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+/goatools-1.3.1.tar.gz
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+%global _empty_manifest_terminate_build 0
+Name:		python-goatools
+Version:	1.3.1
+Release:	1
+Summary:	Python scripts to find enrichment of GO terms
+License:	BSD
+URL:		http://github.com/tanghaibao/goatools
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/43/e0/29f0c8c11c0dc6e8b34f6293b1418144d14d47e3423760691c6304f804d0/goatools-1.3.1.tar.gz
+BuildArch:	noarch
+
+
+%description
+# Tools for Gene Ontology
+
+[![DOI](/doc/images/DOI.svg)](https://www.nature.com/articles/s41598-018-28948-z)
+[![Latest PyPI version](https://img.shields.io/pypi/v/goatools.svg)](https://pypi.python.org/pypi/goatools)
+[![bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/goatools/README.html?highlight=goatools)
+[![Github Actions](https://github.com/tanghaibao/goatools/workflows/build/badge.svg)](https://github.com/tanghaibao/goatools/actions)
+[![Downloads](https://pepy.tech/badge/goatools)](https://pepy.tech/project/goatools)
+
+|         |                                                                       |
+| ------- | --------------------------------------------------------------------- |
+| Authors | Haibao Tang ([tanghaibao](http://github.com/tanghaibao))              |
+|         | DV Klopfenstein ([dvklopfenstein](https://github.com/dvklopfenstein)) |
+|         | Brent Pedersen ([brentp](http://github.com/brentp))                   |
+|         | Fidel Ramirez ([fidelram](https://github.com/fidelram))               |
+|         | Aurelien Naldi ([aurelien-naldi](http://github.com/aurelien-naldi))   |
+|         | Patrick Flick ([patflick](http://github.com/patflick))                |
+|         | Jeff Yunes ([yunesj](http://github.com/yunesj))                       |
+|         | Kenta Sato ([bicycle1885](http://github.com/bicycle1885))             |
+|         | Chris Mungall ([cmungall](https://github.com/cmungall))               |
+|         | Greg Stupp ([stuppie](https://github.com/stuppie))                    |
+|         | David DeTomaso ([deto](https://github.com/deto))                      |
+|         | Olga Botvinnik ([olgabot](https://github.com/olgabot))                |
+| Email   | <tanghaibao@gmail.com>                                                |
+| License | BSD                                                                   |
+
+## Description
+
+This package contains a Python library to
+
+- Process over- and under-representation of certain GO terms, based on
+  Fisher's exact test. With numerous multiple correction routines
+  including locally implemented routines for Bonferroni, Sidak, Holm,
+  and false discovery rate. Also included are multiple test
+  corrections from
+  [statsmodels](http://www.statsmodels.org/stable/index.html): FDR
+  Benjamini/Hochberg, FDR Benjamini/Yekutieli, Holm-Sidak,
+  Simes-Hochberg, Hommel, FDR 2-stage Benjamini-Hochberg, FDR 2-stage
+  Benjamini-Krieger-Yekutieli, FDR adaptive Gavrilov-Benjamini-Sarkar,
+  Bonferroni, Sidak, and Holm.
+
+- Process the obo-formatted file from [Gene Ontology
+  website](http://geneontology.org). The data structure is a directed
+  acyclic graph (DAG) that allows easy traversal from leaf to root.
+
+- Read [GO Association files](http://geneontology.org/page/go-annotation-file-formats):
+
+  - GAF ([GO Annotation
+    File](http://geneontology.org/page/go-annotation-file-gaf-format-21))
+  - GPAD ([Gene Product Association Data](https://geneontology.github.io/docs/gene-product-association-data-gpad-format/))
+  - NCBI's gene2go file
+  - id2gos format. See [example](https://raw.githubusercontent.com/tanghaibao/goatools/main/data/association)
+
+- [Print **_decendants count_** and/or **_information content_**](/notebooks/dcnt_and_tinfo.ipynb)
+  for a list of GO terms
+
+- [Get parents or ancestors for a GO term with or without optional
+  relationships](notebooks/parents_and_ancestors.ipynb), including [Print details about a
+  GO ID's parents](notebooks/parent_go_terms.ipynb)
+
+- Compare two or more lists of GO IDs
+- [Plot GO hierarchies](https://github.com/tanghaibao/goatools#plot-go-lineage)
+- [Write GO hierarchies to an ASCII text file](https://github.com/tanghaibao/goatools#write-go-hierarchy)
+- Group GO terms for easier viewing
+
+- Map GO terms (or protein products with multiple associations to
+  GO terms) to GOslim terms (analog to the map2slim.pl script supplied
+  by geneontology.org)
+
+## To Cite
+
+Klopfenstein DV, Zhang L, Pedersen BS, ... Tang H [GOATOOLS: A Python library for Gene Ontology analyses](https://www.nature.com/articles/s41598-018-28948-z)
+_Scientific reports_ | (2018) 8:10872 | DOI:10.1038/s41598-018-28948-z
+
+- **GO Grouping**:
+  Visualize the major findings in a gene ontology enrichment analysis (GOEA) more easily with grouping.
+  A detailed description of GOATOOLS GO grouping is found in the
+  [manuscript](https://www.nature.com/articles/s41598-018-28948-z).
+- **Compare GO lists**:
+  Compare [two](https://github.com/tanghaibao/goatools/issues/162) or more lists
+  of GO IDs using `compare_gos.py`, which can be used with or without
+  grouping.
+- **Stochastic GOEA simulations**:
+  One of the findings resulting from our simulations is:
+  [Larger study sizes result in higher GOEA sensitivity](https://github.com/dvklopfenstein/goatools_simulation#manuscript-figures),
+  meaning fewer truly significant observations go unreported.
