Goreverselookup

Added total counts of GO Terms and genes to the model and total counts of genes per a single GO term to compare different model results more easily.

--rescore parameter can be used in conjunction with the --full_directory_op parameter. If --rescore True is used, then the first research model that is analysed acts as a base, and the other research models adjust only the p-value and the indirect annotation preferences (more specifically, ModelSettings are transferred from a new model to the base model). This significantly speeds up the time in comparison to re-analyzing each model again and again.

WARNING: This does not work for evidence codes, since they are parsed during GO term querying. Processing models with different accepted evidence codes should not be performed with --rescore.

UniprotApi.py", line 957, in idmapping_batch
request_job_id = request.json()["jobId"]

due to an unhandled http error:

"POST /idmapping/run HTTP/1.1" 500 None
2024-02-07 07:39:12,787 [INFO] idmapping_batch: Attempting batch idmapping from UniProtKB_AC-ID to Ensembl. Url = https://rest.uniprot.org/idmapping/run

is now resolved.

Choosing whether to take GO term parents or children of directly annotated GO terms (to a gene) is now supported. This can be set as the second parameter of the 'include_indirect_annotations' setting, by setting either a "p" (parent) or "c" (child). Example: 'include_indirect_annotations True p'.

For indirect annotations, a max depth setting was implemented, which takes only 'max_depth' indirect annotations, discarding the rest. This is to eliminate GO terms which are high in the Gene Ontology hierarchy (such as "regulation of a biological process") from being included in the gene scoring process. This can be set via the 'indirect_annotations_max_depth' setting. Setting it to -1 means to take the full depth of the hierarchy.

research_models folder contains input files for the presentation research article

versioning: Added GO api version and GO OBO version to research model data (saved into data.json)