summarizeFasta Noncoding not recognized as source

[lydiayliu]

I might be missing something but adding Noncoding as a source in summarizeFasta is not working?

I see it defined tho, maybe cuz the constant is defined in another file
https://github.com/uclahs-cds/private-moPepGen/blob/37f7dc7419a58012d258762e7e791d5a50f52495/moPepGen/aa/PeptidePoolSummarizer.py#L161-L165

Code and error

docker run -u $(id -u):$(id -g) -it --rm -v /hot/:/hot/ blcdsdockerregistry/mopepgen:dev /bin/bash

cd /hot/project/algorithm/moPepGen/CCLE/processed/noncanonical-database/call-nonCanonicalPeptide/GRCh38-EBI-GENCODE34/pipeline-meta-call-NonCanonicalPeptide-0.0.1/
moPepGen summarizeFasta \
    --variant-peptides /hot/project/algorithm/moPepGen/CCLE/processed/noncanonical-database/call-nonCanonicalPeptide/GRCh38-EBI-GENCODE34/pipeline-meta-call-NonCanonicalPeptide-0.0.1/ACH-000004/call-NonCanonicalPeptide-1.0.0/ACH-000004/moPepGen-0.4.1/output/ACH-000004_variant_peptides.fasta \
    --noncoding-peptides /hot/project/algorithm/moPepGen/ref/GRCh38-EBI-GENCODE34/gencode34_default_noncoding_peptides.fa \
    --gvf /hot/project/algorithm/moPepGen/CCLE/processed/noncanonical-database/call-nonCanonicalPeptide/GRCh38-EBI-GENCODE34/pipeline-meta-call-NonCanonicalPeptide-0.0.1/ACH-000004/call-NonCanonicalPeptide-1.0.0/ACH-000004/moPepGen-0.4.1/output/ACH-000004_Fusion_STARFusion.gvf /hot/project/algorithm/moPepGen/CCLE/processed/noncanonical-database/call-nonCanonicalPeptide/GRCh38-EBI-GENCODE34/pipeline-meta-call-NonCanonicalPeptide-0.0.1/ACH-000004/call-NonCanonicalPeptide-1.0.0/ACH-000004/moPepGen-0.4.1/output/ACH-000004_Mutation_VEP.gvf \
    --cleavage-rule trypsin \
    --index-dir /hot/users/yiyangliu/MoPepGen/Index/GRCh38-EBI-GENCODE34/ \
    --output-path ACH-000004/call-NonCanonicalPeptide-1.0.0/ACH-000004/moPepGen-0.4.1/output/ACH-000004_variant_peptides_summary_ordered.txt \
    --order-source Mutation,Fusion,Noncoding

[ 2022-05-11 19:40:47 ] moPepGen summarizeFasta started
[ 2022-05-11 19:42:17 ] Reference indices loaded.
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 89, in main
    args.func(args)
  File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/summarize_fasta.py", line 126, in summarize_fasta
    summarizer.write_summary_table(handle)
  File "/usr/local/lib/python3.8/site-packages/moPepGen/aa/PeptidePoolSummarizer.py", line 225, in write_summary_table
    if self.contains_exclusive_sources(comb):
  File "/usr/local/lib/python3.8/site-packages/moPepGen/aa/PeptidePoolSummarizer.py", line 202, in contains_exclusive_sources
    parser = self.source_parser_map[source]
KeyError: 'Noncoding'

[zhuchcn]

I think that's when == and is make a difference..