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genomeannotation / GAG

Generates an NCBI .tbl file of annotations on a genome.
MIT License
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Error while running GAG2.0.1 #198

Closed sanyalab closed 1 month ago

sanyalab commented 1 month ago

Hello,

I am getting a Tracback error while running the tool. This was not present earlier. 

Traceback (most recent call last):
  File "/SOFTWARE/GAG-2.0.1/gag.py", line 50, in <module>
    main()
  File "/SOFTWARE/GAG-2.0.1/gag.py", line 46, in main
    controller.execute(args)
  File "/SOFTWARE/GAG-2.0.1/src/controller.py", line 74, in execute
    self.read_gff(gffpath, out_dir)
  File "/SOFTWARE/GAG-2.0.1/src/controller.py", line 286, in read_gff
    genes, comments, invalids, ignored = gffreader.read_file(reader)
  File "/SOFTWARE/GAG-2.0.1/src/gff_reader.py", line 336, in read_file
    if len(line) == 0 or line.startswith('#'):
TypeError: startswith first arg must be bytes or a tuple of bytes, not str

I am encountering this for the first time. My gff3 and fasta are properly formatted (checked with Genometools). Python version that I am using is 3.4. However, even with the python updated to 3.14 its not working. Same error. Please advice.

Thanks, Abhijit

sanyalab commented 1 month ago

Found the answer. GAG works with python=2.0. Please write that in bold on the README page here and on the documentation page. Its hardly visible.

Thanks Abhijit