├── .github
└── workflows
│ └── tests.yml
├── .gitignore
├── CONTRIBUTING.md
├── LICENSE
├── MANIFEST.in
├── README.md
├── RELEASING.md
├── deploy.sh
├── develop.sh
├── docs
├── Makefile
├── conf.py
├── index.rst
├── make.bat
├── modules.rst
└── pyensembl.rst
├── lint-and-test.sh
├── lint.sh
├── pyensembl
├── __init__.py
├── common.py
├── database.py
├── download_cache.py
├── ensembl_release.py
├── ensembl_url_templates.py
├── ensembl_versions.py
├── exon.py
├── fasta.py
├── gene.py
├── genome.py
├── locus.py
├── locus_with_genome.py
├── logging.conf
├── normalization.py
├── reference_name.py
├── search.py
├── sequence_data.py
├── shell.py
├── species.py
├── transcript.py
└── version.py
├── pylintrc
├── requirements.txt
├── setup.py
├── test.sh
└── tests
├── __init__.py
├── common.py
├── data.py
├── data
├── gencode.ucsc.small.gtf
├── mouse.ensembl.81.partial.ENSMUSG00000017167.fa
├── mouse.ensembl.81.partial.ENSMUSG00000017167.gtf
├── mouse.ensembl.81.partial.ENSMUSG00000017167.pep
├── mouse.ensembl.81.partial.ncrna.ENSMUSG00000017167.fa
└── refseq.ucsc.small.gtf
├── test_contigs.py
├── test_download_cache.py
├── test_ensembl_gtf.py
├── test_ensembl_object_properties.py
├── test_exon_id.py
├── test_exon_object.py
├── test_gene_ids.py
├── test_gene_names.py
├── test_gene_objects.py
├── test_id_length.py
├── test_locus.py
├── test_missing_genome_sources.py
├── test_mouse.py
├── test_release_versions.py
├── test_search.py
├── test_sequence_data.py
├── test_serialization.py
├── test_shell.py
├── test_string_representation.py
├── test_timings.py
├── test_transcript_ids.py
├── test_transcript_objects.py
├── test_transcript_sequences.py
├── test_transcript_support_level.py
└── test_ucsc_gtf.py
/.github/workflows/tests.yml:
--------------------------------------------------------------------------------
1 | # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
2 | # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
3 |
4 | # TODO:
5 | # - cache this directory $HOME/.cache/pyensembl/
6 | # - update coveralls
7 | # - get a badge for tests passing
8 | # - download binary dependencies from conda
9 | name: Tests
10 | on: [push, pull_request]
11 |
12 | jobs:
13 | build:
14 | runs-on: ubuntu-latest
15 | strategy:
16 | fail-fast: true
17 | matrix:
18 | python-version: ["3.9", "3.10", "3.11"]
19 |
20 | steps:
21 | - name: Checkout repository
22 | uses: actions/checkout@v3
23 | - name: Set up Python ${{ matrix.python-version }}
24 | uses: actions/setup-python@v3
25 | with:
26 | python-version: ${{ matrix.python-version }}
27 | cache: "pip"
28 | - name: Install dependencies
29 | run: |
30 | python -m pip install --upgrade pip
31 | python -m pip install flake8 pytest pytest-cov coveralls
32 | pip install -r requirements.txt
33 | pip install .
34 | - name: Lint with flake8
35 | run: |
36 | # stop the build if there are Python syntax errors or undefined names
37 | flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
38 | # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
39 | flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
40 | - name: Run default linting script
41 | run: |
42 | ./lint.sh
43 | - name: Install Ensembl data
44 | run: |
45 | echo "Before installing Ensembl releases" && df -h
46 | pyensembl install --release 75 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh37.75/
47 | pyensembl install --release 77 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.77/
48 | pyensembl install --release 93 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.93/
49 | pyensembl install --release 93 --species mouse --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.93/
50 | - name: Run unit tests
51 | run: |
52 | ./test.sh
53 | - name: Publish coverage to Coveralls
54 | uses: coverallsapp/github-action@v2.2.3
55 |
--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
1 | # Byte-compiled / optimized / DLL files
2 | __pycache__/
3 | *.py[cod]
4 |
5 | # C extensions
6 | *.so
7 |
8 | # Distribution / packaging
9 | .Python
10 | env/
11 | bin/
12 | build/
13 | develop-eggs/
14 | dist/
15 | eggs/
16 | lib/
17 | lib64/
18 | parts/
19 | sdist/
20 | var/
21 | *.egg-info/
22 | .installed.cfg
23 | *.egg
24 |
25 | # Installer logs
26 | pip-log.txt
27 | pip-delete-this-directory.txt
28 |
29 | # Unit test / coverage reports
30 | htmlcov/
31 | .tox/
32 | .coverage
33 | .cache
34 | nosetests.xml
35 | coverage.xml
36 |
37 | # Translations
38 | *.mo
39 |
40 | # Mr Developer
41 | .mr.developer.cfg
42 | .project
43 | .pydevproject
44 |
45 | # Rope
46 | .ropeproject
47 |
48 | # Django stuff:
49 | *.log
50 | *.pot
51 |
52 | # Sphinx documentation
53 | docs/_build/
54 |
55 |
--------------------------------------------------------------------------------
/CONTRIBUTING.md:
--------------------------------------------------------------------------------
1 | # Contributing to PyEnsembl
2 |
3 | [PyEnsembl](http://www.github.com/hammerlab/pyensembl) is open source software and
4 | we welcome your contributions. This document should help you get started
5 | contributing to PyEnsembl.
6 |
7 | ## Filing Issues
8 |
9 | If you find any bugs or problems while using PyEnsembl or have any feature requests, please feel free to file an issue against the project. When doing so, please follow the guidelines below:
10 |
11 | To report any bugs, issues, or feature requests, please [open an issue](https://github.com/hammerlab/pyensembl/issues)
12 | Please check the [current open issues](https://github.com/hammerlab/pyensembl/issues) to see if the request already exists
13 | If you are filing a bug report, please describe the version of PyEnsembl and Python you are using. If your problem involves a particular gene, transcript, or genomic locus, please include that information (e.g. "Missing transcript sequence for BRCA1-002 for Ensembl release 74").
14 |
15 | ## Coding Guidelines
16 |
17 | - PyEnsembl is written in Python and adheres to the [PEP8](https://www.python.org/dev/peps/pep-0008/)
18 | style guidelines.
19 | - Contributions should come in the form of GitHub pull requests.
20 | - New features should start with a GitHub issue explaining their scope and rationale.
21 | - If the work is based on an existing issue, please reference the issue in the PR.
22 | - All new code should be accompanied by comprehensive unit tests.
23 | - If the PR fixes or implements an issue, please state "Closes #XYZ" or "Fixes #XYZ", where XYZ is the issue number.
24 | - Please ensure that your code works under Python >= 3.7.
25 |
26 | ## Licensing
27 |
28 | PyEnsembl is licensed under the Apache 2.0 license. Your code is assumed to be as well.
29 |
--------------------------------------------------------------------------------
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/MANIFEST.in:
--------------------------------------------------------------------------------
1 | include README.md
2 | include LICENSE
3 |
--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
1 | [](https://github.com/openvax/pyensembl/actions/workflows/tests.yml)
2 | [](https://coveralls.io/github/openvax/pyensembl?branch=main)
3 |
4 |
6 |
7 | # PyEnsembl
8 |
9 | PyEnsembl is a Python interface to [Ensembl](http://www.ensembl.org) reference genome metadata such as exons and transcripts. PyEnsembl downloads [GTF](https://en.wikipedia.org/wiki/Gene_transfer_format) and [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files from the [Ensembl FTP server](ftp://ftp.ensembl.org) and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files.
10 |
11 | # Example Usage
12 |
13 | ```python
14 | from pyensembl import EnsemblRelease
15 |
16 | # release 77 uses human reference genome GRCh38
17 | data = EnsemblRelease(77)
18 |
19 | # will return ['HLA-A']
20 | gene_names = data.gene_names_at_locus(contig=6, position=29945884)
21 |
22 | # get all exons associated with HLA-A
23 | exon_ids = data.exon_ids_of_gene_name('HLA-A')
24 | ```
25 |
26 | # Installation
27 |
28 | You can install PyEnsembl using [pip](https://pip.pypa.io/en/latest/quickstart.html):
29 |
30 | ```sh
31 | pip install pyensembl
32 | ```
33 |
34 | This should also install any required packages such as [datacache](https://github.com/openvax/datacache).
35 |
36 | Before using PyEnsembl, run the following command to download and install
37 | Ensembl data:
38 |
39 | ```
40 | pyensembl install --release --species
41 | ```
42 |
43 | For example, `pyensembl install --release 75 76 --species human` will download and install all
44 | human reference data from Ensembl releases 75 and 76.
45 |
46 | Alternatively, you can create the `EnsemblRelease` object from inside a Python
47 | process and call `ensembl_object.download()` followed by `ensembl_object.index()`.
48 |
49 | ## Cache Location
50 |
51 | By default, PyEnsembl uses the platform-specific `Cache` folder
52 | and caches the files into the `pyensembl` sub-directory.
53 | You can override this default by setting the environment key `PYENSEMBL_CACHE_DIR`
54 | as your preferred location for caching:
55 |
56 | ```sh
57 | export PYENSEMBL_CACHE_DIR=/custom/cache/dir
58 | ```
59 |
60 | or
61 |
62 | ```python
63 | import os
64 |
65 | os.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'
66 | # ... PyEnsembl API usage
67 | ```
68 |
69 | # Usage tips
70 |
71 | ## List installed genomes
72 |
73 | To see the genomes for which PyEnsembl has already downloaded and indexed metadata you can run:
74 |
75 | ```sh
76 | pyensembl list
77 | ```
78 |
79 | Or equivalently do this in Python:
80 |
81 | ```python
82 | from pyensembl.shell import collect_all_installed_ensembl_releases
83 | collect_all_installed_ensembl_releases()
84 | ```
85 |
86 | ## Load genome in Python
87 |
88 | Here's an example Python snippet that loads fly genome data from Ensembl release v100:
89 |
90 | ```python
91 | from pyensembl import EnsemblRelease
92 | data = EnsemblRelease(release=100, species='drosophila_melanogaster')
93 | ```
94 |
95 | ## Data structures
96 |
97 | ### Gene
98 |
99 | ```python
100 | gene = genome.gene_by_id(gene_id='FBgn0011747')
101 | ```
102 |
103 | ### Transcript
104 |
105 | ```python
106 | transcript = gene.transcripts[0]
107 | ```
108 |
109 | ### Protein information
110 |
111 | ```python
112 | transcript.protein_id
113 | transcript.protein_sequence
114 | ```
115 |
116 | # Non-Ensembl Data
117 |
118 | PyEnsembl also allows arbitrary genomes via the specification
119 | of local file paths or remote URLs to both Ensembl and non-Ensembl GTF
120 | and FASTA files. (Warning: GTF formats can vary, and handling of
121 | non-Ensembl data is still very much in development.)
