problems for loading gz files #2
Description
Using your example data, python ACCOST.py 40000 example/bins_chr.txt example/info.tab hIMR90 hESC, I run into the problem when trying to load gz files:
Welcome. Starting ACCOST.
Output will be written to output_dir
/usr/lib/python3/dist-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.17.3 and <1.25.0 is required for this version of SciPy (detected version 1.26.3
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
temp directory currently set to: /tmp/tmpq18rbxs0
Reading bin midpoints and mappability from example/bins_chr.txt
Found 3347 bins, including 113 low mappability bins.
Read 1 pairs of files from example/info.tab.
Loading data
Loading biases from example/hIMR90_chr12_r1.biases.gz
Traceback (most recent call last):
File "/home/nathalie/Downloads/ACCOST/ACCOST_internal.py", line 463, in <module>
main()
File "/home/nathalie/Downloads/ACCOST/ACCOST_internal.py", line 341, in main
matrixA.load_biases(biasfile_A)
File "/home/nathalie/Downloads/ACCOST/contact_counts.py", line 823, in load_biases
if '\t' in line or ',' in line:
TypeError: a bytes-like object is required, not 'str'
/usr/lib/python3/dist-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.17.3 and <1.25.0 is required for this version of SciPy (detected version 1.26.3
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
Traceback (most recent call last):
File "/home/nathalie/Downloads/ACCOST/annotate_pvals.py", line 51, in <module>
main()
File "/home/nathalie/Downloads/ACCOST/annotate_pvals.py", line 22, in main
pvalfh = open(pval_file,'r')
FileNotFoundError: [Errno 2] No such file or directory: 'output_dir/_ln_pvals.txt'
ACCOST Done!
In this precise example, replacing line by line.decode() after lieng 819 of contact_count.py (when relevant) solves the problem but I struggle more with a similar problem due to the use of csv.Sniffer line 106.