Need Nucleotide or protein alphabet

chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R

http://bcbio.wordpress.com

603 stars 243 forks source link

Need Nucleotide or protein alphabet #121

Closed camilo-monge closed 5 years ago

camilo-monge commented 5 years ago

Hello, I'm trying to run gff_to_genbank.py in python3, however, I'm getting the following error. File "/home/camilo/.local/lib/python3.6/site-packages/Bio/SeqIO/InsdcIO.py", line 631, in _write_the_first_line raise ValueError("Need a Nucleotide or Protein alphabet") ValueError: Need a Nucleotide or Protein alphabet Any ideas? Thanks in advance

chapmanb commented 5 years ago

Thanks for the report and sorry about the issue. I'm not able to replicate this with Python 3 and a small test GFF and fasta input file, so not entirely sure what is wrong. Would you be able to share some information to help debug:

What version of bcbio.gff and Biopython are you running?
Do you have a minimal GFF and fasta file input that can replicate the issue we could use for debugging?

Thanks much for the report and help debugging.

camilo-monge commented 5 years ago

I'm sorry, it was my mistake, the gff file had a fasta line at the end.