122 |
123 | For example:
124 |
125 | ```python
126 | from pyensembl import Genome
127 | data = Genome(
128 | reference_name='GRCh38',
129 | annotation_name='my_genome_features',
130 | # annotation_version=None,
131 | gtf_path_or_url='/My/local/gtf/path_to_my_genome_features.gtf', # Path or URL of GTF file
132 | # transcript_fasta_paths_or_urls=None, # List of paths or URLs of FASTA files containing transcript sequences
133 | # protein_fasta_paths_or_urls=None, # List of paths or URLs of FASTA files containing protein sequences
134 | # cache_directory_path=None, # Where to place downloaded and cached files for this genome
135 | )
136 | # parse GTF and construct database of genomic features
137 | data.index()
138 | gene_names = data.gene_names_at_locus(contig=6, position=29945884)
139 | ```
140 |
141 | # API
142 |
143 | The `EnsemblRelease` object has methods to let you access all possible
144 | combinations of the annotation features _gene_name_, _gene_id_,
145 | _transcript_name_, _transcript_id_, _exon_id_ as well as the location of
146 | these genomic elements (contig, start position, end position, strand).
147 |
148 | ## Genes
149 |
150 |
151 | genes(contig=None, strand=None)
152 | Returns a list of Gene objects, optionally restricted to a particular contig
153 | or strand.
154 |
155 | genes_at_locus(contig, position, end=None, strand=None)
156 | Returns a list of Gene objects overlapping a particular position on a contig,
157 | optionally extend into a range with the end parameter and restrict to
158 | forward or backward strand by passing strand='+' or strand='-'.
159 |
160 | gene_by_id(gene_id)
161 | Return a Gene object for given Ensembl gene ID (e.g. "ENSG00000068793").
162 |
163 | gene_names(contig=None, strand=None)
164 | Returns all gene names in the annotation database, optionally restricted
165 | to a particular contig or strand.
166 |
167 | genes_by_name(gene_name)
168 | Get all the unqiue genes with the given name (there might be multiple
169 | due to copies in the genome), return a list containing a Gene object for each
170 | distinct ID.
171 |
172 | gene_by_protein_id(protein_id)
173 | Find Gene associated with the given Ensembl protein ID (e.g. "ENSP00000350283")
174 |
175 | gene_names_at_locus(contig, position, end=None, strand=None)
176 |
177 | Names of genes overlapping with the given locus, optionally restricted by strand.
178 | (returns a list to account for overlapping genes)
179 |
180 | gene_name_of_gene_id(gene_id)
181 |
182 | Returns name of gene with given genen ID.
183 |
184 | gene_name_of_transcript_id(transcript_id)
185 | Returns name of gene associated with given transcript ID.
186 |
187 | gene_name_of_transcript_name(transcript_name)
188 |
189 | Returns name of gene associated with given transcript name.
190 |
191 | gene_name_of_exon_id(exon_id)
192 | Returns name of gene associated with given exon ID.
193 |
194 | gene_ids(contig=None, strand=None)
195 |
196 | Return all gene IDs in the annotation database, optionally restricted by
197 | chromosome name or strand.
198 |
199 | gene_ids_of_gene_name(gene_name)
200 |
201 | Returns all Ensembl gene IDs with the given name.
202 |
203 |
204 |
205 | ## Transcripts
206 |
207 |
208 | transcripts(contig=None, strand=None)
209 | Returns a list of Transcript objects for all transcript entries in the
210 | Ensembl database, optionally restricted to a particular contig or strand.
211 |
212 | transcript_by_id(transcript_id)
213 | Construct a Transcript object for given Ensembl transcript ID (e.g. "ENST00000369985")
214 |
215 | transcripts_by_name(transcript_name)
216 | Returns a list of Transcript objects for every transcript matching the given name.
217 |
218 | transcript_names(contig=None, strand=None)
219 | Returns all transcript names in the annotation database.
220 |
221 | transcript_ids(contig=None, strand=None)
222 | Returns all transcript IDs in the annotation database.
223 |
224 | transcript_ids_of_gene_id(gene_id)
225 | Return IDs of all transcripts associated with given gene ID.
226 |
227 | transcript_ids_of_gene_name(gene_name)
228 | Return IDs of all transcripts associated with given gene name.
229 |
230 | transcript_ids_of_transcript_name(transcript_name)
231 | Find all Ensembl transcript IDs with the given name.
232 |
233 | transcript_ids_of_exon_id(exon_id)
234 | Return IDs of all transcripts associatd with given exon ID.
235 |
236 |
237 | ## Exons
238 |
239 |
240 | exon_ids(contig=None, strand=None)
241 | Returns a list of exons IDs in the annotation database, optionally restricted
242 | by the given chromosome and strand.
243 |
244 | exon_by_id(exon_id)
245 | Construct an Exon object for given Ensembl exon ID (e.g. "ENSE00001209410")
246 |
247 | exon_ids_of_gene_id(gene_id)
248 | Returns a list of exon IDs associated with a given gene ID.
249 |
250 | exon_ids_of_gene_name(gene_name)
251 | Returns a list of exon IDs associated with a given gene name.
252 |
253 | exon_ids_of_transcript_id(transcript_id)
254 | Returns a list of exon IDs associated with a given transcript ID.
255 |
256 | exon_ids_of_transcript_name(transcript_name)
257 | Returns a list of exon IDs associated with a given transcript name.
258 |
259 |
--------------------------------------------------------------------------------
/RELEASING.md:
--------------------------------------------------------------------------------
1 | # Releasing Pyensembl
2 |
3 | This document explains what do once your [Pull Request](https://www.atlassian.com/git/tutorials/making-a-pull-request/) has been reviewed and all final changes applied. Now you're ready merge your branch into master and release it to the world:
4 |
5 | 1. Bump the [version](http://semver.org/) in `version.py`, as part of the PR you want to release.
6 | 2. Merge your branch into master.
7 | 3. Run `deploy.sh`
8 |
--------------------------------------------------------------------------------
/deploy.sh:
--------------------------------------------------------------------------------
1 | ./lint.sh && \
2 | ./test.sh && \
3 | python3 -m pip install --upgrade build && \
4 | python3 -m pip install --upgrade twine && \
5 | rm -rf dist && \
6 | python3 -m build && \
7 | git --version && \
8 | python3 -m twine upload dist/* && \
9 | git tag "$(python3 pyensembl/version.py)" && \
10 | git push --tags
11 |
--------------------------------------------------------------------------------
/develop.sh:
--------------------------------------------------------------------------------
1 | set -e
2 |
3 | pip install -e .
4 |
--------------------------------------------------------------------------------
/docs/Makefile:
--------------------------------------------------------------------------------
1 | # Makefile for Sphinx documentation
2 | #
3 |
4 | # You can set these variables from the command line.
5 | SPHINXOPTS =
6 | SPHINXBUILD = sphinx-build
7 | PAPER =
8 | BUILDDIR = _build
9 |
10 | # User-friendly check for sphinx-build
11 | ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
12 | $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
13 | endif
14 |
15 | # Internal variables.
16 | PAPEROPT_a4 = -D latex_paper_size=a4
17 | PAPEROPT_letter = -D latex_paper_size=letter
18 | ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
19 | # the i18n builder cannot share the environment and doctrees with the others
20 | I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
21 |
22 | .PHONY: help
23 | help:
24 | @echo "Please use \`make ' where is one of"
25 | @echo " html to make standalone HTML files"
26 | @echo " dirhtml to make HTML files named index.html in directories"
27 | @echo " singlehtml to make a single large HTML file"
28 | @echo " pickle to make pickle files"
29 | @echo " json to make JSON files"
30 | @echo " htmlhelp to make HTML files and a HTML help project"
31 | @echo " qthelp to make HTML files and a qthelp project"
32 | @echo " applehelp to make an Apple Help Book"
33 | @echo " devhelp to make HTML files and a Devhelp project"
34 | @echo " epub to make an epub"
35 | @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
36 | @echo " latexpdf to make LaTeX files and run them through pdflatex"
37 | @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
38 | @echo " text to make text files"
39 | @echo " man to make manual pages"
40 | @echo " texinfo to make Texinfo files"
41 | @echo " info to make Texinfo files and run them through makeinfo"
42 | @echo " gettext to make PO message catalogs"
43 | @echo " changes to make an overview of all changed/added/deprecated items"
44 | @echo " xml to make Docutils-native XML files"
45 | @echo " pseudoxml to make pseudoxml-XML files for display purposes"
46 | @echo " linkcheck to check all external links for integrity"
47 | @echo " doctest to run all doctests embedded in the documentation (if enabled)"
48 | @echo " coverage to run coverage check of the documentation (if enabled)"
49 |
50 | .PHONY: clean
51 | clean:
52 | rm -rf $(BUILDDIR)/*
53 |
54 | .PHONY: html
55 | html:
56 | $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
57 | @echo
58 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
59 |
60 | .PHONY: dirhtml
61 | dirhtml:
62 | $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
63 | @echo
64 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
65 |
66 | .PHONY: singlehtml
67 | singlehtml:
68 | $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
69 | @echo
70 | @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
71 |
72 | .PHONY: pickle
73 | pickle:
74 | $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
75 | @echo
76 | @echo "Build finished; now you can process the pickle files."
77 |
78 | .PHONY: json
79 | json:
80 | $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
81 | @echo
82 | @echo "Build finished; now you can process the JSON files."
83 |
84 | .PHONY: htmlhelp
85 | htmlhelp:
86 | $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
87 | @echo
88 | @echo "Build finished; now you can run HTML Help Workshop with the" \
89 | ".hhp project file in $(BUILDDIR)/htmlhelp."
90 |
91 | .PHONY: qthelp
92 | qthelp:
93 | $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
94 | @echo
95 | @echo "Build finished; now you can run "qcollectiongenerator" with the" \
96 | ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
97 | @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pyensembl.qhcp"
98 | @echo "To view the help file:"
99 | @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyensembl.qhc"
100 |
101 | .PHONY: applehelp
102 | applehelp:
103 | $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
104 | @echo
105 | @echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
106 | @echo "N.B. You won't be able to view it unless you put it in" \
107 | "~/Library/Documentation/Help or install it in your application" \
108 | "bundle."
