Goatools

Latest version: v1.4.5

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0.9.9

* **Deprecated**
* *read_ncbi_gene2go* is deprecated and will be removed in the future.
* *get_b2aset* is moved:
* NOW: goatools.utils
* WAS: goatools.associations
* *GoDagTimed* and *prt_hms* is moved:
* NOW: goatools.godag.prttime
* WAS: goatools.test_data.godag_timed
* **Removed**
* All dict entries whose values were an empty set in:
* *gosubdag.rcntobj.go2parents*
* *gosubdag.rcntobj.go2descendants*
* **Added**
* Method to annotation object, *IdToGosReader*, which writes namedtuples into an ASCII file
* **Changed**
* *TermCounts*:
* Added support for optional relationships, like *part_of*.
This is useful for computing termwise and genewise semantic similarities.
* Faster initialization of *TermCounts* object, used in semantic similarity calculations
* *Plotting*:
* Users can now provide a title to be printed in a GO DAG plot
* Users can now provide an *edge2txt* dict to print text on edges between GO Terms
* **Fixed**
* Aspect counts (BP, MF, CC totals) in *TermCounts* object explained in [156](https://github.com/tanghaibao/goatools/issues/156)
* Opened issue:
[2629](https://github.com/geneontology/go-annotation/issues/2629) -> [Help
Desk](https://github.com/geneontology/helpdesk/issues/288)

0.9.7

* **Added**
* Support traversing optional relationships when propagating counts for GOEAs
* Find all ancesters of a GO term using a user-specified list of relationships
[126](https://github.com/tanghaibao/goatools/issues/126#issuecomment-511985524)

Support traversing optional relationships

Support traversing optional relationships, like *part_of* and *regulates*,
when doing propagating counts using these two new arguments in `scripts/find_enrichment.py`:

bash
-r, --relationship Propagate counts up all relationships (default: False)
--relationships [RELATIONSHIPS [RELATIONSHIPS ...]]
Propagate counts up user-specified relationships
(default: None)


[117](https://github.com/tanghaibao/goatools/issues/117#issuecomment-515484624)

0.9.5

* **Added**
* [**Issue 119: Added support for specifying specific evidence codes**](added-support-for-specifying-specific-evidence-codes)
* [**Issue 127: Added splitting GOEA into BP, MF, and CC**](added-splitting-goea-into-bp-mf-and-cc)
* **Fixed**
* [**Issue 120 and 121: Lin similarity is positive**](https://github.com/tanghaibao/goatools/issues/120)

Added support for specifying specific evidence codes

* Specify evidence codes, like EXP (Inferred from Experiment), to exclude or include in a GOEA.
* Specify evidence classes, like Experimental (EXP IDA IPI IMP IGI IEP), which include many evidence codes.
* Get evidence code help:

bash
python3 scripts/find_enrichment.py --ev_help
python3 scripts/find_enrichment.py --ev_help_short


[119](https://github.com/tanghaibao/goatools/issues/119)

Added splitting GOEA into BP, MF, and CC

Split GOEA into three separate analyses by default:

* BP (biological process)
* MF (molecular function)
* CC (cellular component)

[127](https://github.com/tanghaibao/goatools/issues/127#issuecomment-489776548)

0.8.12

0.8.11

0.8.9

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