Complete workflow for Y-STRs using custom sequence ranges #79
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lusSTR/wrappers/filter.py
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| def process_input( | ||
| input_name, | ||
| outpath, | ||
| profile_type, | ||
| data_type, | ||
| output_dir, | ||
| info, | ||
| separate, | ||
| output_type, | ||
| nofilters, | ||
| strand, | ||
| separate, | ||
| custom, | ||
| sex, | ||
| info, | ||
| ): |
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I've never had this happen before- @standage when I specify nofilters as True in the config, it's passed as True to the function but then is changed to False, so the no filters if statement is bypassed. Why is that happening?
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I do notice that you name the parameter filters in the Snakemake rule params block, but nofilters in the config file and the Python code. That's a possible source of confusion, but it doesn't explain this behavior. And otherwise I can't see any obvious reason the variable's value would be changed.
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if I do print(nofilters) in main() it's True, if I print it in process_input() it's False. 🫤
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I had changed the order of the function arguments..... 🤦♀️
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Ah, that'll do it. For functions with that many arguments, I almost always try to find which arguments have a reasonable default value and convert them to keyword arguments, which reduces that kind of issue.
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I added some keyword arguments.
| try: | ||
| final_df = final_df.astype({"CE_Allele": "float64", "Reads": "int"}) | ||
| except KeyError: | ||
| final_df = None | ||
| return final_df, flags_df |
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I added this to skip by any samples with no YSTR data without erring out.
|
This is ready for review @standage |
| if len(sequence) > 14: | ||
| final_string = ( | ||
| f"{collapse_repeats_by_length(sequence[:14], 4)} " | ||
| f"{collapse_repeats_by_length(sequence[14:], 4)}" | ||
| ) | ||
| else: | ||
| final_string = collapse_repeats_by_length(sequence, 4) |
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I'm curious about the significance of the value 14 here.
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It's ensuring the beginning of the bracketed form looks like this [GAAA]3 AG GAAG ....
lusSTR/wrappers/filter.py
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| def process_strs(dict_loc, datatype, seq_col, brack_col): | ||
| def process_strs(dict_loc, datatype, seq_col, brack_col, sex): |
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It doesn't look like the sex argument is used in this function. Did I miss something, or is it really unnecessary?
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Yup, you're right! I've removed it.
| process_input( | ||
| input_name, | ||
| outpath, | ||
| profile_type, | ||
| data_type, | ||
| output_type, | ||
| strand=strand, | ||
| nofiltering=nofilters, | ||
| separate=separate, | ||
| custom=custom, | ||
| sex=sex, | ||
| info=info, | ||
| ) |
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This is called whether sex is true or false? To make sure I understand, enabling sex includes processing of the Y-STRs in addition to the autosomals?
Completing the workflow for Y-STRs using PowerSeq custom sequence ranges. Y-STRs have to be incorporated into the
filterstep.