109 |
110 | .PHONY: devhelp
111 | devhelp:
112 | $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
113 | @echo
114 | @echo "Build finished."
115 | @echo "To view the help file:"
116 | @echo "# mkdir -p $$HOME/.local/share/devhelp/pyensembl"
117 | @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyensembl"
118 | @echo "# devhelp"
119 |
120 | .PHONY: epub
121 | epub:
122 | $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
123 | @echo
124 | @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
125 |
126 | .PHONY: latex
127 | latex:
128 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
129 | @echo
130 | @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
131 | @echo "Run \`make' in that directory to run these through (pdf)latex" \
132 | "(use \`make latexpdf' here to do that automatically)."
133 |
134 | .PHONY: latexpdf
135 | latexpdf:
136 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
137 | @echo "Running LaTeX files through pdflatex..."
138 | $(MAKE) -C $(BUILDDIR)/latex all-pdf
139 | @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
140 |
141 | .PHONY: latexpdfja
142 | latexpdfja:
143 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
144 | @echo "Running LaTeX files through platex and dvipdfmx..."
145 | $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
146 | @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
147 |
148 | .PHONY: text
149 | text:
150 | $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
151 | @echo
152 | @echo "Build finished. The text files are in $(BUILDDIR)/text."
153 |
154 | .PHONY: man
155 | man:
156 | $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
157 | @echo
158 | @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
159 |
160 | .PHONY: texinfo
161 | texinfo:
162 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
163 | @echo
164 | @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
165 | @echo "Run \`make' in that directory to run these through makeinfo" \
166 | "(use \`make info' here to do that automatically)."
167 |
168 | .PHONY: info
169 | info:
170 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
171 | @echo "Running Texinfo files through makeinfo..."
172 | make -C $(BUILDDIR)/texinfo info
173 | @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
174 |
175 | .PHONY: gettext
176 | gettext:
177 | $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
178 | @echo
179 | @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
180 |
181 | .PHONY: changes
182 | changes:
183 | $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
184 | @echo
185 | @echo "The overview file is in $(BUILDDIR)/changes."
186 |
187 | .PHONY: linkcheck
188 | linkcheck:
189 | $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
190 | @echo
191 | @echo "Link check complete; look for any errors in the above output " \
192 | "or in $(BUILDDIR)/linkcheck/output.txt."
193 |
194 | .PHONY: doctest
195 | doctest:
196 | $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
197 | @echo "Testing of doctests in the sources finished, look at the " \
198 | "results in $(BUILDDIR)/doctest/output.txt."
199 |
200 | .PHONY: coverage
201 | coverage:
202 | $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
203 | @echo "Testing of coverage in the sources finished, look at the " \
204 | "results in $(BUILDDIR)/coverage/python.txt."
205 |
206 | .PHONY: xml
207 | xml:
208 | $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
209 | @echo
210 | @echo "Build finished. The XML files are in $(BUILDDIR)/xml."
211 |
212 | .PHONY: pseudoxml
213 | pseudoxml:
214 | $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
215 | @echo
216 | @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
217 |
--------------------------------------------------------------------------------
/docs/conf.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | #
3 | # pyensembl documentation build configuration file, created by
4 | # sphinx-quickstart on Sat Mar 26 22:47:25 2016.
5 | #
6 | # This file is execfile()d with the current directory set to its
7 | # containing dir.
8 | #
9 | # Note that not all possible configuration values are present in this
10 | # autogenerated file.
11 | #
12 | # All configuration values have a default; values that are commented out
13 | # serve to show the default.
14 |
15 | import sys
16 | import os
17 |
18 | # If extensions (or modules to document with autodoc) are in another directory,
19 | # add these directories to sys.path here. If the directory is relative to the
20 | # documentation root, use os.path.abspath to make it absolute, like shown here.
21 | sys.path.insert(0, os.path.abspath('..'))
22 |
23 | # -- General configuration ------------------------------------------------
24 |
25 | # If your documentation needs a minimal Sphinx version, state it here.
26 | #needs_sphinx = '1.0'
27 |
28 | # Add any Sphinx extension module names here, as strings. They can be
29 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
30 | # ones.
31 | extensions = [
32 | 'sphinx.ext.autodoc',
33 | ]
34 |
35 | # Add any paths that contain templates here, relative to this directory.
36 | templates_path = ['_templates']
37 |
38 | # The suffix(es) of source filenames.
39 | # You can specify multiple suffix as a list of string:
40 | # source_suffix = ['.rst', '.md']
41 | source_suffix = '.rst'
42 |
43 | # The encoding of source files.
44 | #source_encoding = 'utf-8-sig'
45 |
46 | # The master toctree document.
47 | master_doc = 'index'
48 |
49 | # General information about the project.
50 | project = u'pyensembl'
51 | copyright = u'2016, Hammer Lab'
52 | author = u'Hammer Lab'
53 |
54 | # The version info for the project you're documenting, acts as replacement for
55 | # |version| and |release|, also used in various other places throughout the
56 | # built documents.
57 | #
58 | # The short X.Y version.
59 | version = u'0.8.10'
60 | # The full version, including alpha/beta/rc tags.
61 | release = u'0.8.10'
62 |
63 | # The language for content autogenerated by Sphinx. Refer to documentation
64 | # for a list of supported languages.
65 | #
66 | # This is also used if you do content translation via gettext catalogs.
67 | # Usually you set "language" from the command line for these cases.
68 | language = None
69 |
70 | # There are two options for replacing |today|: either, you set today to some
71 | # non-false value, then it is used:
72 | #today = ''
73 | # Else, today_fmt is used as the format for a strftime call.
74 | #today_fmt = '%B %d, %Y'
75 |
76 | # List of patterns, relative to source directory, that match files and
77 | # directories to ignore when looking for source files.
78 | exclude_patterns = ['_build']
79 |
80 | # The reST default role (used for this markup: `text`) to use for all
81 | # documents.
82 | #default_role = None
83 |
84 | # If true, '()' will be appended to :func: etc. cross-reference text.
85 | #add_function_parentheses = True
86 |
87 | # If true, the current module name will be prepended to all description
88 | # unit titles (such as .. function::).
89 | #add_module_names = True
90 |
91 | # If true, sectionauthor and moduleauthor directives will be shown in the
92 | # output. They are ignored by default.
93 | #show_authors = False
94 |
95 | # The name of the Pygments (syntax highlighting) style to use.
96 | pygments_style = 'sphinx'
97 |
98 | # A list of ignored prefixes for module index sorting.
99 | #modindex_common_prefix = []
100 |
101 | # If true, keep warnings as "system message" paragraphs in the built documents.
102 | #keep_warnings = False
103 |
104 | # If true, `todo` and `todoList` produce output, else they produce nothing.
105 | todo_include_todos = False
106 |
107 |
108 | # -- Options for HTML output ----------------------------------------------
109 |
110 | # The theme to use for HTML and HTML Help pages. See the documentation for
111 | # a list of builtin themes.
112 | html_theme = 'alabaster'
113 |
114 | # Theme options are theme-specific and customize the look and feel of a theme
115 | # further. For a list of options available for each theme, see the
116 | # documentation.
117 | #html_theme_options = {}
118 |
119 | # Add any paths that contain custom themes here, relative to this directory.
120 | #html_theme_path = []
121 |
122 | # The name for this set of Sphinx documents. If None, it defaults to
123 | # " v documentation".
124 | #html_title = None
125 |
126 | # A shorter title for the navigation bar. Default is the same as html_title.
127 | #html_short_title = None
128 |
129 | # The name of an image file (relative to this directory) to place at the top
130 | # of the sidebar.
131 | #html_logo = None
132 |
133 | # The name of an image file (relative to this directory) to use as a favicon of
134 | # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
135 | # pixels large.
136 | #html_favicon = None
137 |
138 | # Add any paths that contain custom static files (such as style sheets) here,
139 | # relative to this directory. They are copied after the builtin static files,
140 | # so a file named "default.css" will overwrite the builtin "default.css".
141 | html_static_path = ['_static']
142 |
143 | # Add any extra paths that contain custom files (such as robots.txt or
144 | # .htaccess) here, relative to this directory. These files are copied
145 | # directly to the root of the documentation.
146 | #html_extra_path = []
147 |
148 | # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
149 | # using the given strftime format.
150 | #html_last_updated_fmt = '%b %d, %Y'
151 |
152 | # If true, SmartyPants will be used to convert quotes and dashes to
153 | # typographically correct entities.
154 | #html_use_smartypants = True
155 |
156 | # Custom sidebar templates, maps document names to template names.
157 | #html_sidebars = {}
158 |
159 | # Additional templates that should be rendered to pages, maps page names to
160 | # template names.
161 | #html_additional_pages = {}
162 |
163 | # If false, no module index is generated.
164 | #html_domain_indices = True
165 |
166 | # If false, no index is generated.
167 | #html_use_index = True
168 |
169 | # If true, the index is split into individual pages for each letter.
170 | #html_split_index = False
171 |
172 | # If true, links to the reST sources are added to the pages.
173 | #html_show_sourcelink = True
174 |
175 | # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
176 | #html_show_sphinx = True
177 |
178 | # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
179 | #html_show_copyright = True
180 |
181 | # If true, an OpenSearch description file will be output, and all pages will
182 | # contain a ` where ^ is one of
21 | echo. html to make standalone HTML files
22 | echo. dirhtml to make HTML files named index.html in directories
23 | echo. singlehtml to make a single large HTML file
24 | echo. pickle to make pickle files
25 | echo. json to make JSON files
26 | echo. htmlhelp to make HTML files and a HTML help project
27 | echo. qthelp to make HTML files and a qthelp project
28 | echo. devhelp to make HTML files and a Devhelp project
29 | echo. epub to make an epub
30 | echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
31 | echo. text to make text files
32 | echo. man to make manual pages
33 | echo. texinfo to make Texinfo files
34 | echo. gettext to make PO message catalogs
35 | echo. changes to make an overview over all changed/added/deprecated items
36 | echo. xml to make Docutils-native XML files
37 | echo. pseudoxml to make pseudoxml-XML files for display purposes
38 | echo. linkcheck to check all external links for integrity
39 | echo. doctest to run all doctests embedded in the documentation if enabled
40 | echo. coverage to run coverage check of the documentation if enabled
41 | goto end
42 | )
43 |
44 | if "%1" == "clean" (
45 | for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
46 | del /q /s %BUILDDIR%\*
47 | goto end
48 | )
49 |
50 |
51 | REM Check if sphinx-build is available and fallback to Python version if any
52 | %SPHINXBUILD% 1>NUL 2>NUL
53 | if errorlevel 9009 goto sphinx_python
54 | goto sphinx_ok
55 |
56 | :sphinx_python
57 |
58 | set SPHINXBUILD=python -m sphinx.__init__
59 | %SPHINXBUILD% 2> nul
60 | if errorlevel 9009 (
61 | echo.
