Goatools

* **Added**
* Support for GAF 2.2 [201](https://github.com/tanghaibao/goatools/issues/201)
* **Changed**
* The "Compare GO terms" script now can use GO terms stored in files of any name. [187](https://github.com/tanghaibao/goatools/issues/187)
* Improved documentation about using the optional attribute, definition. [204](https://github.com/tanghaibao/goatools/issues/204)

* **Added**
* Added Wang's semantic similarity calculator
* Added a script to duplicate Table 2 in the [GOATOOLS publication](https://www.nature.com/articles/s41598-018-28948-z) [#171](https://github.com/tanghaibao/goatools/issues/171)
* Added clear documentation to explain GO term text (D and R) in plots [178](https://github.com/tanghaibao/goatools/issues/178)
* **Changed**
* Workarounds for errors in the Gene Ontology Consortium (GOC) annotations and opened these issues with GOC.
NOTE: Report annotation issues to [Help Desk](https://github.com/geneontology/helpdesk/)
* [Incorrect taxon format](https://github.com/geneontology/go-annotation/issues/3373) [GO helpdesk #287](https://github.com/geneontology/helpdesk/issues/287)
* [Obsolete GOs seen in gaf files](https://github.com/geneontology/go-annotation/issues/3523)
* Moved calculating the depth using optional relationships from GODag to its own module [188](https://github.com/tanghaibao/goatools/issues/188)

* **Fixed**
* The `scripts/wr_hier.pyi` script can now print the hierarchy for GO IDs in all namespaces. [163](https://github.com/tanghaibao/goatools/issues/163)
* The semantic_similarity function upon comparing a GO term to itself. [150](https://github.com/tanghaibao/goatools/issues/150)
* **Added**
* Added a new notebook showing how to download background genes from NCBI.
* Added arg, `--prt_study_gos_only`, to script, `scripts/find_enrichment.py`
to print only study GOs when printing all GO terms, regardless of their significance (`--pval=1.0`):
`find_enrichment.py study_genes.txt human_genes.txt gene2go --pval=1.0 --prt_study_gos_only`
* **Changed**
* Remove trailing divider ("NOT|"), if it exists in the gpad file ([go-annotation 2885](https://github.com/geneontology/go-annotation/issues/2885))

* **Added**
* Added quiet mode when running GOEAs using the function, *run_goea*.
Examples are in section **5a. Quietly Run a GOEA** of the
[**GOEA Jupyter notebook**](https://github.com/tanghaibao/goatools/blob/main/notebooks/goea_nbt3102.ipynb).
re: See comments ([1](https://github.com/tanghaibao/goatools/issues/133#issuecomment-598334391) and
[2](https://github.com/tanghaibao/goatools/issues/133#issuecomment-598844019)) in
[**133**](https://github.com/tanghaibao/goatools/issues/133)

* **Added**
* New [Jupyter notebook](https://github.com/tanghaibao/goatools/blob/main/notebooks/godag_obsolete_terms.ipynb) showing how to work with obsolete GO terms.
[**153**](https://github.com/tanghaibao/goatools/issues/153)
[**154**](https://github.com/tanghaibao/goatools/issues/154)
[**155**](https://github.com/tanghaibao/goatools/issues/155)
* [**Issue 154**](https://github.com/tanghaibao/goatools/issues/154) Support for optional GO term attributes, *consider* and *replaced_by*
* **Deprecated**
* Renamed internal data variable:
* NOW: *gosubdag.rcntobj.go2ancestors*
* WAS: *gosubdag.rcntobj.go2parents*
* **Changed**
* [**Issue 148**](https://github.com/tanghaibao/goatools/issues/148)
Return None for Lin's semantic similarity calculations if one or both of the GO terms is not annotated.
This will be updated in the future to have the option to assign a count of 1 to GO terms that are not annotated,
indicating the annotation of a mock gene to allow the researcher to get a rough idea of the similarity.
* [**Issue 142**](https://github.com/tanghaibao/goatools/issues/142)
* Write GO hierachy to a file now writes a file when using Python3
* Gaf reader defaults to gaf file version of 2.1 if no version line if found