Goreverselookup

Python version 3.12 was excluded, since it is new and might be erroneous with some dependencies, so that it prevents a successful push to TestPypi and Pypi.

GOReverseLookup now supports full taxon modularity using the _target_taxon_ and _ortholog_organisms_ settings, for example:

target_organism homo_sapiens|UniProtKB|NCBITaxon:9606 format: organism_label|organism_database|ncbi_taxon
ortholog_organisms danio_rerio|ZFIN|NCBITaxon:7955,rattus_norvegicus|RGD|NCBITaxon:10116,mus_musculus|MGI|NCBITaxon:10090,xenopus_tropicalis|Xenbase|NCBITaxon:8364

Evidence code filtering is now supported to query only annotations between genes and GO terms with evidence codes that satisfy the user-defined valid evidence codes. Example setting that includes only the TAS author statement evidence code, excludes the ND evidence code from curator statement and excludes all electronic (IEA) evidence codes:

evidence_codes experimental(~),phylogenetic(~),computational_analysis(~),author_statement(TAS),!curator_statement(ND),!electronic(~)

GOReverseLookup now has a script entry-point, so the program can now be started using the following command:

goreverselookup <input_file_filepath>

Implemented gOrth from https://biit.cs.ut.ee/gprofiler/orth into the workflow.

Various minor bugfixes and improvements.

request_params={"rows": 50000, "taxon": "NCBITaxon:9606"} was faulty in fetch_all_go_term_products. Must be: request_params={"rows": 10000000}. Before, only homo sapiens uniprotkb genes were returned. Now, all genes (ZFIN,MGI, etc) are correctly returned when querying genes annotated to GO Terms.

The D (bottom-right) value in the contingency table was being calculated as:

num_goterms_all_general - (num_goterms_all_process - num_goterms_product_process)

now it is corrected to be calculated as:

num_goterms_all_general - num_goterms_product_general - (num_goterms_all_process - num_goterms_product_process)

The functions get_all_products_for_goterm and get_all_terms_for_product of the GOAF can now work with indirect annotations.