62 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
63 | echo.installed, then set the SPHINXBUILD environment variable to point
64 | echo.to the full path of the 'sphinx-build' executable. Alternatively you
65 | echo.may add the Sphinx directory to PATH.
66 | echo.
67 | echo.If you don't have Sphinx installed, grab it from
68 | echo.http://sphinx-doc.org/
69 | exit /b 1
70 | )
71 |
72 | :sphinx_ok
73 |
74 |
75 | if "%1" == "html" (
76 | %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
77 | if errorlevel 1 exit /b 1
78 | echo.
79 | echo.Build finished. The HTML pages are in %BUILDDIR%/html.
80 | goto end
81 | )
82 |
83 | if "%1" == "dirhtml" (
84 | %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
85 | if errorlevel 1 exit /b 1
86 | echo.
87 | echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
88 | goto end
89 | )
90 |
91 | if "%1" == "singlehtml" (
92 | %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
93 | if errorlevel 1 exit /b 1
94 | echo.
95 | echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
96 | goto end
97 | )
98 |
99 | if "%1" == "pickle" (
100 | %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
101 | if errorlevel 1 exit /b 1
102 | echo.
103 | echo.Build finished; now you can process the pickle files.
104 | goto end
105 | )
106 |
107 | if "%1" == "json" (
108 | %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
109 | if errorlevel 1 exit /b 1
110 | echo.
111 | echo.Build finished; now you can process the JSON files.
112 | goto end
113 | )
114 |
115 | if "%1" == "htmlhelp" (
116 | %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
117 | if errorlevel 1 exit /b 1
118 | echo.
119 | echo.Build finished; now you can run HTML Help Workshop with the ^
120 | .hhp project file in %BUILDDIR%/htmlhelp.
121 | goto end
122 | )
123 |
124 | if "%1" == "qthelp" (
125 | %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
126 | if errorlevel 1 exit /b 1
127 | echo.
128 | echo.Build finished; now you can run "qcollectiongenerator" with the ^
129 | .qhcp project file in %BUILDDIR%/qthelp, like this:
130 | echo.^> qcollectiongenerator %BUILDDIR%\qthelp\pyensembl.qhcp
131 | echo.To view the help file:
132 | echo.^> assistant -collectionFile %BUILDDIR%\qthelp\pyensembl.ghc
133 | goto end
134 | )
135 |
136 | if "%1" == "devhelp" (
137 | %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
138 | if errorlevel 1 exit /b 1
139 | echo.
140 | echo.Build finished.
141 | goto end
142 | )
143 |
144 | if "%1" == "epub" (
145 | %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
146 | if errorlevel 1 exit /b 1
147 | echo.
148 | echo.Build finished. The epub file is in %BUILDDIR%/epub.
149 | goto end
150 | )
151 |
152 | if "%1" == "latex" (
153 | %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
154 | if errorlevel 1 exit /b 1
155 | echo.
156 | echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
157 | goto end
158 | )
159 |
160 | if "%1" == "latexpdf" (
161 | %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
162 | cd %BUILDDIR%/latex
163 | make all-pdf
164 | cd %~dp0
165 | echo.
166 | echo.Build finished; the PDF files are in %BUILDDIR%/latex.
167 | goto end
168 | )
169 |
170 | if "%1" == "latexpdfja" (
171 | %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
172 | cd %BUILDDIR%/latex
173 | make all-pdf-ja
174 | cd %~dp0
175 | echo.
176 | echo.Build finished; the PDF files are in %BUILDDIR%/latex.
177 | goto end
178 | )
179 |
180 | if "%1" == "text" (
181 | %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
182 | if errorlevel 1 exit /b 1
183 | echo.
184 | echo.Build finished. The text files are in %BUILDDIR%/text.
185 | goto end
186 | )
187 |
188 | if "%1" == "man" (
189 | %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
190 | if errorlevel 1 exit /b 1
191 | echo.
192 | echo.Build finished. The manual pages are in %BUILDDIR%/man.
193 | goto end
194 | )
195 |
196 | if "%1" == "texinfo" (
197 | %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
198 | if errorlevel 1 exit /b 1
199 | echo.
200 | echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
201 | goto end
202 | )
203 |
204 | if "%1" == "gettext" (
205 | %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
206 | if errorlevel 1 exit /b 1
207 | echo.
208 | echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
209 | goto end
210 | )
211 |
212 | if "%1" == "changes" (
213 | %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
214 | if errorlevel 1 exit /b 1
215 | echo.
216 | echo.The overview file is in %BUILDDIR%/changes.
217 | goto end
218 | )
219 |
220 | if "%1" == "linkcheck" (
221 | %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
222 | if errorlevel 1 exit /b 1
223 | echo.
224 | echo.Link check complete; look for any errors in the above output ^
225 | or in %BUILDDIR%/linkcheck/output.txt.
226 | goto end
227 | )
228 |
229 | if "%1" == "doctest" (
230 | %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
231 | if errorlevel 1 exit /b 1
232 | echo.
233 | echo.Testing of doctests in the sources finished, look at the ^
234 | results in %BUILDDIR%/doctest/output.txt.
235 | goto end
236 | )
237 |
238 | if "%1" == "coverage" (
239 | %SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage
240 | if errorlevel 1 exit /b 1
241 | echo.
242 | echo.Testing of coverage in the sources finished, look at the ^
243 | results in %BUILDDIR%/coverage/python.txt.
244 | goto end
245 | )
246 |
247 | if "%1" == "xml" (
248 | %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
249 | if errorlevel 1 exit /b 1
250 | echo.
251 | echo.Build finished. The XML files are in %BUILDDIR%/xml.
252 | goto end
253 | )
254 |
255 | if "%1" == "pseudoxml" (
256 | %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
257 | if errorlevel 1 exit /b 1
258 | echo.
259 | echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
260 | goto end
261 | )
262 |
263 | :end
264 |
--------------------------------------------------------------------------------
/docs/modules.rst:
--------------------------------------------------------------------------------
1 | pyensembl
2 | =========
3 |
4 | .. toctree::
5 | :maxdepth: 4
6 |
7 | pyensembl
8 |
--------------------------------------------------------------------------------
/docs/pyensembl.rst:
--------------------------------------------------------------------------------
1 | pyensembl package
2 | =================
3 |
4 | Submodules
5 | ----------
6 |
7 | pyensembl.biotypes module
8 | -------------------------
9 |
10 | .. automodule:: pyensembl.biotypes
11 | :members:
12 | :undoc-members:
13 | :show-inheritance:
14 |
15 | pyensembl.common module
16 | -----------------------
17 |
18 | .. automodule:: pyensembl.common
19 | :members:
20 | :undoc-members:
21 | :show-inheritance:
22 |
23 | pyensembl.database module
24 | -------------------------
25 |
26 | .. automodule:: pyensembl.database
27 | :members:
28 | :undoc-members:
29 | :show-inheritance:
30 |
31 | pyensembl.download_cache module
32 | -------------------------------
33 |
34 | .. automodule:: pyensembl.download_cache
35 | :members:
36 | :undoc-members:
37 | :show-inheritance:
38 |
39 | pyensembl.ensembl_release module
40 | --------------------------------
41 |
42 | .. automodule:: pyensembl.ensembl_release
43 | :members:
44 | :undoc-members:
45 | :show-inheritance:
46 |
47 | pyensembl.ensembl_versions module
48 | -----------------------------------------
49 |
50 | .. automodule:: pyensembl.ensembl_versions
51 | :members:
52 | :undoc-members:
53 | :show-inheritance:
54 |
55 | pyensembl.ensembl_url_templates module
56 | --------------------------------------
57 |
58 | .. automodule:: pyensembl.ensembl_url_templates
59 | :members:
60 | :undoc-members:
61 | :show-inheritance:
62 |
63 | pyensembl.exon module
64 | ---------------------
65 |
66 | .. automodule:: pyensembl.exon
67 | :members:
68 | :undoc-members:
69 | :show-inheritance:
70 |
71 | pyensembl.gene module
72 | ---------------------
73 |
74 | .. automodule:: pyensembl.gene
75 | :members:
76 | :undoc-members:
77 | :show-inheritance:
78 |
79 | pyensembl.genome module
80 | -----------------------
81 |
82 | .. automodule:: pyensembl.genome
83 | :members:
84 | :undoc-members:
85 | :show-inheritance:
86 |
87 | pyensembl.gtf module
88 | --------------------
89 |
90 | .. automodule:: pyensembl.gtf
91 | :members:
92 | :undoc-members:
93 | :show-inheritance:
94 |
95 | pyensembl.locus module
96 | ----------------------
97 |
98 | .. automodule:: pyensembl.locus
99 | :members:
100 | :undoc-members:
101 | :show-inheritance:
102 |
103 | pyensembl.memory_cache module
104 | -----------------------------
105 |
106 | .. automodule:: pyensembl.memory_cache
107 | :members:
108 | :undoc-members:
109 | :show-inheritance:
110 |
111 | pyensembl.search module
112 | -----------------------
113 |
114 | .. automodule:: pyensembl.search
115 | :members:
116 | :undoc-members:
117 | :show-inheritance:
118 |
119 | pyensembl.sequence_data module
120 | ------------------------------
121 |
122 | .. automodule:: pyensembl.sequence_data
123 | :members:
124 | :undoc-members:
125 | :show-inheritance:
126 |
127 | pyensembl.shell module
128 | ----------------------
129 |
130 | .. automodule:: pyensembl.shell
131 | :members:
132 | :undoc-members:
133 | :show-inheritance:
134 |
135 | pyensembl.species module
136 | ------------------------
137 |
138 | .. automodule:: pyensembl.species
139 | :members:
140 | :undoc-members:
141 | :show-inheritance:
142 |
143 | pyensembl.transcript module
144 | ---------------------------
145 |
146 | .. automodule:: pyensembl.transcript
147 | :members:
148 | :undoc-members:
149 | :show-inheritance:
150 |
151 |
152 | Module contents
153 | ---------------
154 |
155 | .. automodule:: pyensembl
156 | :members:
157 | :undoc-members:
158 | :show-inheritance:
159 |
--------------------------------------------------------------------------------
/lint-and-test.sh:
--------------------------------------------------------------------------------
1 | ./lint.sh && ./test.sh
2 |
--------------------------------------------------------------------------------
/lint.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 | set -o errexit
3 |
4 |
5 | # disabling several categories of errors due to false positives in pylint,
6 | # see these issues:
7 | # - https://bitbucket.org/logilab/pylint/issues/701/false-positives-with-not-an-iterable-and
8 | # - https://bitbucket.org/logilab/pylint/issues/58
9 |
10 | find pyensembl -name '*.py' \
11 | | xargs pylint \
12 | --errors-only \
13 | --disable=unsubscriptable-object,not-an-iterable,no-member
14 |
15 | echo 'Passes pylint check'
16 |
--------------------------------------------------------------------------------
/pyensembl/__init__.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | from .database import Database
14 | from .download_cache import DownloadCache
15 | from .ensembl_release import EnsemblRelease, cached_release
16 | from .ensembl_versions import MAX_ENSEMBL_RELEASE
17 | from .exon import Exon
18 | from .genome import Genome
19 | from .gene import Gene
20 | from .locus import Locus
21 | from .reference_name import (
22 | ensembl_grch36,
23 | ensembl_grch37,
24 | ensembl_grch38,
25 | normalize_reference_name,
26 | find_species_by_reference,
27 | which_reference,
28 | genome_for_reference_name,
29 | )
30 |
31 | from .search import find_nearest_locus
32 | from .sequence_data import SequenceData
33 | from .species import find_species_by_name, check_species_object, normalize_species_name
34 | from .transcript import Transcript
35 | from .version import __version__
36 |
37 | __all__ = [
38 | "__version__",
39 | "DownloadCache",
40 | "Database",
41 | "EnsemblRelease",
42 | "cached_release",
43 | "MAX_ENSEMBL_RELEASE",
44 | "Gene",
45 | "Transcript",
46 | "Exon",
47 | "SequenceData",
48 | "find_nearest_locus",
49 | "find_species_by_name",
50 | "find_species_by_reference",
51 | "genome_for_reference_name",
52 | "which_reference",
53 | "check_species_object",
54 | "normalize_reference_name",
55 | "normalize_species_name",
56 | "Genome",
57 | "Locus",
58 | "Exon",
59 | "ensembl_grch36",
60 | "ensembl_grch37",
61 | "ensembl_grch38",
62 | ]
63 |
--------------------------------------------------------------------------------
/pyensembl/common.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | import pickle
14 |
15 | from functools import wraps
16 |
17 |
18 | def dump_pickle(obj, filepath):
19 | with open(filepath, "wb") as f:
20 | # use lower protocol for compatibility between Python 2 and Python 3
21 | pickle.dump(obj, file=f, protocol=2)
22 |
23 |
24 | def load_pickle(filepath):
25 | with open(filepath, "rb") as f:
26 | obj = pickle.load(f)
27 | return obj
28 |
29 |
30 | def _memoize_cache_key(args, kwargs):
31 | """Turn args tuple and kwargs dictionary into a hashable key.
