refactor: Updated the counts-umi-smk rule and it's scripts to python3 #93
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….py to update the script to python3.
…adsBAM_python3.py
…as it is needed in the FastQ2doubleIndexBAM_python3.py script.
File "/home/ali/Documents/MPRAsnakeflow/workflow/rules/../scripts/count/FastQ2doubleIndexBAM_python3.py", line 281, in <module>
outfiles[None][0].write(forward)
File "pysam/libcalignmentfile.pyx", line 1710, in pysam.libcalignmentfile.AlignmentFile.write
File "pysam/libcalignmentfile.pyx", line 1742, in pysam.libcalignmentfile.AlignmentFile.write
OSError: sam_write1 failed with error code -1
[E::bgzf_close] File write failed
Ampholyt
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Jan 24, 2024
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I add it here because it is a minor thing (actually because of the Snakefile): change regex strings in the Snakefile to raw strings as mentioned here
visze
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to visze/MPRAsnakeflow
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Jul 31, 2024
…k-script-update refactor: Updated the counts-umi-smk rule and it's scripts to python3
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Created new files for scripts with the suffix _python3 and also added the pysam library in the python3 environment that was needed by the python scripts