+  The code for the stochastic GOEA simulations
+  described in the paper is found [here](https://github.com/dvklopfenstein/goatools_simulation)
+
+## Installation
+
+Make sure your Python version >= 3.7, and download an
+`.obo` file of the most current
+[GO](http://geneontology.org/docs/download-ontology):
+
+```bash
+wget http://current.geneontology.org/ontology/go-basic.obo
+```
+
+or `.obo` file for the most current [GO
+Slim](http://geneontology.org/docs/go-subset-guide/) terms (e.g.
+generic GOslim) :
+
+```bash
+wget http://current.geneontology.org/ontology/subsets/goslim_generic.obo
+```
+
+
+
+### [PyPI](https://pypi.org/project/goatools/)
+
+```bash
+pip install goatools
+```
+
+To install the development version:
+
+```bash
+pip install git+git://github.com/tanghaibao/goatools.git
+```
+
+### [Bioconda](http://bioconda.github.io/recipes/goatools/README.html?highlight=goatools)
+```bash
+conda install -c bioconda goatools
+```
+
+## Dependencies
+
+When installing via PyPI or Bioconda as described above, all dependencies are automatically downloaded.
+Alternatively, you can manually install:
+
+- For statistical testing of GO enrichment:
+  - [`scipy.stats.fisher_exact`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html)
+  - `statsmodels` (optional) for access to a variety of statistical tests for GOEA
+
+
+- To plot the ontology lineage, install one of these two options:
+  - [Graphviz](http://www.graphviz.org/), for graph visualization.
+  - [pygraphviz](http://networkx.lanl.gov/pygraphviz/), Python binding for communicating with Graphviz:
+  - [pydot](https://code.google.com/p/pydot/), a Python interface to Graphviz's Dot language.
+
+## Cookbook
+
+`run.sh` contains example cases, which calls the utility scripts in the
+`scripts` folder.
+
+### Find GO enrichment of genes under study
+
+See examples in [find_enrichment](/doc/md/README_find_enrichment.md)
+
+The `find_enrichment.py` takes as arguments files
+containing:
+
+- gene names in a study
+- gene names in population (or other study if `--compare` is specified)
+- an association file that maps a gene name to a GO category.
+
+Please look at `tests/data` folder to see examples on how to make these
+files. when ready, the command looks like:
+
+```bash
+python scripts/find_enrichment.py --pval=0.05 --indent data/study \
+                                  data/population data/association
+```
+
+and can filter on the significance of (e)nrichment or (p)urification. it
+can report various multiple testing corrected p-values as well as the
+false discovery rate.
+
+The `e` in the "Enrichment" column means "enriched" - the concentration
+of GO term in the study group is significantly _higher_ than those in
+the population. The "p" stands for "purified" - significantly _lower_
+concentration of the GO term in the study group than in the population.
+
+**Important note**: by default, `find_enrichment.py` propagates counts
+to all the parents of a GO term. As a result, users may find terms in
+the output that are not present in their `association` file. Use
+`--no_propagate_counts` to disable this behavior.
+
+### Write GO hierarchy
+
+- [`wr_hier.py`](doc/md/README_wr_hier.md): Given a GO ID, write the hierarchy below (default)
+  or above (`--up`) the given GO.
+
+### Plot GO lineage
+
+- [`go_plot.py`](doc/md/README_go_plot.md):
+  - Plots user-specified GO term(s) up to root
+  - Multiple user-specified GOs
+  - User-defined colors
+  - Plot relationships (`-r`)
+  - Optionally plot children of user-specfied GO terms
+- `plot_go_term.py` can plot the lineage
+of a certain GO term, by:
+
+```bash
+python scripts/plot_go_term.py --term=GO:0008135
+```
+
+This command will plot the following image.
+
+![GO term lineage](https://www.dropbox.com/s/4zbqx8sqcls3mge/gograph.png?raw=1)
+
+Sometimes people like to stylize the graph themselves, use option
+`--gml` to generate a GML output which can then be used in an external
+graph editing software like [Cytoscape](http://www.cytoscape.org/). The
+following image is produced by importing the GML file into Cytoscape
+using yFile orthogonal layout and solid VizMapping. Note that the [GML
+reader plugin](https://code.google.com/p/graphmlreader/) may need to be
+downloaded and installed in the `plugins` folder of Cytoscape:
+
+```bash
+python scripts/plot_go_term.py --term=GO:0008135 --gml
+```
+
+![GO term lineage (Cytoscape)](https://www.dropbox.com/s/ueov2ioxl063q8h/gograph-gml.png?raw=1)
+
+### Map GO terms to GOslim terms
+
+See `map_to_slim.py` for usage. As arguments it takes the gene ontology
+files:
+
+- the current gene ontology file `go-basic.obo`
+- the GOslim file to be used (e.g. `goslim_generic.obo` or any other GOslim file)
+
+The script either maps one GO term to its GOslim terms, or protein
+products with multiple associations to all its GOslim terms.
+
+To determine the GOslim terms for a single GO term, you can use the
+following command:
+
+```bash
+python scripts/map_to_slim.py --term=GO:0008135 go-basic.obo goslim_generic.obo
+```
+
+To determine the GOslim terms for protein products with multiple
+associations:
+
+```bash
+python scripts/map_to_slim.py --association_file=data/association go-basic.obo goslim_generic.obo
+```
+
+Where the `association` file has the same format as used for
+`find_enrichment.py`.
+
+The implementation is similar to
+[map2slim](http://search.cpan.org/~cmungall/go-perl/scripts/map2slim).
