Installation error with pyx
Closed this issue · 2 comments
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).
Seems to be related to numpy version (tensorflow/tensorflow#559), please reopen if the update does not resolve the issue (without modifying CRISPResso2Align.pyx)
This error happens with unspecified bases in FASTQ, leading to alignment score over/underflow. Currently bean only supports A/C/T/G for bases. If you need to accommodate special bases, please edit output_path/.aln_mat.txt (
crispr-bean/bean/mapping/GuideEditCounter.py
Line 248 in fb67667