs/crispr—bean/include/python3.9 -c ./src/shared_array.c -o build/temp.1
inux-x86_64-cpython-39/./src/shared_array.o
gcc -pthread -B /home/1ud200@5/.conda/envs/crispr—bean/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -02 -Wall
-fPIC -02 -isystem /home/1ud2005/.conda/envs/crispr—bean/include -I/home/1ud20@5/.conda/envs/crispr—bean/include -fPIC -02 -isyst
em /home/1ud2005/.conda/envs/crispr—bean/include -fPIC -I/scratch/1ud2005_11425453/pip—build—env-i7eammi4/overlay/lib/python3.9/s
ite-packages/numpy/core/include —I/home/1ud2005/.conda/envs/crispr—bean/include/python3.9 -c ./src/shared_array_attach.c -o build
/temp.linux-x86_64-cpython-39/./src/shared_array_attach.o
./src/shared_array_attach.c: In function ‘do_attach’:
./src/shared_array_attach.c:99:2: error: ‘for’ loop initial declarations are only allowed in C99 mode
for (int i = 0; i < meta—>ndims; i++)
rn
./src/shared_array_attach.c:99:2: note: use option -std=c99 or -std=gnu99 to compile your code
error: command '/usr/bin/gcc' failed with exit code 1
: This error originates from a subprocess, and is likely not a problem with pip.
Failed to build sharedarray
This comes from C version, providing -std=c99 or std-gnu99 resolves the issue (link).
CFLAGS='-std=c99' python -m pip install .
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