+
+## Technical notes
+
+### Available statistical tests for calculating uncorrected p-values
+
+For calculating uncorrected p-values, we use SciPy:
+
+- [`scipy.stats.fisher_exact`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html)
+
+### Available multiple test corrections
+
+We have implemented several significance tests:
+
+- `bonferroni`, bonferroni correction
+- `sidak`, sidak correction
+- `holm`, hold correction
+- `fdr`, false discovery rate (fdr) implementation using resampling
+
+Additional methods are available if `statsmodels` is installed:
+
+- `sm_bonferroni`, bonferroni one-step correction
+- `sm_sidak`, sidak one-step correction
+- `sm_holm-sidak`, holm-sidak step-down method using Sidak adjustments
+- `sm_holm`, holm step-down method using Bonferroni adjustments
+- `simes-hochberg`, simes-hochberg step-up method (independent)
+- `hommel`, hommel closed method based on Simes tests (non-negative)
+- `fdr_bh`, fdr correction with Benjamini/Hochberg (non-negative)
+- `fdr_by`, fdr correction with Benjamini/Yekutieli (negative)
+- `fdr_tsbh`, two stage fdr correction (non-negative)
+- `fdr_tsbky`, two stage fdr correction (non-negative)
+- `fdr_gbs`, fdr adaptive Gavrilov-Benjamini-Sarkar
+
+In total 15 tests are available, which can be selected using option
+`--method`. Please note that the default FDR (`fdr`) uses a resampling
+strategy which may lead to slightly different q-values between runs.
+
+## iPython [Notebooks](notebooks)
+
+### Optional attributes
+
+[definition](notebooks/Optional_attribute_definition.ipynb)
+
+### Run a Ontology Enrichment Analysis (GOEA)
+
+[goea_nbt3102](notebooks/goea_nbt3102.ipynb)
+[human phenotype ontologies](notebooks/Enrichment_analyses_human_phenotype_ontology.ipynb)
+
+### Show many study genes are associated with RNA, translation, mitochondria, and ribosomal
+
+[goea_nbt3102_group_results](notebooks/goea_nbt3102_group_results.ipynb)
+
+### Report level and depth counts of a set of GO terms
+
+[report_depth_level](notebooks/report_depth_level.ipynb)
+
+### Find all human protein-coding genes associated with cell cycle
+
+[cell_cycle](notebooks/cell_cycle.ipynb)
+
+### Calculate annotation coverage of GO terms on various species
+
+[annotation_coverage](notebooks/annotation_coverage.ipynb)
+
+### Determine the semantic similarities between GO terms
+
+[semantic_similarity](notebooks/semantic_similarity.ipynb) [semantic_similarity_wang](notebooks/semantic_similarity_wang.ipynb)
+
+### Obsolete GO terms are loaded upon request
+
+[godag_obsolete_terms](notebooks/godag_obsolete_terms.ipynb)
+
+## Want to Help?
+
+Prior to submitting your pull request, please add a test which verifies your code, and run:
+
+```console
+make test
+```
+
+Items that we know we need include:
+
+- Add code coverage runs
+- Edit tests in the `makefile` under the comment
+- Help setting up [documentation](http://goatools.readthedocs.io/en/latest/). We
+  are using Sphinx and Python docstrings to create documentation.
+  For documentation practice, use make targets:
+
+  ```bash
+  make mkdocs_practice
+  ```
+
+  To remove practice documentation:
+
+  ```bash
+  make rmdocs_practice
+  ```
+
+  Once you are happy with the documentation do:
+
+  ```bash
+  make gh-pages
+  ```
+
+Copyright (C) 2010-2021, Haibao Tang et al. All rights reserved.
+
+
+%package -n python3-goatools
+Summary:	Python scripts to find enrichment of GO terms
+Provides:	python-goatools
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-goatools
+# Tools for Gene Ontology
+
+[![DOI](/doc/images/DOI.svg)](https://www.nature.com/articles/s41598-018-28948-z)
+[![Latest PyPI version](https://img.shields.io/pypi/v/goatools.svg)](https://pypi.python.org/pypi/goatools)
+[![bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/goatools/README.html?highlight=goatools)
+[![Github Actions](https://github.com/tanghaibao/goatools/workflows/build/badge.svg)](https://github.com/tanghaibao/goatools/actions)
+[![Downloads](https://pepy.tech/badge/goatools)](https://pepy.tech/project/goatools)
+
+|         |                                                                       |
+| ------- | --------------------------------------------------------------------- |
+| Authors | Haibao Tang ([tanghaibao](http://github.com/tanghaibao))              |
+|         | DV Klopfenstein ([dvklopfenstein](https://github.com/dvklopfenstein)) |
+|         | Brent Pedersen ([brentp](http://github.com/brentp))                   |
+|         | Fidel Ramirez ([fidelram](https://github.com/fidelram))               |
+|         | Aurelien Naldi ([aurelien-naldi](http://github.com/aurelien-naldi))   |
+|         | Patrick Flick ([patflick](http://github.com/patflick))                |
+|         | Jeff Yunes ([yunesj](http://github.com/yunesj))                       |
+|         | Kenta Sato ([bicycle1885](http://github.com/bicycle1885))             |
+|         | Chris Mungall ([cmungall](https://github.com/cmungall))               |
+|         | Greg Stupp ([stuppie](https://github.com/stuppie))                    |
+|         | David DeTomaso ([deto](https://github.com/deto))                      |
+|         | Olga Botvinnik ([olgabot](https://github.com/olgabot))                |
+| Email   | <tanghaibao@gmail.com>                                                |
+| License | BSD                                                                   |
+
+## Description
+
+This package contains a Python library to
+
+- Process over- and under-representation of certain GO terms, based on
+  Fisher's exact test. With numerous multiple correction routines
+  including locally implemented routines for Bonferroni, Sidak, Holm,
+  and false discovery rate. Also included are multiple test
+  corrections from
+  [statsmodels](http://www.statsmodels.org/stable/index.html): FDR
+  Benjamini/Hochberg, FDR Benjamini/Yekutieli, Holm-Sidak,
+  Simes-Hochberg, Hommel, FDR 2-stage Benjamini-Hochberg, FDR 2-stage
+  Benjamini-Krieger-Yekutieli, FDR adaptive Gavrilov-Benjamini-Sarkar,
+  Bonferroni, Sidak, and Holm.
