Closed miseminger closed 7 months ago
noncomprehensive list of delins amino acid names that aren't delins at nt level (might be fine, but to look into):
/home/miseminger/projects/def-virusmvp/shared_data/latest_gvfs/BA.4_annotated.gvf
nt_name=g.CATGGTCATGTTA241_253AATG;aa_name=p.H81_M85delinsNV
/home/miseminger/projects/def-virusmvp/shared_data/latest_gvfs/BA.5_annotated.gvf
nt_name=g.173_181delAAGGCGTTT;aa_name=p.K58_L61delinsM
/home/miseminger/projects/def-virusmvp/shared_data/latest_gvfs/BA.5.1.2_annotated.gvf
nt_name=g.50_52delGTT;aa_name=p.S17_L18delinsM
/home/miseminger/projects/def-virusmvp/shared_data/latest_gvfs/BA.1.1.1_annotated.gvf
nt_name=g.245_253delGTCATGTTA;aa_name=p.G82_M85delinsV
This was a regex issue: df["hgvs_nucleotide"] = df["hgvs_nucleotide"].str.replace("n.", "g.", regex=True)
changed "ins" to "ig.". Solved by changing to regex=False
.
Closed with commit (611e3b23df56bf537fc1ca7023f99695a593f38d)[https://github.com/cidgoh/nf-ncov-voc/pull/149/commits/611e3b23df56bf537fc1ca7023f99695a593f38d]
Insertion at pos 6500, ln 38 in
/home/miseminger/projects/def-virusmvp/shared_data/latest_gvfs/BF.11_annotated.gvf
:nt_name=g.6237_6238ig.TCTTCA;aa_name=p.P2079_A2080insSS
nt name format is unknown, @miseminger will keep looking into it.