Choosing the Correct Adjacent Exon along Exon Boundaries

[jarbesfeld]

Describe the bug

The get_adjacent_exon method needs to be updated to consider edge cases where start or end occurs along the boundaries of the exon.

Steps to reproduce

N/A

Expected behavior

If a segment starts at alt_end_ion the positive strand, the next exon should be selected.
If a segment ends at alt_end_ion the positive strand, the current exon should be selected.
If a segment ends at alt_start_i on exon 1, the following error message should be returned:
"Invalid input. The segment cannot end at the first position on the first exon"
If a segment starts at alt_end_i on the last exon, the following error message should be returned:
"Invalid input. The segment cannot start at the end position on the last exon"

If a segment ends at alt_start_i on the negative strand, the current exon should be selected.
If a segment starts at alt_start_i on the negative strand, the next exon should be selected.
If a segment ends at alt_end_i on exon 1, the following error message should be returned:
"Invalid input. The segment cannot end at the first position on the first exon"
If a segment starts at alt_start_i on the last exon, the following error message should be returned:
"Invalid input. The segment cannot start at the end position on the last exon"

Current behavior

The current logic does not consider these edge cases

Possible reason(s)

N/A

Suggested fix

See expected behavior

Branch, commit, and/or version

issue-224-new-structure

Screenshots

N/A

Environment details

M1 Mac

Additional details

No response

Contribution

None

[korikuzma]

Current implementation returns first exon with offset when passed:

r = await mapper.genomic_to_tx_segment(
  genomic_ac="NC_000001.11",
  seg_end_genomic=154192100,
  transcript="NM_152263.4",
)

However, it should return the above error message since the output does not make biological sense.

[korikuzma]

For tx_segment_to_genomic regardless of strand orientation:

If exon_start is 1 and exon_end is None, the exon start offset must be >= 0.
If exon_end is the last exon and exon_start is None, the exon end offset must be <= 0

[korikuzma]

    # Positive strand, start == alt_start_i
    resp = test_egc_mapper._get_adjacent_exon(
        tx_exons_genomic_coords=nm_001105539_exons_genomic_coords,
        start=80486225,
        strand=Strand.POSITIVE,
    )
    assert resp == 0

This currently returns exon 1 (0 index) but it should return exon 0.