changing values in the config files have no effect

[husensofteng]

The values are not used as specified in the configuration file!

Example, changing the --num_orfs parameter in the config/ensembl_config.yaml has no effect.

pypgatk_cli.py dnaseq-to-proteindb 
--config_file config/ensembl_config.yaml 
--input_fasta Meleagris_gallopavo.Turkey_5.1.106.fa 
--output_proteindb lncRNAs.fa 
--include_biotypes lncRNA

Produces 1703*3 = 5109 proteins since there are 1703 lncRNA transcripts in the fasta file and num_ofrs is set to 3 as default value here.

pypgatk_cli.py dnaseq-to-proteindb --config_file config/ensembl_config.yaml --input_fasta Meleagris_gallopavo.Turkey_5.1.106.fa --output_proteindb lncRNAs.fa --include_biotypes lncRNA --num_orfs 1

Produces 1703 proteins since there are only 1703 lncRNAs in the fasta file.

However changing the same parameter in the config/ensembl_config.yaml file still produces 5109 proteins.