feat: Determine adjacent exon for fusions with non-exonic breakpoint #268
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… message, and update docstrings
…e optional parameter, and correct chromosome accession warning statement
…provided, modify docstrings
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I believe the original positions were correct.
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@korikuzma I thought the positions needed to be increased by 1 as I got the following assertion error when the entered start position was 80514010:
Full diff:
E - GenomicData(gene='ZBTB10', chr='NC_000008.11', start=None, end=80514008, exon_start=None, exon_start_offset=None, exon_end=3, exon_end_offset=100, transcript='NM_001105539.3', strand=<Strand.POSITIVE: 1>)
E ? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
E + GenomicData(gene='ZBTB10', chr='NC_000008.11', start=None, end=80514009, exon_start=None, exon_start_offset=None, exon_end=3, exon_end_offset=100, transcript='NM_001105539.3', strand=<Strand.POSITIVE: 1>)
E ? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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@jarbesfeld That means that you will have to change something in your code. I will let you try to resolve on your own first.
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Stick with the values provided by UTA.
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@korikuzma I think I'm confused about what the position should be. For example, if the supplied value for "end"by the user is 80514010, that would be reduced by 1 to 80514009 by this line (https://github.com/GenomicMedLab/cool-seq-tool/blob/main/src/cool_seq_tool/mappers/exon_genomic_coords.py#L292). So I thought the value for end in the test fixture should be 80514009?
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@jarbesfeld I am also confused. My main question is why did you change the values in the tests if the input positions in your test did not change?
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@korikuzma When using _set_exon_offset, I changed it so params["pos"] = pos (i.e. the breakpoint entered by the user). Before params["pos"] was set to tx_genomic_coords[exon - 1][3] (start of exon) or tx_genomic_coords[exon - 1][4] (end of exon) so I changed the value of the position in the tests to reflect this change. I think the old position values came from when pos was set to the start or end of an exon.
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Right. I will have to look at this again when I am not as busy so I can understand your changes. I just left quick reviews initially.
Closes #266
Allows for the adjacent exon to be determined for fusions with breakpoints that do not occur on an exon