Refactorization of Analyze schema #11
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| from setuptools import setup, find_packages | ||
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| version = "2.2.0" |
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Yes, changed to version 3.0.0
| # for schema_file in schema_files: | ||
| results = [] | ||
| start = time.perf_counter() | ||
| with concurrent.futures.ProcessPoolExecutor() as executor: |
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Please include the parameter for setting the threads you want to use so we can test it on the HPC
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Included parameter for cpu used. Prokka usage cpus was set to 3. more testing is required to getting the optimize value
| a_quality[record.id] = {"quality": "Good quality", "reason": "-"} | ||
| allele_seq[record.id] = str(record.seq) | ||
| a_quality[record.id]["length"] = len(str(record.seq)) | ||
| if len(record.seq) % 3 != 0: |
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Have you checked that the translate protein function of biopython only fails with not a 3 multiple. It would make sense to me but just in case. Also I think that keeping he protein info output could be interesting as it was in the previous code.
Can you run the previous code for analyze schema so we can check the output and see if we are missing something?
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This part of the code is replaced now for using biopython
| a_quality[record.id]["length"] = len(str(record.seq)) | ||
| if len(record.seq) % 3 != 0: | ||
| a_quality[record.id]["quality"] = "Bad quality" | ||
| a_quality[record.id]["reason"] = "Can not be converted to protein" |
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I would call this as in the previous code : Not a CDS, cannot be converted to protein. Or something like this
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error messages are collected from biopython text message
| ): | ||
| bad_quality_record.append(record.id) | ||
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| if self.remove_duplicated: |
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duplicates and subset checkings must be done all times, when you use remove_duplicated or remove_subset etc.. it's only for removing them from the schema, but the statistics and que quality flag should be there indicating that there is a duplicate or a subset
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duplicated and subset alleles are showed in quality data
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After checking the new and old code, I would add also information about different number of proteins found per gene, and some graphs and stats about the lenght variability of the alleles for each gene as in previous code |
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In the pie graph: |
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In the good quality/bad quality pie, The bad quality (if any) I assume that all the possibilities would appear, right? |
Testing result of 70 Locus.
statistics.csv