32 |
33 | Expects that all arguments to a memoized function are either hashable
34 | or can be uniquely identified from type(arg) and repr(arg).
35 | """
36 | cache_key_list = []
37 |
38 | # hack to get around the unhashability of lists,
39 | # add a special case to convert them to tuples
40 | for arg in args:
41 | if type(arg) is list:
42 | cache_key_list.append(tuple(arg))
43 | else:
44 | cache_key_list.append(arg)
45 | for k, v in sorted(kwargs.items()):
46 | if type(v) is list:
47 | cache_key_list.append((k, tuple(v)))
48 | else:
49 | cache_key_list.append((k, v))
50 | return tuple(cache_key_list)
51 |
52 |
53 | def memoize(fn):
54 | """Simple reset-able memoization decorator for functions and methods,
55 | assumes that all arguments to the function can be hashed and
56 | compared.
57 | """
58 | cache = {}
59 |
60 | @wraps(fn)
61 | def wrapped_fn(*args, **kwargs):
62 | cache_key = _memoize_cache_key(args, kwargs)
63 | try:
64 | return cache[cache_key]
65 | except KeyError:
66 | value = fn(*args, **kwargs)
67 | cache[cache_key] = value
68 | return value
69 |
70 | def clear_cache():
71 | cache.clear()
72 |
73 | # Needed to ensure that EnsemblRelease.clear_cache
74 | # is able to clear memoized values from each of its methods
75 | wrapped_fn.clear_cache = clear_cache
76 | # expose the cache so we can check if an item has already been computed
77 | wrapped_fn.cache = cache
78 | # if we want to check whether an item is in the cache, first need
79 | # to construct the same cache key as used by wrapped_fn
80 | wrapped_fn.make_cache_key = _memoize_cache_key
81 | return wrapped_fn
82 |
--------------------------------------------------------------------------------
/pyensembl/ensembl_release.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | """
14 | Contains the EnsemblRelease class, which extends the Genome class
15 | to be specific to a particular release of Ensembl.
16 | """
17 | from weakref import WeakValueDictionary
18 |
19 | from .genome import Genome
20 | from .ensembl_versions import check_release_number, MAX_ENSEMBL_RELEASE
21 | from .species import check_species_object, human
22 |
23 | from .ensembl_url_templates import ENSEMBL_FTP_SERVER, make_gtf_url, make_fasta_url
24 |
25 |
26 | class EnsemblRelease(Genome):
27 | """
28 | Bundles together the genomic annotation and sequence data associated with
29 | a particular release of the Ensembl database.
30 | """
31 |
32 | @classmethod
33 | def normalize_init_values(cls, release, species, server):
34 | """
35 | Normalizes the arguments which uniquely specify an EnsemblRelease
36 | genome.
37 | """
38 | release = check_release_number(release)
39 | species = check_species_object(species)
40 | return (release, species, server)
41 |
42 | # Using a WeakValueDictionary instead of an ordinary dict to prevent a
43 | # memory leak in cases where we test many different releases in sequence.
44 | # When all the references to a particular EnsemblRelease die then that
45 | # genome should also be removed from this cache.
46 | _genome_cache = WeakValueDictionary()
47 |
48 | @classmethod
49 | def cached(
50 | cls, release=MAX_ENSEMBL_RELEASE, species=human, server=ENSEMBL_FTP_SERVER
51 | ):
52 | """
53 | Construct EnsemblRelease if it's never been made before, otherwise
54 | return an old instance.
55 | """
56 | init_args_tuple = cls.normalize_init_values(release, species, server)
57 | if init_args_tuple in cls._genome_cache:
58 | genome = cls._genome_cache[init_args_tuple]
59 | else:
60 | genome = cls._genome_cache[init_args_tuple] = cls(*init_args_tuple)
61 | return genome
62 |
63 | def __init__(
64 | self, release=MAX_ENSEMBL_RELEASE, species=human, server=ENSEMBL_FTP_SERVER
65 | ):
66 | self.release, self.species, self.server = self.normalize_init_values(
67 | release=release, species=species, server=server
68 | )
69 |
70 | self.gtf_url = make_gtf_url(
71 | ensembl_release=self.release, species=self.species, server=self.server
72 | )
73 |
74 | self.transcript_fasta_urls = [
75 | make_fasta_url(
76 | ensembl_release=self.release,
77 | species=self.species.latin_name,
78 | sequence_type="cdna",
79 | server=server,
80 | is_plant = self.species.is_plant,
81 | ),
82 | make_fasta_url(
83 | ensembl_release=self.release,
84 | species=self.species.latin_name,
85 | sequence_type="ncrna",
86 | server=server,
87 | is_plant = self.species.is_plant,
88 | ),
89 | ]
90 |
91 | self.protein_fasta_urls = [
92 | make_fasta_url(
93 | ensembl_release=self.release,
94 | species=self.species.latin_name,
95 | sequence_type="pep",
96 | server=self.server,
97 | is_plant = self.species.is_plant,
98 | )
99 | ]
100 |
101 | self.reference_name = self.species.which_reference(self.release)
102 |
103 | Genome.__init__(
104 | self,
105 | reference_name=self.reference_name,
106 | annotation_name="ensembl",
107 | annotation_version=self.release,
108 | gtf_path_or_url=self.gtf_url,
109 | transcript_fasta_paths_or_urls=self.transcript_fasta_urls,
110 | protein_fasta_paths_or_urls=self.protein_fasta_urls,
111 | )
112 |
113 | def install_string(self):
114 | return "pyensembl install --release %d --species %s" % (
115 | self.release,
116 | self.species.latin_name,
117 | )
118 |
119 | def __str__(self):
120 | return "EnsemblRelease(release=%d, species='%s')" % (
121 | self.release,
122 | self.species.latin_name,
123 | )
124 |
125 | def __eq__(self, other):
126 | return (
127 | other.__class__ is EnsemblRelease
128 | and self.release == other.release
129 | and self.species == other.species
130 | )
131 |
132 | def __hash__(self):
133 | return hash((self.release, self.species))
134 |
135 | def to_dict(self):
136 | return {"release": self.release, "species": self.species, "server": self.server}
137 |
138 | @classmethod
139 | def from_dict(cls, state_dict):
140 | """
141 | Deserialize EnsemblRelease without creating duplicate instances.
142 | """
143 | return cls.cached(**state_dict)
144 |
145 |
146 | def cached_release(release, species="human"):
147 | """
148 | Create an EnsemblRelease instance only if it's hasn't already been made,
149 | otherwise returns the old instance.
150 | Keeping this function for backwards compatibility but this functionality
151 | has been moving into the cached method of EnsemblRelease.
152 | """
153 | return EnsemblRelease.cached(release=release, species=species)
154 |
--------------------------------------------------------------------------------
/pyensembl/ensembl_url_templates.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | """
14 | Templates for URLs and paths to specific relase, species, and file type
15 | on the Ensembl ftp server.
16 |
17 | For example, the human chromosomal DNA sequences for release 78 are in:
18 |
19 | https://ftp.ensembl.org/pub/release-78/fasta/homo_sapiens/dna/
20 |
21 | """
22 |
23 | from .species import Species, find_species_by_name
24 | from .ensembl_versions import check_release_number
25 |
26 | ENSEMBL_FTP_SERVER = "https://ftp.ensembl.org"
27 | ENSEMBL_PLANTS_FTP_SERVER = "https://ftp.ensemblgenomes.ebi.ac.uk/"
28 |
29 | # Example directories
30 | # FASTA files: /pub/release-78/fasta/homo_sapiens/
31 | # GTF annotation files: /pub/release-78/gtf/homo_sapiens/
32 | FASTA_SUBDIR_TEMPLATE = "/pub/release-%(release)d/fasta/%(species)s/%(type)s/"
33 | PLANTS_FASTA_SUBDIR_TEMPLATE = "/pub/release-%(release)d/plants/fasta/%(species)s/%(type)s/"
34 | GTF_SUBDIR_TEMPLATE = "/pub/release-%(release)d/gtf/%(species)s/"
35 | PLANTS_GTF_SUBDIR_TEMPLATE = "/pub/release-%(release)d/plants/gtf/%(species)s/"
36 |
37 | #List plants
38 | #Lest do a vector with all the plants species that we added to make the custom url
39 | lPlants = ("arabidopsis_thaliana","arabidopsis")
40 |
41 | def normalize_release_properties(ensembl_release, species):
42 | """
43 | Make sure a given release is valid, normalize it to be an integer,
44 | normalize the species name, and get its associated reference.
