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sjteresi / TE_Density

Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
GNU General Public License v3.0
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fleshout exception message on import_filtered_genes #141

Closed teresi closed 7 months ago

teresi commented 11 months ago

I wanted to quickly fleshout the exception given the issue I saw posted

note that the info message says what it's reading, but having it in the error message is more complete and the guy that posted his issue didn't include the info message in his post

testing

do the tests pass?

if you raise something in import_filtered_genes does it print?

[cmd]▸$ ./process_genome.py ..//TE_Density_Filtered_Gene_and_TE_Annotations/Cleaned_TAIR10_GFF3_genes_main_chromosomes.tsv ../TE_Density_Filtered_Gene_and_TE_Annotations/Cleaned_TAIR10_chr_main_chromosomes.fas.mod.EDTA.TEanno.tsv adiposetoperus -n 4 --output_dir ../TE_Density_Filtered_Gene_and_TE_Annotations/results
2023-06-01 21:39:09 GOKU __main__[2817920] INFO preprocessing...
2023-06-01 21:39:09 GOKU PreProcessor[2817920] INFO Reading pre-filtered gene annotation file: /data/genes/TE_Density_Filtered_Gene_and_TE_Annotations/Cleaned_TAIR10_GFF3_genes_main_chromosomes.tsv
2023-06-01 21:39:09 GOKU PreProcessor[2817920] CRITICAL
            Error occurred while trying to read preprocessed gene
            annotation file into a Pandas dataframe, please refer
            to the README as to what information is expected
            input file: /data/genes/TE_Density_Filtered_Gene_and_TE_Annotations/Cleaned_TAIR10_GFF3_genes_main_chromosomes.tsv