+
+- Process the obo-formatted file from [Gene Ontology
+  website](http://geneontology.org). The data structure is a directed
+  acyclic graph (DAG) that allows easy traversal from leaf to root.
+
+- Read [GO Association files](http://geneontology.org/page/go-annotation-file-formats):
+
+  - GAF ([GO Annotation
+    File](http://geneontology.org/page/go-annotation-file-gaf-format-21))
+  - GPAD ([Gene Product Association Data](https://geneontology.github.io/docs/gene-product-association-data-gpad-format/))
+  - NCBI's gene2go file
+  - id2gos format. See [example](https://raw.githubusercontent.com/tanghaibao/goatools/main/data/association)
+
+- [Print **_decendants count_** and/or **_information content_**](/notebooks/dcnt_and_tinfo.ipynb)
+  for a list of GO terms
+
+- [Get parents or ancestors for a GO term with or without optional
+  relationships](notebooks/parents_and_ancestors.ipynb), including [Print details about a
+  GO ID's parents](notebooks/parent_go_terms.ipynb)
+
+- Compare two or more lists of GO IDs
+- [Plot GO hierarchies](https://github.com/tanghaibao/goatools#plot-go-lineage)
+- [Write GO hierarchies to an ASCII text file](https://github.com/tanghaibao/goatools#write-go-hierarchy)
+- Group GO terms for easier viewing
+
+- Map GO terms (or protein products with multiple associations to
+  GO terms) to GOslim terms (analog to the map2slim.pl script supplied
+  by geneontology.org)
+
+## To Cite
+
+Klopfenstein DV, Zhang L, Pedersen BS, ... Tang H [GOATOOLS: A Python library for Gene Ontology analyses](https://www.nature.com/articles/s41598-018-28948-z)
+_Scientific reports_ | (2018) 8:10872 | DOI:10.1038/s41598-018-28948-z
+
+- **GO Grouping**:
+  Visualize the major findings in a gene ontology enrichment analysis (GOEA) more easily with grouping.
+  A detailed description of GOATOOLS GO grouping is found in the
+  [manuscript](https://www.nature.com/articles/s41598-018-28948-z).
+- **Compare GO lists**:
+  Compare [two](https://github.com/tanghaibao/goatools/issues/162) or more lists
+  of GO IDs using `compare_gos.py`, which can be used with or without
+  grouping.
+- **Stochastic GOEA simulations**:
+  One of the findings resulting from our simulations is:
+  [Larger study sizes result in higher GOEA sensitivity](https://github.com/dvklopfenstein/goatools_simulation#manuscript-figures),
+  meaning fewer truly significant observations go unreported.
+  The code for the stochastic GOEA simulations
+  described in the paper is found [here](https://github.com/dvklopfenstein/goatools_simulation)
+
+## Installation
+
+Make sure your Python version >= 3.7, and download an
+`.obo` file of the most current
+[GO](http://geneontology.org/docs/download-ontology):
+
+```bash
+wget http://current.geneontology.org/ontology/go-basic.obo
+```
+
+or `.obo` file for the most current [GO
+Slim](http://geneontology.org/docs/go-subset-guide/) terms (e.g.
+generic GOslim) :
+
+```bash
+wget http://current.geneontology.org/ontology/subsets/goslim_generic.obo
+```
+
+
+
+### [PyPI](https://pypi.org/project/goatools/)
+
+```bash
+pip install goatools
+```
+
+To install the development version:
+
+```bash
+pip install git+git://github.com/tanghaibao/goatools.git
+```
+
+### [Bioconda](http://bioconda.github.io/recipes/goatools/README.html?highlight=goatools)
+```bash
+conda install -c bioconda goatools
+```
+
+## Dependencies
+
+When installing via PyPI or Bioconda as described above, all dependencies are automatically downloaded.
+Alternatively, you can manually install:
+
+- For statistical testing of GO enrichment:
+  - [`scipy.stats.fisher_exact`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html)
+  - `statsmodels` (optional) for access to a variety of statistical tests for GOEA
+
+
+- To plot the ontology lineage, install one of these two options:
+  - [Graphviz](http://www.graphviz.org/), for graph visualization.
+  - [pygraphviz](http://networkx.lanl.gov/pygraphviz/), Python binding for communicating with Graphviz:
+  - [pydot](https://code.google.com/p/pydot/), a Python interface to Graphviz's Dot language.
+
+## Cookbook
+
+`run.sh` contains example cases, which calls the utility scripts in the
+`scripts` folder.
+
+### Find GO enrichment of genes under study
+
+See examples in [find_enrichment](/doc/md/README_find_enrichment.md)
+
+The `find_enrichment.py` takes as arguments files
+containing:
+
+- gene names in a study
+- gene names in population (or other study if `--compare` is specified)
+- an association file that maps a gene name to a GO category.