45 | """
46 | ensembl_release = check_release_number(ensembl_release)
47 | if not isinstance(species, Species):
48 | species = find_species_by_name(species)
49 | reference_name = species.which_reference(ensembl_release)
50 | return ensembl_release, species.latin_name, reference_name
51 |
52 |
53 | # GTF annotation file example: Homo_sapiens.GTCh38.gtf.gz
54 | GTF_FILENAME_TEMPLATE = "%(Species)s.%(reference)s.%(release)d.gtf.gz"
55 |
56 |
57 | def make_gtf_filename(ensembl_release, species):
58 | """
59 | Return GTF filename expect on Ensembl FTP server for a specific
60 | species/release combination
61 | """
62 | ensembl_release, species, reference_name = normalize_release_properties(
63 | ensembl_release, species
64 | )
65 | return GTF_FILENAME_TEMPLATE % {
66 | "Species": species.capitalize(),
67 | "reference": reference_name,
68 | "release": ensembl_release,
69 | }
70 |
71 |
72 | def make_gtf_url(ensembl_release, species, server=ENSEMBL_FTP_SERVER, gtf_subdir=GTF_SUBDIR_TEMPLATE):
73 | """
74 | Returns a URL and a filename, which can be joined together.
75 | """
76 | if species.is_plant:
77 | server = ENSEMBL_PLANTS_FTP_SERVER
78 | gtf_subdir = PLANTS_GTF_SUBDIR_TEMPLATE
79 | #else:
80 | #print(f"[+] {species.latin_name} it is not a plant", flush=True)
81 |
82 | ensembl_release, species, _ = normalize_release_properties(ensembl_release, species)
83 | subdir = gtf_subdir % {"release": ensembl_release, "species": species}
84 | filename = make_gtf_filename(ensembl_release=ensembl_release, species=species)
85 | return server + subdir + filename
86 |
87 |
88 | # cDNA & protein FASTA file for releases before (and including) Ensembl 75
89 | # example: Homo_sapiens.NCBI36.54.cdna.all.fa.gz
90 | OLD_FASTA_FILENAME_TEMPLATE = (
91 | "%(Species)s.%(reference)s.%(release)d.%(sequence_type)s.all.fa.gz"
92 | )
93 |
94 | # ncRNA FASTA file for releases before (and including) Ensembl 75
95 | # example: Homo_sapiens.NCBI36.54.ncrna.fa.gz
96 |
97 | OLD_FASTA_FILENAME_TEMPLATE_NCRNA = "%(Species)s.%(reference)s.%(release)d.ncrna.fa.gz"
98 |
99 | # cDNA & protein FASTA file for releases after Ensembl 75
100 | # example: Homo_sapiens.GRCh37.cdna.all.fa.gz
101 | NEW_FASTA_FILENAME_TEMPLATE = "%(Species)s.%(reference)s.%(sequence_type)s.all.fa.gz"
102 |
103 | # ncRNA FASTA file for releases after Ensembl 75
104 | # example: Homo_sapiens.GRCh37.ncrna.fa.gz
105 | NEW_FASTA_FILENAME_TEMPLATE_NCRNA = "%(Species)s.%(reference)s.ncrna.fa.gz"
106 |
107 |
108 | def make_fasta_filename(ensembl_release, species, sequence_type, is_plant):
109 | ensembl_release, species, reference_name = normalize_release_properties(
110 | ensembl_release, species
111 | )
112 | if ensembl_release <= 75 and not is_plant:
113 | if sequence_type == "ncrna":
114 | return OLD_FASTA_FILENAME_TEMPLATE_NCRNA % {
115 | "Species": species.capitalize(),
116 | "reference": reference_name,
117 | "release": ensembl_release,
118 | }
119 | else:
120 | return OLD_FASTA_FILENAME_TEMPLATE % {
121 | "Species": species.capitalize(),
122 | "reference": reference_name,
123 | "release": ensembl_release,
124 | "sequence_type": sequence_type,
125 | }
126 | else:
127 | if sequence_type == "ncrna":
128 | return NEW_FASTA_FILENAME_TEMPLATE_NCRNA % {
129 | "Species": species.capitalize(),
130 | "reference": reference_name,
131 | }
132 | else:
133 | return NEW_FASTA_FILENAME_TEMPLATE % {
134 | "Species": species.capitalize(),
135 | "reference": reference_name,
136 | "sequence_type": sequence_type,
137 | }
138 |
139 |
140 | def make_fasta_url(ensembl_release, species, sequence_type, is_plant, server=ENSEMBL_FTP_SERVER, fasta_subdir=FASTA_SUBDIR_TEMPLATE):
141 | """Construct URL to FASTA file with cDNA transcript or protein sequences
142 |
143 | Parameter examples:
144 | ensembl_release = 75
145 | species = "Homo_sapiens"
146 | sequence_type = "cdna" (other option: "pep")
147 | """
148 | ensembl_release, species, reference_name = normalize_release_properties(
149 | ensembl_release, species
150 | )
151 |
152 | if is_plant:
153 | server = ENSEMBL_PLANTS_FTP_SERVER
154 | fasta_subdir = PLANTS_FASTA_SUBDIR_TEMPLATE
155 |
156 | subdir = fasta_subdir % {
157 | "release": ensembl_release,
158 | "species": species,
159 | "type": sequence_type,
160 | }
161 | filename = make_fasta_filename(
162 | ensembl_release=ensembl_release, species=species, sequence_type=sequence_type, is_plant = is_plant
163 | )
164 | return server + subdir + filename
165 |
--------------------------------------------------------------------------------
/pyensembl/ensembl_versions.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | MIN_ENSEMBL_RELEASE = 40
14 | MAX_ENSEMBL_RELEASE = 111
15 | MAX_PLANTS_ENSEMBL_RELEASE = 58
16 |
17 | def check_release_number(release):
18 | """
19 | Check to make sure a release is in the valid range of
20 | Ensembl releases.
21 | """
22 | try:
23 | release = int(release)
24 | except:
25 | raise ValueError("Invalid Ensembl release: %s" % release)
26 |
27 | if release < MIN_ENSEMBL_RELEASE:
28 | raise ValueError(
29 | "Invalid Ensembl releases %d, must be greater than %d"
30 | % (release, MIN_ENSEMBL_RELEASE)
31 | )
32 | return release
33 |
--------------------------------------------------------------------------------
/pyensembl/exon.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 |
14 | from .locus import Locus
15 |
16 |
17 | class Exon(Locus):
18 | def __init__(self, exon_id, contig, start, end, strand, gene_name, gene_id):
19 | Locus.__init__(self, contig, start, end, strand)
20 | self.exon_id = exon_id
21 | self.gene_name = gene_name
22 | self.gene_id = gene_id
23 |
24 | @property
25 | def id(self):
26 | """
27 | Alias for exon_id necessary for backward compatibility.
28 | """
29 | return self.exon_id
30 |
31 | def __str__(self):
32 | return (
33 | "Exon(exon_id='%s',"
34 | " gene_id='%s',"
35 | " gene_name='%s',"
36 | " contig='%s',"
37 | " start=%d,"
38 | " end=%s,"
39 | " strand='%s')"
40 | ) % (
41 | self.exon_id,
42 | self.gene_id,
43 | self.gene_name,
44 | self.contig,
45 | self.start,
46 | self.end,
47 | self.strand,
48 | )
49 |
50 | def __eq__(self, other):
51 | if not isinstance(other, Exon):
52 | raise TypeError(
53 | "Cannot compare %s and %s"
54 | % (self.__class__.__name__, other.__class.__name__)
55 | )
56 | return (
57 | self.contig == other.contig
58 | and self.start == other.start
59 | and self.end == other.end
60 | and self.strand == other.strand
61 | and self.id == other.id
62 | )
63 |
64 | def __hash__(self):
65 | return hash(self.id)
66 |
67 | def to_dict(self):
68 | state_dict = Locus.to_dict(self)
69 | state_dict["exon_id"] = self.id
70 | state_dict["gene_name"] = self.gene_name
71 | state_dict["gene_id"] = self.gene_id
72 | return state_dict
73 |
--------------------------------------------------------------------------------
/pyensembl/fasta.py:
--------------------------------------------------------------------------------
1 | # Copyright (c) 2015-2016. Mount Sinai School of Medicine
2 | #
3 | # Licensed under the Apache License, Version 2.0 (the "License");
4 | # you may not use this file except in compliance with the License.
5 | # You may obtain a copy of the License at
6 | #
7 | # http://www.apache.org/licenses/LICENSE-2.0
8 | #
9 | # Unless required by applicable law or agreed to in writing, software
10 | # distributed under the License is distributed on an "AS IS" BASIS,
11 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12 | # See the License for the specific language governing permissions and
13 | # limitations under the License.
14 |
15 | """
16 | The worse sin in bioinformatics is to write your own FASTA parser.
17 | Unfortunately, small errors creep in to different FASTA files on the
18 | Ensembl FTP server that no proper FASTA parser lets you skip over.
19 | """
20 |
21 |
22 | from gzip import GzipFile
23 | import logging
24 |
25 |
26 | logger = logging.getLogger(__name__)
27 |
28 |
29 | def _parse_header_id(line):
30 | """
31 | Pull the transcript or protein identifier from the header line
32 | which starts with '>'
33 | """
34 | if type(line) is not bytes:
35 | raise TypeError(
36 | "Expected header line to be of type %s but got %s" % (bytes, type(line))
37 | )
38 |
39 | if len(line) <= 1:
40 | raise ValueError("No identifier on FASTA line")
41 |
42 | # split line at first space to get the unique identifier for
43 | # this sequence
44 | space_index = line.find(b" ")
45 | if space_index >= 0:
46 | identifier = line[1:space_index]
47 | else:
48 | identifier = line[1:]
49 |
50 | # annoyingly Ensembl83 reformatted the transcript IDs of its
51 | # cDNA FASTA to include sequence version numbers
52 | # .e.g.
