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liguowang / cpgtools

Python package to analyze DNA methylation data
GNU General Public License v3.0
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Difficulty running test #7

Open annajellemabutler opened 4 months ago

annajellemabutler commented 4 months ago

I installed using pip3. I am trying to run the CpG_aggregation.py test. I downloaded the test files, and am now running CpG_aggregation.py -b hg19.RefSeq.union.1Kpromoter.bed.gz -i test_03_RRBS.bed -o out. However, the output I get is just the help message. There are no errors or any other output. Any suggestions?

liguowang commented 4 months ago

It seems you have to provide value to "-t" or "--type". The accepted value is "count" (if it is RRBS/WGBS) or "beta" (if it is EPIC array data).