+
+Please look at `tests/data` folder to see examples on how to make these
+files. when ready, the command looks like:
+
+```bash
+python scripts/find_enrichment.py --pval=0.05 --indent data/study \
+                                  data/population data/association
+```
+
+and can filter on the significance of (e)nrichment or (p)urification. it
+can report various multiple testing corrected p-values as well as the
+false discovery rate.
+
+The `e` in the "Enrichment" column means "enriched" - the concentration
+of GO term in the study group is significantly _higher_ than those in
+the population. The "p" stands for "purified" - significantly _lower_
+concentration of the GO term in the study group than in the population.
+
+**Important note**: by default, `find_enrichment.py` propagates counts
+to all the parents of a GO term. As a result, users may find terms in
+the output that are not present in their `association` file. Use
+`--no_propagate_counts` to disable this behavior.
+
+### Write GO hierarchy
+
+- [`wr_hier.py`](doc/md/README_wr_hier.md): Given a GO ID, write the hierarchy below (default)
+  or above (`--up`) the given GO.
+
+### Plot GO lineage
+
+- [`go_plot.py`](doc/md/README_go_plot.md):
+  - Plots user-specified GO term(s) up to root
+  - Multiple user-specified GOs
+  - User-defined colors
+  - Plot relationships (`-r`)
+  - Optionally plot children of user-specfied GO terms
+- `plot_go_term.py` can plot the lineage
+of a certain GO term, by:
+
+```bash
+python scripts/plot_go_term.py --term=GO:0008135
+```
+
+This command will plot the following image.
+
+![GO term lineage](https://www.dropbox.com/s/4zbqx8sqcls3mge/gograph.png?raw=1)
+
+Sometimes people like to stylize the graph themselves, use option
+`--gml` to generate a GML output which can then be used in an external
+graph editing software like [Cytoscape](http://www.cytoscape.org/). The
+following image is produced by importing the GML file into Cytoscape
+using yFile orthogonal layout and solid VizMapping. Note that the [GML
+reader plugin](https://code.google.com/p/graphmlreader/) may need to be
+downloaded and installed in the `plugins` folder of Cytoscape:
+
+```bash
+python scripts/plot_go_term.py --term=GO:0008135 --gml
+```
+
+![GO term lineage (Cytoscape)](https://www.dropbox.com/s/ueov2ioxl063q8h/gograph-gml.png?raw=1)
+
+### Map GO terms to GOslim terms
+
+See `map_to_slim.py` for usage. As arguments it takes the gene ontology
+files:
+
+- the current gene ontology file `go-basic.obo`
+- the GOslim file to be used (e.g. `goslim_generic.obo` or any other GOslim file)
+
+The script either maps one GO term to its GOslim terms, or protein
+products with multiple associations to all its GOslim terms.
+
+To determine the GOslim terms for a single GO term, you can use the
+following command:
+
+```bash
+python scripts/map_to_slim.py --term=GO:0008135 go-basic.obo goslim_generic.obo
+```
+
+To determine the GOslim terms for protein products with multiple
+associations:
+
+```bash
+python scripts/map_to_slim.py --association_file=data/association go-basic.obo goslim_generic.obo
+```
+
+Where the `association` file has the same format as used for
+`find_enrichment.py`.
+
+The implementation is similar to
+[map2slim](http://search.cpan.org/~cmungall/go-perl/scripts/map2slim).
+
+## Technical notes
+
+### Available statistical tests for calculating uncorrected p-values
+
+For calculating uncorrected p-values, we use SciPy:
+
+- [`scipy.stats.fisher_exact`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html)
+
+### Available multiple test corrections
+
+We have implemented several significance tests:
+
+- `bonferroni`, bonferroni correction
+- `sidak`, sidak correction
+- `holm`, hold correction
+- `fdr`, false discovery rate (fdr) implementation using resampling
+
+Additional methods are available if `statsmodels` is installed:
+
+- `sm_bonferroni`, bonferroni one-step correction
+- `sm_sidak`, sidak one-step correction
+- `sm_holm-sidak`, holm-sidak step-down method using Sidak adjustments
+- `sm_holm`, holm step-down method using Bonferroni adjustments
+- `simes-hochberg`, simes-hochberg step-up method (independent)
+- `hommel`, hommel closed method based on Simes tests (non-negative)
+- `fdr_bh`, fdr correction with Benjamini/Hochberg (non-negative)
+- `fdr_by`, fdr correction with Benjamini/Yekutieli (negative)
+- `fdr_tsbh`, two stage fdr correction (non-negative)
+- `fdr_tsbky`, two stage fdr correction (non-negative)
+- `fdr_gbs`, fdr adaptive Gavrilov-Benjamini-Sarkar
+
+In total 15 tests are available, which can be selected using option
+`--method`. Please note that the default FDR (`fdr`) uses a resampling
+strategy which may lead to slightly different q-values between runs.
+
+## iPython [Notebooks](notebooks)
+
+### Optional attributes
+
+[definition](notebooks/Optional_attribute_definition.ipynb)
+
+### Run a Ontology Enrichment Analysis (GOEA)
+
+[goea_nbt3102](notebooks/goea_nbt3102.ipynb)
+[human phenotype ontologies](notebooks/Enrichment_analyses_human_phenotype_ontology.ipynb)
+
+### Show many study genes are associated with RNA, translation, mitochondria, and ribosomal
+
+[goea_nbt3102_group_results](notebooks/goea_nbt3102_group_results.ipynb)
+
+### Report level and depth counts of a set of GO terms
+
+[report_depth_level](notebooks/report_depth_level.ipynb)
+
+### Find all human protein-coding genes associated with cell cycle
+
+[cell_cycle](notebooks/cell_cycle.ipynb)
+
+### Calculate annotation coverage of GO terms on various species
+
+[annotation_coverage](notebooks/annotation_coverage.ipynb)
+
+### Determine the semantic similarities between GO terms
+
+[semantic_similarity](notebooks/semantic_similarity.ipynb) [semantic_similarity_wang](notebooks/semantic_similarity_wang.ipynb)
+
+### Obsolete GO terms are loaded upon request
+
+[godag_obsolete_terms](notebooks/godag_obsolete_terms.ipynb)
+
+## Want to Help?
