Wrong location in ExonGenomicCoordsMapper.transcript_to_genomic_coordinates

[jsstevenson]

Describe the bug

The genomic location for an exon in the following lookup appears to be incorrect.

Steps to reproduce

run this

from cool_seq_tool.app import CoolSeqTool
import asyncio

async def do_thing():
    egc = CoolSeqTool().ex_g_coords_mapper
    result = await egc.transcript_to_genomic_coordinates(
        "NM_002529.4",  # latest NTRK1 transcript ac
        "NTRK1",
        exon_start=1
    )
    print(result.genomic_data.start)  # 156861145
    print(result.genomic_data.strand)  # 1 (ie positive)

asyncio.run(do_thing())

Expected behavior

I think this is the ending coordinate of exon 1, not the starting coordinate.

1. see this screenshot from the ncbi genome data viewer

2. take a look at the result of this UTA query:

SELECT * FROM tx_exon_aln_v WHERE tx_ac = 'NM_002529.4' AND alt_aln_method='splign' AND alt_ac = 'NC_000001.11' AND ord = 0;

Also, I don't think this would matter, but this transcript aligns to the positive strand of chr1 (am I saying that right?) so there shouldn't be any weird "end is start and start is end" issues here

Current behavior

As noted above, the returned starting location is 156861145

Possible reason(s)

No response

Suggested fix

No response

Branch, commit, and/or version

The 0.5.1 release (it's what we have pinned for fusions) but I don't think it would be different on 0.6.0

Screenshots

No response

Environment details

mac

Additional details

No response

Contribution

Yes, I can create a PR for this fix.

[korikuzma]

@jsstevenson I am resolving this in #224 . This was when we didn't know when to use start or end for the exon. @jarbesfeld has helped clear things up in the past few weeks!

[korikuzma]

@jarbesfeld says this output from #352 is correct

{
  "gene": "NTRK1",
  "genomic_ac": "NC_000001.11",
  "tx_ac": "NM_002529.4",
  "seg_start": {
    "exon_ord": 0,
    "offset": 0,
    "genomic_location": {
      "type": "SequenceLocation",
      "sequenceReference": {
        "type": "SequenceReference",
        "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"
      },
      "start": 156860864
    }
  }
}

[github-actions]

Closed by #352.