Development of somalier_wrapper.py#1
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This is a really good readme, very comprehensive!
| "--fasta", help="Path to reference genome", required=True | ||
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| argument_parser.add_argument("--sites", help="Path to sites file", required=True) | ||
| argument_parser.add_argument("--prefix", help="Prefix for results", required=True) |
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for any of these required arguments that'll be the same every time (e.g. sites file), we add a default so we don't need to give the arguments every time? or if you want it to be more general, we could put those arguments in a config to pass in. Not a necessity though, just a suggestion
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could you add versions for the dependencies
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really good commenting throughout here, it's easy to pick this up and follow what you're doing
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| # Gather command line arguments | ||
| args = parse_arguments() |
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Do we want to do an upfront check that if you're running with relatedness turned on that you've supplied all three arguments? Would save running something long for it to crash part way
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Initial review of logic, will check with test data post-move. This is a really good script, clearly written and it's easy to follow what's going on. I agree with your suggestion that Nextflow would probably be a better approach for comparing many many samples, but this should work well in Python for comparing within a run or between a couple of runs. I think the best next step is working out some thresholds for each of the different assays so we can look at implementing this in the pipelines. |
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Hi @Istaisa, thank you for code review. Your comments will be really helpful as I continue to develop somalier_wrapper.py. I will make the relevant changes over the next week 😄 |
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somalier_wrapper.py is a wrapper script for streamlining the execution of somalier extract, relate, and ancestry commands into a single command. It provides a stand alone method of assessing sample relatedness outside of existing bioinformatics pipelines that can be used when addressing ad hoc queries regarding relationships between samples.