+
+Prior to submitting your pull request, please add a test which verifies your code, and run:
+
+```console
+make test
+```
+
+Items that we know we need include:
+
+- Add code coverage runs
+- Edit tests in the `makefile` under the comment
+- Help setting up [documentation](http://goatools.readthedocs.io/en/latest/). We
+  are using Sphinx and Python docstrings to create documentation.
+  For documentation practice, use make targets:
+
+  ```bash
+  make mkdocs_practice
+  ```
+
+  To remove practice documentation:
+
+  ```bash
+  make rmdocs_practice
+  ```
+
+  Once you are happy with the documentation do:
+
+  ```bash
+  make gh-pages
+  ```
+
+Copyright (C) 2010-2021, Haibao Tang et al. All rights reserved.
+
+
+%package help
+Summary:	Development documents and examples for goatools
+Provides:	python3-goatools-doc
+%description help
+# Tools for Gene Ontology
+
+[![DOI](/doc/images/DOI.svg)](https://www.nature.com/articles/s41598-018-28948-z)
+[![Latest PyPI version](https://img.shields.io/pypi/v/goatools.svg)](https://pypi.python.org/pypi/goatools)
+[![bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/goatools/README.html?highlight=goatools)
+[![Github Actions](https://github.com/tanghaibao/goatools/workflows/build/badge.svg)](https://github.com/tanghaibao/goatools/actions)
+[![Downloads](https://pepy.tech/badge/goatools)](https://pepy.tech/project/goatools)
+
+|         |                                                                       |
+| ------- | --------------------------------------------------------------------- |
+| Authors | Haibao Tang ([tanghaibao](http://github.com/tanghaibao))              |
+|         | DV Klopfenstein ([dvklopfenstein](https://github.com/dvklopfenstein)) |
+|         | Brent Pedersen ([brentp](http://github.com/brentp))                   |
+|         | Fidel Ramirez ([fidelram](https://github.com/fidelram))               |
+|         | Aurelien Naldi ([aurelien-naldi](http://github.com/aurelien-naldi))   |
+|         | Patrick Flick ([patflick](http://github.com/patflick))                |
+|         | Jeff Yunes ([yunesj](http://github.com/yunesj))                       |
+|         | Kenta Sato ([bicycle1885](http://github.com/bicycle1885))             |
+|         | Chris Mungall ([cmungall](https://github.com/cmungall))               |
+|         | Greg Stupp ([stuppie](https://github.com/stuppie))                    |
+|         | David DeTomaso ([deto](https://github.com/deto))                      |
+|         | Olga Botvinnik ([olgabot](https://github.com/olgabot))                |
+| Email   | <tanghaibao@gmail.com>                                                |
+| License | BSD                                                                   |
+
+## Description
+
+This package contains a Python library to
+
+- Process over- and under-representation of certain GO terms, based on
+  Fisher's exact test. With numerous multiple correction routines
+  including locally implemented routines for Bonferroni, Sidak, Holm,
+  and false discovery rate. Also included are multiple test
+  corrections from
+  [statsmodels](http://www.statsmodels.org/stable/index.html): FDR
+  Benjamini/Hochberg, FDR Benjamini/Yekutieli, Holm-Sidak,
+  Simes-Hochberg, Hommel, FDR 2-stage Benjamini-Hochberg, FDR 2-stage
+  Benjamini-Krieger-Yekutieli, FDR adaptive Gavrilov-Benjamini-Sarkar,
+  Bonferroni, Sidak, and Holm.
+
+- Process the obo-formatted file from [Gene Ontology
+  website](http://geneontology.org). The data structure is a directed
+  acyclic graph (DAG) that allows easy traversal from leaf to root.
+
+- Read [GO Association files](http://geneontology.org/page/go-annotation-file-formats):
+
+  - GAF ([GO Annotation
+    File](http://geneontology.org/page/go-annotation-file-gaf-format-21))
+  - GPAD ([Gene Product Association Data](https://geneontology.github.io/docs/gene-product-association-data-gpad-format/))
+  - NCBI's gene2go file
+  - id2gos format. See [example](https://raw.githubusercontent.com/tanghaibao/goatools/main/data/association)
+
+- [Print **_decendants count_** and/or **_information content_**](/notebooks/dcnt_and_tinfo.ipynb)
+  for a list of GO terms
+
+- [Get parents or ancestors for a GO term with or without optional
+  relationships](notebooks/parents_and_ancestors.ipynb), including [Print details about a
+  GO ID's parents](notebooks/parent_go_terms.ipynb)
+
+- Compare two or more lists of GO IDs
+- [Plot GO hierarchies](https://github.com/tanghaibao/goatools#plot-go-lineage)
+- [Write GO hierarchies to an ASCII text file](https://github.com/tanghaibao/goatools#write-go-hierarchy)
+- Group GO terms for easier viewing
+
+- Map GO terms (or protein products with multiple associations to
+  GO terms) to GOslim terms (analog to the map2slim.pl script supplied
+  by geneontology.org)
+
+## To Cite
+
+Klopfenstein DV, Zhang L, Pedersen BS, ... Tang H [GOATOOLS: A Python library for Gene Ontology analyses](https://www.nature.com/articles/s41598-018-28948-z)
+_Scientific reports_ | (2018) 8:10872 | DOI:10.1038/s41598-018-28948-z
+
+- **GO Grouping**:
+  Visualize the major findings in a gene ontology enrichment analysis (GOEA) more easily with grouping.
