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CLI #7
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I have some code review bandwidth and am interested in isovar. Does this PR represent the latest state of the project? |
Not quite, there are some fragments not checked in. I'll give you something
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@iskandr ready for review? |
@hammer Not yet, still working through some edge cases I thought of last night. The parts that don't interact with read data (such as the |
@hammer |
@tavinathanson @ihodes @hammer If you all want to start reviewing, anything other than I added some explanation of the design to the README but it's worth repeating a little here:
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chromosome : str | ||
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base1_position_before_variant : int |
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Just poking around; noticed that you have two base1_position_before_variants
s vs. after
.
…p to help validate the process
… tested and run separately from rest of protein_sequence module
… VariantSequence objects, got rid of partially matching reads, added more tests for interbase range of variants on transcripts, found a bug in pyensembl's contig normalization
… rid of ReferenceContextWithORF
Changes Unknown when pulling c8ee0bf on cli into * on master*. |
Changes Unknown when pulling 3959de7 on cli into * on master*. |
Changes Unknown when pulling 1706af7 on cli into * on master*. |
Changes Unknown when pulling 1706af7 on cli into * on master*. |
@iskandr I'm running into |
…n code, separating Translation from ProteinSequence
Changes Unknown when pulling bdd3125 on cli into * on master*. |
Changes Unknown when pulling 4910ded on cli into * on master*. |
Changes Unknown when pulling d06c34e on cli into * on master*. |
Changes Unknown when pulling a38fe9d on cli into * on master*. |
Gives isovar a commandline interface and CSV output (#6)