zwdzwd / transvar

TransVar - multiway annotator for precision medicine

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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 and Lys 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!