Annotation source None not supported

[lydiayliu]

I regenerated the index for mouse using

refdir=/hot/project/method/AlgorithmDevelopment/ALGO-000074-moPepGen/ref/GRCm38-EBI-ENSEMBL102/

## set up index
docker run -u $(id -u):$(id -g) --rm -v /hot/:/hot/ ghcr.io/uclahs-cds/mopepgen:1.1.0 \
moPepGen generateIndex \
    --genome-fasta ${refdir}/Mus_musculus_GRCm38_dna_primary_assembly.fa \
    --annotation-gtf ${refdir}/Mus_musculus.GRCm38.102.gtf \
    --proteome-fasta ${refdir}/Mus_musculus.GRCm38.pep.all.fa \
    --reference-source ensembl \
    --invalid-protein-as-noncoding \
    --output-dir ${refdir}/index

But when I go ahead and use that index directory to run callNoncoding, I got the following error

docker run -u $(id -u):$(id -g) --rm -v /hot/:/hot/ ghcr.io/uclahs-cds/mopepgen:1.1.0 \
moPepGen callNoncoding \
    --output-path ${refdir}/noncoding/min.fa \
    --output-orf ${refdir}/noncoding/min.orf.fa \
    --index-dir ${refdir}/index/
    --orf-assignment min

Traceback (most recent call last):
  File "/usr/local/bin/moPepGen", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/__main__.py", line 92, in main
    args.func(args)
  File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_noncoding_peptide.py", line 128, in call_noncoding_peptide
    tx_model.transcript.biotype in exclusion_biotypes:
  File "/usr/local/lib/python3.8/site-packages/moPepGen/gtf/GTFSeqFeature.py", line 22, in biotype
    raise ValueError(f'Annotation source {self.source} not supported')
ValueError: Annotation source None not supported

I assume that is related to reference-source
https://github.com/uclahs-cds/private-moPepGen/blob/f107557c63ea1afa33be75507f09bf4feb0d65a4/moPepGen/cli/common.py#L51-L57

But I've never previously had to input the value when using the index dir?

edit: nvm I tried it with reference-source and no difference was made...

[lydiayliu]

Update!

With the following workflow

refdir=/hot/project/method/AlgorithmDevelopment/ALGO-000074-moPepGen/ref/GRCm38-EBI-ENSEMBL102/

## set up index
docker run -u $(id -u):$(id -g) --rm -v /hot/:/hot/ ghcr.io/uclahs-cds/mopepgen:dev \
moPepGen generateIndex \
    --genome-fasta ${refdir}/Mus_musculus_GRCm38_dna_primary_assembly.fa \
    --annotation-gtf ${refdir}/Mus_musculus.GRCm38.102.gtf \
    --proteome-fasta ${refdir}/Mus_musculus.GRCm38.pep.all.fa \
    --reference-source ensembl \
    --invalid-protein-as-noncoding \
    --output-dir ${refdir}/index

## call noncoding peptides
docker run -u $(id -u):$(id -g) --rm -v /hot/:/hot/ ghcr.io/uclahs-cds/mopepgen:dev \
moPepGen callNoncoding \
    --output-path ${refdir}/noncoding/min.fa \
    --output-orf ${refdir}/noncoding/min.orf.fa \
    --index-dir ${refdir}/index/ \
    --orf-assignment min

I'm getting

Traceback (most recent call last):
  File "/usr/local/bin/moPepGen", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/__main__.py", line 92, in main
    args.func(args)
  File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_noncoding_peptide.py", line 128, in call_noncoding_peptide
    tx_model.transcript.biotype in exclusion_biotypes:
  File "/usr/local/lib/python3.8/site-packages/moPepGen/gtf/GTFSeqFeature.py", line 22, in biotype
    raise ValueError(f'Annotation source {self.source} not supported')
ValueError: Annotation source ensembl not supported

Is --reference-source ensembl incorrect?