Missing some characters of amino acid name when use `panno`
wei-linlin opened this issue · comments
Hi,
When I tried to annotate a protein by panno
, I found this problem:
use --aa3
option for 3 letters code, but the output with one letter.
$ transvar panno -i 'JAK2:F537_K539delinsL' --ucsc --aa3
input transcript gene strand coordinates(gDNA/cDNA/protein) region info
JAK2:F537_K539delinsL NM_004972 (protein_coding) JAK2 + chr9:g.5070022_5070027delTCACAA/c.1611_1616delTCACAA/p.Phe537_Lys539delinsL inside_[cds_in_exon_12] CSQN=MultiAAMissense;left_align_gDNA=g.5070022_5070027delTCACAA;unaligned_gDNA=g.5070022_5070027delTCACAA;left_align_cDNA=c.1611_1616delTCACAA;unalign_cDNA=c.1611_1616delTCACAA;candidate_alternative_sequence=CTT/CTG/CTA/CTC/TTA/TTG;source=UCSCRefGene
- submitted mutation:
JAK2:F537_K539delinsL
(amino acid with one letter) with option--aa3
- output protein change:
p.Phe537_Lys539delinsL
(correct:p.Phe537_Lys539delinsLeu
) - missing:
eu
[Leu/Leucine/L] (Phe
andLys
are correct)
Is there a character length limit when output? In other words, whether the character length of protein change or coordinates
column exceeds the length threashold?
Thanks!