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acorg / midtools

Multiple Infection Detection - Python for detecting multiple infections from sequence reads and trying to pick them apart

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Attribute error in Significant-base-frequencies.py

TaliVeith opened this issue · comments

commented

significant-base-frequencies.py --samFile 190802_15-against-Adeno.sam > out

Error message:

Traceback (most recent call last):
File "/home/tali/Darkmatter/env/bin/significant-base-frequencies.py", line 63, in
significantOffsets) = parseCommandLineOptions(args)
File "/home/tali/Darkmatter/env/lib/python3.6/site-packages/midtools/options.py", line 61, in parseCommandLineOptions
paddedSAM = PaddedSAM(args.samFile)
File "/home/tali/Darkmatter/env/lib/python3.6/site-packages/dark/sam.py", line 428, in init
referenceLengths = samFilter.referenceLengths()
AttributeError: 'str' object has no attribute 'referenceLengths'

commented

You need to run pip install -U dark-matter. If you first run the command dark-matter-version.py you'll see what version you have installed. Latest is 3.0.78.

commented

This was fixed but not pushed to PyPI. Closing.