Fix multi-exon HGVSp parsing

[nuno-agostinho]

ENSVAR-6167

Motivation

When a HGVSp like ENSP00000346614.5:p.D237G contains an amino acid whose codon sequence spans two exons, VEP gets the wrong reference sequence (GAG) instead of the expected (GAT):

MSG: Sequence translated from reference (GAG -> E) does not match input sequence (D)

This occurs because VEP is fetching the sequence from the exon and the intron, instead of skipping the intron sequence:
GAgtaagtggcgtatgtaaaattgtcattctacacaaaaaatcacgagcagagggcaaagtgaaatcgtggctgctttatcattaattttgcatgtgcagcggagagcttgtcctttgtgctctaaatccttgctacaaacggttacataaaagatctaagaaagtggagacaaaggaaggtgggtaaagttagaaggaaaaaaagagctagaaaagtgtgcaagtcacttcatacctgaattcttgacatttgactggaattgttctgattagaccatggtcctcaaggcatttcacagttttttttaagtctgcgctgccttaggggattttatccttgagacatccactggcttaactcaagtttccttcaaaatatgtagctaaatacagctgttcagctaatagctcagaggttctttggagaacaaatggaatgttatttactaatattacttgtggcatgttagcacttttgtgttctgccaagtgcttttgggtccattctcaaagccgccatggctaagctggtagtacgttggcgatggcccatatgggaagtggaagtggtagatcttcaggggactttcaaaatgctttgaatttaactctttcttcccctttattctaattcctagT

Logic

This issue was fixed by:

• Fetching the cDNA sequence (i.e., ignoring the intron) before checking what are the nucleotide changes between the reference and replacement amino acids
• Fetching the sequence (including the whole intron) as the reference allele

Testing

Examples of HGVSp where the codon spans two exons:

ENSP00000346614.5:p.Asp237Gly

ENSP00000489869.1:p.V108A
ENSP00000489869.1:p.V108S
ENSP00000489869.1:p.V108I
ENSP00000489869.1:p.H123T
ENSP00000489869.1:p.R136A
 
ENSP00000297350.4:p.G134I
ENSP00000297350.4:p.D273F
 
ENSP00000381693.2:p.P936S

Please also test with other HGVSp examples, such as those listed in https://www.ebi.ac.uk/seqdb/confluence/display/EV/HGVS#HGVS-SupportedHGVS

[nakib103]

LGTM!~ code change make sense and everything works fine!

[nakib103]

merged to main and postrealasefix/112