zwdzwd / transvar

TransVar - multiway annotator for precision medicine
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Missing some characters of amino acid name when use `panno` #45

Open wei-linlin opened 4 years ago

wei-linlin commented 4 years ago

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

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!