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parklab / MosaicForecast

A mosaic detecting software based on phasing and random forest
MIT License
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37th line of args_generator.py #37

Closed dongjuleem closed 1 year ago

dongjuleem commented 1 year ago

Thank you for providing this grate tool. I encountered an issue while using the args_generator.py file. As far as I understand, the problem seems to occur when loading X.intervals.list and Y.intervals.list within the intervals folder.

In the 37th line of args_generator.py instead of pattern=re.compile(r'([0-9]+)\.intervals\.list') I'd like to ask if it's okay to change to pattern = re.compile(r'([0-9XY]+)\.intervals\.list') and use it.

douym commented 1 year ago

Thank you for providing this grate tool. I encountered an issue while using the args_generator.py file. As far as I understand, the problem seems to occur when loading X.intervals.list and Y.intervals.list within the intervals folder.

In the 37th line of args_generator.py instead of pattern=re.compile(r'([0-9]+)\.intervals\.list') I'd like to ask if it's okay to change to pattern = re.compile(r'([0-9XY]+)\.intervals\.list') and use it.

Hi @dongjuleem ,

Thanks for your message. It should be ok to run the prediction model on haploid chromosomes, but the haplotype phasing by "Phase.py" would be different compared with diploid chromosomes.

Best, Y.

dongjuleem commented 1 year ago

Hi, Sorry for the basic question. I would like to apply the model to diploid chromosomes. In that case, is it advisable to apply it only to chromosomes 1 through 22, excluding X and Y from the intervals list?

douym commented 1 year ago

Hi, Sorry for the basic question. I would like to apply the model to diploid chromosomes. In that case, is it advisable to apply it only to chromosomes 1 through 22, excluding X and Y from the intervals list?

Hi @dongjuleem ,

In that case, maybe you could exclude X and Y from Males and exclude Y from females.

Best wishes,

Y.

dongjuleem commented 1 year ago

i appreciate your time.