53 | # "ENST00000448914.1" instead of "ENST00000448914"
54 | # So now we have to parse out the identifier
55 |
56 | # only split name of ENSEMBL naming. In other database, such as TAIR,
57 | # the '.1' notation is the isoform not the version.
58 | if identifier.startswith(b"ENS"):
59 | dot_index = identifier.find(b".")
60 | if dot_index >= 0:
61 | identifier = identifier[:dot_index]
62 |
63 | return identifier.decode("ascii")
64 |
65 |
66 | class FastaParser(object):
67 | """
68 | FastaParser object consumes lines of a FASTA file incrementally
69 | while building up a dictionary mapping sequence identifiers to sequences.
70 | """
71 |
72 | def __init__(self):
73 | self.current_id = None
74 | self.current_lines = []
75 |
76 | def read_file(self, fasta_path):
77 | """
78 | Read the contents of a FASTA file into a dictionary
79 | """
80 | fasta_dictionary = {}
81 | for identifier, sequence in self.iterate_over_file(fasta_path):
82 | fasta_dictionary[identifier] = sequence
83 | return fasta_dictionary
84 |
85 | def iterate_over_file(self, fasta_path):
86 | """
87 | Generator that yields identifiers paired with sequences.
88 | """
89 | with self._open(fasta_path) as f:
90 | for line in f:
91 | line = line.rstrip()
92 |
93 | if len(line) == 0:
94 | continue
95 |
96 | # have to slice into a bytes object or else I get a single integer
97 | first_char = line[0:1]
98 |
99 | if first_char == b">":
100 | id_and_seq = self._read_header(line)
101 | if id_and_seq is not None:
102 | yield id_and_seq
103 |
104 | elif first_char == b";":
105 | # semicolon are comment characters
106 | continue
107 | else:
108 | self.current_lines.append(line)
109 | # the last sequence is still in the lines buffer after we're done with
110 | # the file so make sure to yield it
111 | id_and_seq = self._current_entry()
112 | if id_and_seq is not None:
113 | yield id_and_seq
114 |
115 | def _open(self, fasta_path):
116 | """
117 | Open either a text file or compressed gzip file as a stream of bytes.
118 | """
119 | if fasta_path.endswith("gz") or fasta_path.endswith("gzip"):
120 | return GzipFile(fasta_path, "rb")
121 | else:
122 | return open(fasta_path, "rb")
123 |
124 | def _current_entry(self):
125 | # when we hit a new entry, if this isn't the first
126 | # entry of the file then put the last one in the dictionary
127 | if self.current_id:
128 | if len(self.current_lines) == 0:
129 | logger.warn("No sequence data for '%s'", self.current_id)
130 | else:
131 | sequence = b"".join(self.current_lines)
132 | sequence = sequence.decode("ascii")
133 | return self.current_id, sequence
134 |
135 | def _read_header(self, line):
136 | previous_entry = self._current_entry()
137 |
138 | self.current_id = _parse_header_id(line)
139 |
140 | if len(self.current_id) == 0:
141 | logger.warn("Unable to parse ID from header line: %s", line)
142 |
143 | self.current_lines = []
144 | return previous_entry
145 |
146 |
147 | def parse_fasta_dictionary(fasta_path):
148 | """
149 | Given a path to a FASTA (or compressed FASTA) file, returns a dictionary
150 | mapping its sequence identifiers to sequences.
151 |
152 | Parameters
153 | ----------
154 | fasta_path : str
155 | Path to the FASTA file.
156 |
157 | Returns dictionary from string identifiers to string sequences.
158 | """
159 | parser = FastaParser()
160 | return parser.read_file(fasta_path)
161 |
--------------------------------------------------------------------------------
/pyensembl/gene.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 |
14 | from memoized_property import memoized_property
15 |
16 | from .locus_with_genome import LocusWithGenome
17 |
18 |
19 | class Gene(LocusWithGenome):
20 | def __init__(self, gene_id, gene_name, contig, start, end, strand, biotype, genome):
21 | LocusWithGenome.__init__(
22 | self,
23 | contig=contig,
24 | start=start,
25 | end=end,
26 | strand=strand,
27 | biotype=biotype,
28 | genome=genome,
29 | )
30 | self.gene_id = gene_id
31 | self.gene_name = gene_name
32 |
33 | @property
34 | def id(self):
35 | """
36 | Alias for gene_id necessary for backwards compatibility.
37 | """
38 | return self.gene_id
39 |
40 | @property
41 | def name(self):
42 | """
43 | Alias for gene_name necessary for backwards compatibility.
44 | """
45 | return self.gene_name
46 |
47 | def __str__(self):
48 | return (
49 | "Gene(gene_id='%s',"
50 | " gene_name='%s',"
51 | " biotype='%s',"
52 | " contig='%s',"
53 | " start=%d,"
54 | " end=%d, strand='%s', genome='%s')"
55 | ) % (
56 | self.gene_id,
57 | self.gene_name,
58 | self.biotype,
59 | self.contig,
60 | self.start,
61 | self.end,
62 | self.strand,
63 | self.genome.reference_name,
64 | )
65 |
66 | def __eq__(self, other):
67 | return (
68 | other.__class__ is Gene
69 | and self.id == other.id
70 | and self.genome == other.genome
71 | )
72 |
73 | def __hash__(self):
74 | return hash(self.id)
75 |
76 | def to_dict(self):
77 | state_dict = LocusWithGenome.to_dict(self)
78 | state_dict["gene_id"] = self.gene_id
79 | state_dict["gene_name"] = self.gene_name
80 | return state_dict
81 |
82 | @memoized_property
83 | def transcripts(self):
84 | """
85 | Property which dynamically construct transcript objects for all
86 | transcript IDs associated with this gene.
87 | """
88 | transcript_id_results = self.db.query(
89 | select_column_names=["transcript_id"],
90 | filter_column="gene_id",
91 | filter_value=self.id,
92 | feature="transcript",
93 | distinct=False,
94 | required=False,
95 | )
96 |
97 | # We're doing a SQL query for each transcript ID to fetch
98 | # its particular information, might be more efficient if we
99 | # just get all the columns here, but how do we keep that modular?
100 | return [
101 | self.genome.transcript_by_id(result[0]) for result in transcript_id_results
102 | ]
103 |
104 | @memoized_property
105 | def exons(self):
106 | exon_set = set([])
107 | for transcript in self.transcripts:
108 | for exon in transcript.exons:
109 | exon_set.add(exon)
110 | return list(sorted(exon_set))
111 |
--------------------------------------------------------------------------------
/pyensembl/locus.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | from serializable import Serializable
14 |
15 | from .normalization import normalize_chromosome, normalize_strand
16 |
17 |
18 | class Locus(Serializable):
19 | """
20 | Base class for any entity which can be localized at a range of positions
21 | on a particular strand of a chromosome/contig.
22 | """
23 |
24 | def __init__(self, contig, start, end, strand):
25 | """
26 | contig : str
27 | Chromosome or other sequence name in the reference assembly
28 |
29 | start : int
30 | Start position of locus on the contig
31 |
32 | end : int
33 | Inclusive end position on the contig
34 |
35 | strand : str
36 | Should we read the locus forwards ('+') or backwards ('-')?
37 | """
38 |
39 | self.contig = normalize_chromosome(contig)
40 | self.strand = normalize_strand(strand)
41 |
42 | start = int(start)
43 | end = int(end)
44 |
45 | if start == 0:
46 | raise ValueError("Expected start > 0 (using base 1 coordinates)")
47 | elif end == 0:
48 | raise ValueError("Expected end > 0 (using base 1 coordinates)")
49 |
50 | if end < start:
51 | raise ValueError(
52 | "Expected start <= end, got start = %d, end = %d" % (start, end)
53 | )
54 | self.start = start
55 | self.end = end
56 |
57 | def __str__(self):
58 | return "Locus(contig='%s', start=%d, end=%d, strand='%s')" % (
59 | self.contig,
60 | self.start,
61 | self.end,
62 | self.strand,
63 | )
64 |
65 | def __len__(self):
66 | return self.end - self.start + 1
67 |
68 | def __eq__(self, other):
69 | if not isinstance(other, Locus):
70 | raise TypeError(
71 | "Cannot compare %s and %s"
72 | % (self.__class__.__name__, other.__class.__name__)
73 | )
74 | return (
75 | self.contig == other.contig
76 | and self.start == other.start
77 | and self.end == other.end
78 | and self.strand == other.strand
79 | )
80 |
81 | def to_tuple(self):
82 | return (self.contig, self.start, self.end, self.strand)
83 |
84 | def __lt__(self, other):
85 | if not isinstance(other, Locus):
86 | raise TypeError(
87 | "Cannot compare %s and %s"
88 | % (self.__class__.__name__, other.__class.__name__)
89 | )
90 | return self.to_tuple() < other.to_tuple()
91 |
92 | def __le__(self, other):
93 | return (self == other) or (self < other)
94 |
95 | def __gt__(self, other):
96 | if not isinstance(other, Locus):
97 | raise TypeError(
98 | "Cannot compare %s and %s"
99 | % (self.__class__.__name__, other.__class.__name__)
100 | )
101 | return self.to_tuple() > other.to_tuple()
102 |
103 | def __ge__(self, other):
104 | return (self == other) or (self > other)
105 |
106 | def to_dict(self):
107 | return {
108 | "contig": self.contig,
109 | "start": self.start,
110 | "end": self.end,
111 | "strand": self.strand,
112 | }
113 |
114 | @property
115 | def length(self):
116 | return self.end - self.start + 1
117 |
118 | def offset(self, position):
119 | """Offset of given position from stranded start of this locus.
120 |
121 | For example, if a Locus goes from 10..20 and is on the negative strand,
122 | then the offset of position 13 is 7, whereas if the Locus is on the
123 | positive strand, then the offset is 3.
124 | """
125 | if position > self.end or position < self.start:
126 | raise ValueError(
127 | "Position %d outside valid range %d..%d of %s"
128 | % (position, self.start, self.end, self)
129 | )
130 | elif self.on_forward_strand:
131 | return position - self.start
132 | else:
133 | return self.end - position
134 |
135 | def offset_range(self, start, end):
136 | """
137 | Database start/end entries are always ordered such that
138 | start < end. This makes computing a relative position (e.g. of a stop
139 | codon relative to its transcript) complicated since the "end"
140 | position of a backwards locus is actually earlir on the strand.
141 | This function correctly selects a start vs. end value depending
142 | on this locuses's strand and determines that position's offset from
143 | the earliest position in this locus.
