Kyle Tretina

icon company NVIDIA icon location Boston, MA icon location Product Marketing Lead @NVIDIA | PhD @UMBaltimore | omics, immuno/micro, AI/ML | 🇺🇸🇸🇰 | Opinions are my own views, not those of my employer.

Results 4 issues of Kyle Tretina

biocodeutils.py add error output mRNA ID

When the biocodeutils function called "translate" finds an unknown codon, it currently will deal with it like this: print("WARN: Encountered unknown codon during translation: {0}".format(seq[x:x+3])) Could you please add the...

correct_gff_feature_order.pl misplacing ##FASTA

Hello, While the script seems to work as advertised otherwise, when given a GFF file with a FASTA at the end of the file, correct_gff_feature_order.pl places the "##FASTA" header in...

GFF3 validator

1 comment

We have talked before about writing a script to confirm full gff3 format agreement, and I have found someone else's attempt at doing this (link below). This might be a...

enhancement

convert_gff3_to_gbk.py with no embedded FASTA

convert_gff3_to_gbk.py currently does not support GFF3 files without embedded FASTA sequences. Here is the error that I got: "raise Exception("ERROR: CDS.get_residues() requested but its molecule {0} has no stored residues".format(mol.id))"...

bug