+  A detailed description of GOATOOLS GO grouping is found in the
+  [manuscript](https://www.nature.com/articles/s41598-018-28948-z).
+- **Compare GO lists**:
+  Compare [two](https://github.com/tanghaibao/goatools/issues/162) or more lists
+  of GO IDs using `compare_gos.py`, which can be used with or without
+  grouping.
+- **Stochastic GOEA simulations**:
+  One of the findings resulting from our simulations is:
+  [Larger study sizes result in higher GOEA sensitivity](https://github.com/dvklopfenstein/goatools_simulation#manuscript-figures),
+  meaning fewer truly significant observations go unreported.
+  The code for the stochastic GOEA simulations
+  described in the paper is found [here](https://github.com/dvklopfenstein/goatools_simulation)
+
+## Installation
+
+Make sure your Python version >= 3.7, and download an
+`.obo` file of the most current
+[GO](http://geneontology.org/docs/download-ontology):
+
+```bash
+wget http://current.geneontology.org/ontology/go-basic.obo
+```
+
+or `.obo` file for the most current [GO
+Slim](http://geneontology.org/docs/go-subset-guide/) terms (e.g.
+generic GOslim) :
+
+```bash
+wget http://current.geneontology.org/ontology/subsets/goslim_generic.obo
+```
+
+
+
+### [PyPI](https://pypi.org/project/goatools/)
+
+```bash
+pip install goatools
+```
+
+To install the development version:
+
+```bash
+pip install git+git://github.com/tanghaibao/goatools.git
+```
+
+### [Bioconda](http://bioconda.github.io/recipes/goatools/README.html?highlight=goatools)
+```bash
+conda install -c bioconda goatools
+```
+
+## Dependencies
+
+When installing via PyPI or Bioconda as described above, all dependencies are automatically downloaded.
+Alternatively, you can manually install:
+
+- For statistical testing of GO enrichment:
+  - [`scipy.stats.fisher_exact`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html)
+  - `statsmodels` (optional) for access to a variety of statistical tests for GOEA
+
+
+- To plot the ontology lineage, install one of these two options:
+  - [Graphviz](http://www.graphviz.org/), for graph visualization.
+  - [pygraphviz](http://networkx.lanl.gov/pygraphviz/), Python binding for communicating with Graphviz:
+  - [pydot](https://code.google.com/p/pydot/), a Python interface to Graphviz's Dot language.
+
+## Cookbook
+
+`run.sh` contains example cases, which calls the utility scripts in the
+`scripts` folder.
+
+### Find GO enrichment of genes under study
+
+See examples in [find_enrichment](/doc/md/README_find_enrichment.md)
+
+The `find_enrichment.py` takes as arguments files
+containing:
+
+- gene names in a study
+- gene names in population (or other study if `--compare` is specified)
+- an association file that maps a gene name to a GO category.
+
+Please look at `tests/data` folder to see examples on how to make these
+files. when ready, the command looks like:
+
+```bash
+python scripts/find_enrichment.py --pval=0.05 --indent data/study \
+                                  data/population data/association
+```
+
+and can filter on the significance of (e)nrichment or (p)urification. it
+can report various multiple testing corrected p-values as well as the
+false discovery rate.
+
+The `e` in the "Enrichment" column means "enriched" - the concentration
+of GO term in the study group is significantly _higher_ than those in
+the population. The "p" stands for "purified" - significantly _lower_
+concentration of the GO term in the study group than in the population.
+
+**Important note**: by default, `find_enrichment.py` propagates counts
+to all the parents of a GO term. As a result, users may find terms in
+the output that are not present in their `association` file. Use
+`--no_propagate_counts` to disable this behavior.
+
+### Write GO hierarchy
+
+- [`wr_hier.py`](doc/md/README_wr_hier.md): Given a GO ID, write the hierarchy below (default)
+  or above (`--up`) the given GO.
+
+### Plot GO lineage
+
+- [`go_plot.py`](doc/md/README_go_plot.md):
+  - Plots user-specified GO term(s) up to root
+  - Multiple user-specified GOs
+  - User-defined colors
+  - Plot relationships (`-r`)
+  - Optionally plot children of user-specfied GO terms
+- `plot_go_term.py` can plot the lineage
+of a certain GO term, by:
+
+```bash
+python scripts/plot_go_term.py --term=GO:0008135
+```
+
+This command will plot the following image.
+
+![GO term lineage](https://www.dropbox.com/s/4zbqx8sqcls3mge/gograph.png?raw=1)
+
+Sometimes people like to stylize the graph themselves, use option
+`--gml` to generate a GML output which can then be used in an external
+graph editing software like [Cytoscape](http://www.cytoscape.org/). The
+following image is produced by importing the GML file into Cytoscape
+using yFile orthogonal layout and solid VizMapping. Note that the [GML
+reader plugin](https://code.google.com/p/graphmlreader/) may need to be
+downloaded and installed in the `plugins` folder of Cytoscape:
+
+```bash
+python scripts/plot_go_term.py --term=GO:0008135 --gml
+```
+
+![GO term lineage (Cytoscape)](https://www.dropbox.com/s/ueov2ioxl063q8h/gograph-gml.png?raw=1)
+
+### Map GO terms to GOslim terms
+
+See `map_to_slim.py` for usage. As arguments it takes the gene ontology
+files:
+
+- the current gene ontology file `go-basic.obo`
+- the GOslim file to be used (e.g. `goslim_generic.obo` or any other GOslim file)
+
+The script either maps one GO term to its GOslim terms, or protein
+products with multiple associations to all its GOslim terms.
