PEPPAN fails with UnboundLocalError using PGAP-annotated gff/fna files

[MrTomRod]

Describe the bug PEPPAN fails with "UnboundLocalError: local variable 'name' referenced before assignment"

To Reproduce 1) Install PEPPAN

# install via conda
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda create --prefix ./conda-envs/peppan python=3.9
conda activate /data/users/username/conda-envs/peppan
conda install mmseqs2 blast diamond rapidnj fasttree
pip3 install peppan

# quickstart
PEPPAN --testunit
PEPPAN -p examples/ST131 -P examples/GCF_000010485.combined.gff.gz examples/*.gff.gz > 1_PEPPAN.out 2>&1
PEPPAN_parser -g examples/ST131.PEPPAN.gff -s examples/PEPPAN_out -t -c -a 95 > 2_PEPPAN_parser.out 2>&1

2) Download data

• FAM14217: gff, fna
• FAM15300: gff, fna

3) Run PEPPAN

$ conda activate /data/users/username/conda-envs/peppan
$ cd /data/users/username/genome_datasets
$ PEPPAN \
> --prefix PEPPAN_50/my-prefix \
> --genes \
> in/FAM14217-p1-1.1.gff,in/FAM14217-p1-1.1.fna \
> in/FAM15300-i1-1.1.gff,in/FAM15300-i1-1.1.fna

2023-03-02 16:33:51.941180      COMMAND: /data/users/username/conda-envs/peppan/bin/PEPPAN --prefix PEPPAN_50/my-prefix --genes in/FAM14217-p1-1.1.gff,in/FAM14217-p1-1.1.fna in/FAM15300-i1-1.1.gff,in/FAM15300-i1-1.1.fna
Traceback (most recent call last):
  File "/data/users/username/conda-envs/peppan/bin/PEPPAN", line 8, in <module>
    sys.exit(ortho())
  File "/data/users/username/conda-envs/peppan/lib/python3.9/site-packages/PEPPAN/PEPPAN.py", line 1845, in ortho
    genes = addGenes(genes, params['genes'], params['gtable'])
  File "/data/users/username/conda-envs/peppan/lib/python3.9/site-packages/PEPPAN/PEPPAN.py", line 1017, in addGenes
    ng = readFasta(gfile)
  File "/data/users/username/conda-envs/peppan/lib/python3.9/site-packages/PEPPAN/modules/configure.py", line 126, in readFasta
    sequence[name].extend(line.strip().split())
UnboundLocalError: local variable 'name' referenced before assignment