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grch38_to_mane_c_p should validate input arguments #457

@korikuzma

Description

@korikuzma

Describe the bug

grch38_to_mane_c_p method accepts GRCh37 (and other assemblies) when try_longest_compatible is set to True, which is misleading IMO.

Steps to reproduce

from cool_seq_tool import CoolSeqTool

cst = CoolSeqTool()

await cst.mane_transcript.grch38_to_mane_c_p("NC_000007.13", 140453136, 140453136, try_longest_compatible=True)

returns:

ProteinAndCdnaRepresentation(protein=DataRepresentation(gene=None, refseq='NP_001361187.1', ensembl=None, pos=(639, 640), strand=<Strand.NEGATIVE: -1>, status=<TranscriptPriority.LONGEST_COMPATIBLE_REMAINING: 'longest_compatible_remaining'>), cdna=CdnaRepresentation(gene='BRAF', refseq='NM_001374258.1', ensembl=None, pos=(1918, 1919), strand=<Strand.NEGATIVE: -1>, status=<TranscriptPriority.LONGEST_COMPATIBLE_REMAINING: 'longest_compatible_remaining'>, coding_start_site=226, coding_end_site=2650, alt_ac=None))

Acceptance Criteria

await cst.mane_transcript.grch38_to_mane_c_p("NC_000007.13", 140453136, 140453136, try_longest_compatible=True) should not return a result

Possible reason(s)/Suggested Fix

In a separate issue, I think we may also consider adding a new method for g_to_mane_c_p to accept either GRCh37 or GRCh38 and deprecating grch38_to_mane_c_p.

Environment & Version

version: 0.15.3

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