+
+To determine the GOslim terms for a single GO term, you can use the
+following command:
+
+```bash
+python scripts/map_to_slim.py --term=GO:0008135 go-basic.obo goslim_generic.obo
+```
+
+To determine the GOslim terms for protein products with multiple
+associations:
+
+```bash
+python scripts/map_to_slim.py --association_file=data/association go-basic.obo goslim_generic.obo
+```
+
+Where the `association` file has the same format as used for
+`find_enrichment.py`.
+
+The implementation is similar to
+[map2slim](http://search.cpan.org/~cmungall/go-perl/scripts/map2slim).
+
+## Technical notes
+
+### Available statistical tests for calculating uncorrected p-values
+
+For calculating uncorrected p-values, we use SciPy:
+
+- [`scipy.stats.fisher_exact`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html)
+
+### Available multiple test corrections
+
+We have implemented several significance tests:
+
+- `bonferroni`, bonferroni correction
+- `sidak`, sidak correction
+- `holm`, hold correction
+- `fdr`, false discovery rate (fdr) implementation using resampling
+
+Additional methods are available if `statsmodels` is installed:
+
+- `sm_bonferroni`, bonferroni one-step correction
+- `sm_sidak`, sidak one-step correction
+- `sm_holm-sidak`, holm-sidak step-down method using Sidak adjustments
+- `sm_holm`, holm step-down method using Bonferroni adjustments
+- `simes-hochberg`, simes-hochberg step-up method (independent)
+- `hommel`, hommel closed method based on Simes tests (non-negative)
+- `fdr_bh`, fdr correction with Benjamini/Hochberg (non-negative)
+- `fdr_by`, fdr correction with Benjamini/Yekutieli (negative)
+- `fdr_tsbh`, two stage fdr correction (non-negative)
+- `fdr_tsbky`, two stage fdr correction (non-negative)
+- `fdr_gbs`, fdr adaptive Gavrilov-Benjamini-Sarkar
+
+In total 15 tests are available, which can be selected using option
+`--method`. Please note that the default FDR (`fdr`) uses a resampling
+strategy which may lead to slightly different q-values between runs.
+
+## iPython [Notebooks](notebooks)
+
+### Optional attributes
+
+[definition](notebooks/Optional_attribute_definition.ipynb)
+
+### Run a Ontology Enrichment Analysis (GOEA)
+
+[goea_nbt3102](notebooks/goea_nbt3102.ipynb)
+[human phenotype ontologies](notebooks/Enrichment_analyses_human_phenotype_ontology.ipynb)
+
+### Show many study genes are associated with RNA, translation, mitochondria, and ribosomal
+
+[goea_nbt3102_group_results](notebooks/goea_nbt3102_group_results.ipynb)
+
+### Report level and depth counts of a set of GO terms
+
+[report_depth_level](notebooks/report_depth_level.ipynb)
+
+### Find all human protein-coding genes associated with cell cycle
+
+[cell_cycle](notebooks/cell_cycle.ipynb)
+
+### Calculate annotation coverage of GO terms on various species
+
+[annotation_coverage](notebooks/annotation_coverage.ipynb)
+
+### Determine the semantic similarities between GO terms
+
+[semantic_similarity](notebooks/semantic_similarity.ipynb) [semantic_similarity_wang](notebooks/semantic_similarity_wang.ipynb)
+
+### Obsolete GO terms are loaded upon request
+
+[godag_obsolete_terms](notebooks/godag_obsolete_terms.ipynb)
+
+## Want to Help?
+
+Prior to submitting your pull request, please add a test which verifies your code, and run:
+
+```console
+make test
+```
+
+Items that we know we need include:
+
+- Add code coverage runs
+- Edit tests in the `makefile` under the comment
+- Help setting up [documentation](http://goatools.readthedocs.io/en/latest/). We
+  are using Sphinx and Python docstrings to create documentation.
+  For documentation practice, use make targets:
+
+  ```bash
+  make mkdocs_practice
+  ```
+
+  To remove practice documentation:
+
+  ```bash
+  make rmdocs_practice
+  ```
+
+  Once you are happy with the documentation do:
+
+  ```bash
+  make gh-pages
+  ```
+
+Copyright (C) 2010-2021, Haibao Tang et al. All rights reserved.
+
+
+%prep
+%autosetup -n goatools-1.3.1
+
+%build
+%py3_build
+
+%install
+%py3_install
+install -d -m755 %{buildroot}/%{_pkgdocdir}
+if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
+if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
+if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
+if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
+pushd %{buildroot}
+if [ -d usr/lib ]; then
+	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/lib64 ]; then
+	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/bin ]; then
+	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/sbin ]; then
+	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+touch doclist.lst
+if [ -d usr/share/man ]; then
+	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
+fi
+popd
+mv %{buildroot}/filelist.lst .
+mv %{buildroot}/doclist.lst .
+
+%files -n python3-goatools -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Wed May 17 2023 Python_Bot <Python_Bot@openeuler.org> - 1.3.1-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..867494a
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+beeadd4efc40ee1f3d7fd0949d59e76b  goatools-1.3.1.tar.gz