Expand CLI #208
Expand CLI #208
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Nice job @adrosenbaum . Could you add some tests for the new mixin classes? Also there is a dependency problem on travis, maybe you saw it?
chanjo/calculate.py
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| TranscriptStat.transcript, | ||
| ).filter( | ||
| TranscriptStat.sample_id.in_(sample_ids), | ||
| Transcript.gene_id.in_(OMIM_GENE_IDS), |
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Have you checked the performance for this query? Feels like it can take some time to calculate?
chanjo/cli/db.py
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| @db_cmd.command() | ||
| @click.option('--group-id', '-g') |
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Could you add a help what this option means?
| @click.option('--sample-id', '-s') | ||
| @click.option('--pretty', '-p', is_flag=True) | ||
| @click.pass_context | ||
| def samples(context, group_id, sample_id, pretty): |
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What happens if samples=None or of the sample does not exists? Could you add a test or two?
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You feel ready with this @adrosenbaum ? |
Yes, I'm only working on some listing issues I missed. However I'm thinking of testing this before by installing chanjo on its own condo environment on hasta. I'll let you know when this is done. |
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@moonso this is ready to be deployed I think. |
We need to decouple chanjo from cg. This requires that all operations that cg does through the chanjo API can be made from the CLI.
** How to test **
chanjo db samples -g <case_id> --prettychanjo db samples -s <sample_id> --prettychanjo calculate coverage -s <sample_id_1> -s <sample_id_2> --omim --prettyExpected results
chanjo db samples -g <case_id> --prettyshould return all samples in the casechanjo db samples -s <sample_id> --prettyshould return the samplechanjo calculate coverage -s <sample_id_1> -s <sample_id_2> --omim --prettyShould return the mean coverage, and completeness for the samplesReview:
This is a minor version change because new functionality is added in a backward compatible manner