144 | """
145 | if start > end:
146 | raise ValueError(
147 | "Locus should always have start <= end, got start=%d, end=%d"
148 | % (start, end)
149 | )
150 |
151 | if start < self.start or end > self.end:
152 | raise ValueError("Range (%d, %d) falls outside %s" % (start, end, self))
153 |
154 | if self.on_forward_strand:
155 | return (start - self.start, end - self.start)
156 |
157 | else:
158 | return (self.end - end, self.end - start)
159 |
160 | def on_contig(self, contig):
161 | return normalize_chromosome(contig) == self.contig
162 |
163 | def on_strand(self, strand):
164 | return normalize_strand(strand) == self.strand
165 |
166 | @property
167 | def on_forward_strand(self):
168 | return self.on_strand("+")
169 |
170 | @property
171 | def on_positive_strand(self):
172 | return self.on_forward_strand
173 |
174 | @property
175 | def on_backward_strand(self):
176 | return self.on_strand("-")
177 |
178 | @property
179 | def on_negative_strand(self):
180 | return self.on_backward_strand
181 |
182 | def can_overlap(self, contig, strand=None):
183 | """
184 | Is this locus on the same contig and (optionally) on the same strand?
185 | """
186 | return self.on_contig(contig) and (strand is None or self.on_strand(strand))
187 |
188 | def distance_to_interval(self, start, end):
189 | """
190 | Find the distance between intervals [start1, end1] and [start2, end2].
191 | If the intervals overlap then the distance is 0.
192 | """
193 | if self.start > end:
194 | # interval is before this exon
195 | return self.start - end
196 | elif self.end < start:
197 | # exon is before the interval
198 | return start - self.end
199 | else:
200 | return 0
201 |
202 | def distance_to_locus(self, other):
203 | if not self.can_overlap(other.contig, other.strand):
204 | # if two loci are on different contigs or strands,
205 | # can't compute a distance between them
206 | return float("inf")
207 | return self.distance_to_interval(other.start, other.end)
208 |
209 | def overlaps(self, contig, start, end, strand=None):
210 | """
211 | Does this locus overlap with a given range of positions?
212 |
213 | Since locus position ranges are inclusive, we should make sure
214 | that e.g. chr1:10-10 overlaps with chr1:10-10
215 | """
216 | return (
217 | self.can_overlap(contig, strand)
218 | and self.distance_to_interval(start, end) == 0
219 | )
220 |
221 | def overlaps_locus(self, other_locus):
222 | return self.overlaps(
223 | other_locus.contig, other_locus.start, other_locus.end, other_locus.strand
224 | )
225 |
226 | def contains(self, contig, start, end, strand=None):
227 | return (
228 | self.can_overlap(contig, strand) and start >= self.start and end <= self.end
229 | )
230 |
231 | def contains_locus(self, other_locus):
232 | return self.contains(
233 | other_locus.contig, other_locus.start, other_locus.end, other_locus.strand
234 | )
235 |
--------------------------------------------------------------------------------
/pyensembl/locus_with_genome.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 |
14 | from .locus import Locus
15 |
16 |
17 | class LocusWithGenome(Locus):
18 | """
19 | Common base class for Gene and Transcript to avoid copying
20 | their shared logic.
21 | """
22 |
23 | def __init__(self, contig, start, end, strand, biotype, genome):
24 | Locus.__init__(self, contig, start, end, strand)
25 | self.genome = genome
26 | self.db = self.genome.db
27 | self.biotype = biotype
28 |
29 | def to_dict(self):
30 | return dict(
31 | contig=self.contig,
32 | start=self.start,
33 | end=self.end,
34 | strand=self.strand,
35 | biotype=self.biotype,
36 | genome=self.genome,
37 | )
38 |
39 | @property
40 | def is_protein_coding(self):
41 | """
42 | We're not counting immunoglobulin-like genes from the T-cell receptor or
43 | or antibodies since they occur in fragments that must be recombined.
44 | It might be worth consider counting non-sense mediated decay and
45 | non-stop decay since variants in these could potentially make a
46 | functional protein. To read more about the biotypes used in Ensembl:
47 | http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html
48 | http://www.gencodegenes.org/gencode_biotypes.html
49 |
50 | For now let's stick with the simple category of 'protein_coding', which
51 | means that there is an open reading frame in this gene/transcript
52 | whose successful transcription has been observed.
53 | """
54 | return self.biotype == "protein_coding"
55 |
--------------------------------------------------------------------------------
/pyensembl/logging.conf:
--------------------------------------------------------------------------------
1 | [loggers]
2 | keys=root,pyensembl,datacache
3 |
4 | [formatters]
5 | keys=simpleFormatter
6 |
7 | [handlers]
8 | keys=consoleHandler,consoleHandlerCritical
9 |
10 | [logger_root]
11 | level=INFO
12 | handlers=consoleHandlerCritical
13 |
14 | [handler_consoleHandler]
15 | class=StreamHandler
16 | level=INFO
17 | formatter=simpleFormatter
18 | args=(sys.stdout,)
19 |
20 | [handler_consoleHandlerCritical] # only for root logger: essentially silent
21 | class=StreamHandler
22 | level=CRITICAL
23 | formatter=simpleFormatter
24 | args=(sys.stdout,)
25 |
26 | [formatter_simpleFormatter]
27 | format=%(asctime)s - %(name)s - %(levelname)s - %(message)s
28 | datefmt=
29 |
30 | # pyensembl
31 |
32 | [logger_pyensembl]
33 | level=DEBUG
34 | qualname=pyensembl
35 | handlers=consoleHandler
36 |
37 | # datacache
38 |
39 | [logger_datacache]
40 | level=DEBUG
41 | qualname=datacache
42 | handlers=consoleHandler
43 |
--------------------------------------------------------------------------------
/pyensembl/normalization.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | from sys import intern
14 | from typechecks import is_string, is_integer
15 |
16 | # Manually memoizing here, since our simple common.memoize function has
17 | # noticable overhead in this instance.
18 | NORMALIZE_CHROMOSOME_CACHE = {}
19 |
20 |
21 | def normalize_chromosome(c):
22 | try:
23 | return NORMALIZE_CHROMOSOME_CACHE[c]
24 | except KeyError:
25 | pass
26 |
27 | if not (is_string(c) or is_integer(c)):
28 | raise TypeError("Chromosome cannot be '%s' : %s" % (c, type(c)))
29 |
30 | result = str(c)
31 |
32 | if result == "0":
33 | raise ValueError("Chromosome name cannot be 0")
34 | elif result == "":
35 | raise ValueError("Chromosome name cannot be empty")
36 |
37 | if result.startswith("chr") and "_" not in result:
38 | # excluding "_" for names like "chrUn_gl000212"
39 | # capitalize "chrx" -> "chrX"
40 | result = "chr" + result[3:].upper()
41 | elif result.isalpha():
42 | # capitalize e.g. "x" -> "X"
43 | result = result.upper()
44 |
45 | # interning strings since the chromosome names probably get constructed
46 | # or parsed millions of times, can save memory in tight situations
47 | # (such as parsing GTF files)
48 | result = intern(result)
49 |
50 | NORMALIZE_CHROMOSOME_CACHE[c] = result
51 |
52 | return result
53 |
54 |
55 | def normalize_strand(strand):
56 | if strand == "+" or strand == 1 or strand == "+1" or strand == "1":
57 | return "+"
58 | elif strand == "-" or strand == -1 or strand == "-1":
59 | return "-"
60 | raise ValueError("Invalid strand: %s" % (strand,))
61 |
--------------------------------------------------------------------------------
/pyensembl/reference_name.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | from .ensembl_release import EnsemblRelease
14 | from .species import Species, find_species_by_name
15 |
16 |
17 | def normalize_reference_name(name):
18 | """
19 | Search the dictionary of species-specific references to find a reference
20 | name that matches aside from capitalization.
21 |
22 | If no matching reference is found, raise an exception.
23 | """
24 | lower_name = name.strip().lower()
25 | for reference in Species._reference_names_to_species.keys():
26 | if reference.lower() == lower_name:
27 | return reference
28 | raise ValueError("Reference genome '%s' not found" % name)
29 |
30 |
31 | def find_species_by_reference(reference_name):
32 | return Species._reference_names_to_species[normalize_reference_name(reference_name)]
33 |
34 |
35 | def which_reference(species_name, ensembl_release):
36 | return find_species_by_name(species_name).which_reference(ensembl_release)
37 |
38 |
39 | def max_ensembl_release(reference_name):
40 | species = find_species_by_reference(reference_name)
41 | (_, max_release) = species.reference_assemblies[reference_name]
42 | return max_release
43 |
44 |
45 | def genome_for_reference_name(reference_name, allow_older_downloaded_release=True):
46 | """
47 | Given a genome reference name, such as "GRCh38", returns the
48 | corresponding Ensembl Release object.
49 |
50 | If `allow_older_downloaded_release` is True, and some older releases have
51 | been downloaded, then return the most recent locally available release.
52 |
53 | Otherwise, return the newest release of Ensembl (even if its data hasn't
54 | already been downloaded).
55 | """
56 | reference_name = normalize_reference_name(reference_name)
57 | species = find_species_by_reference(reference_name)
58 | (min_ensembl_release, max_ensembl_release) = species.reference_assemblies[
59 | reference_name
60 | ]
61 | if allow_older_downloaded_release:
62 | # go through candidate releases in descending order
63 | for release in reversed(range(min_ensembl_release, max_ensembl_release + 1)):
64 | # check if release has been locally downloaded
65 | candidate = EnsemblRelease.cached(release=release, species=species)
66 | if candidate.required_local_files_exist():
67 | return candidate
68 | # see if any of the releases between [max, min] are already locally
69 | # available
70 | return EnsemblRelease.cached(release=max_ensembl_release, species=species)
71 |
72 |
73 | ensembl_grch36 = genome_for_reference_name("ncbi36")
74 | ensembl_grch37 = genome_for_reference_name("grch37")
75 | ensembl_grch38 = genome_for_reference_name("grch38")
76 |
--------------------------------------------------------------------------------
/pyensembl/search.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | """
14 | Helper functions for searching over collections of PyEnsembl objects
15 | """
16 |
17 |
18 | def find_nearest_locus(start, end, loci):
19 | """
20 | Finds nearest locus (object with method `distance_to_interval`) to the
21 | interval defined by the given `start` and `end` positions.
22 | Returns the distance to that locus, along with the locus object itself.
23 | """
24 | best_distance = float("inf")
25 | best_locus = None
26 | for locus in loci:
27 | distance = locus.distance_to_interval(start, end)
28 | if best_distance > distance:
29 | best_distance = distance
30 | best_locus = locus
31 | return best_distance, best_locus
32 |
--------------------------------------------------------------------------------
/pyensembl/sequence_data.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | from os import remove
14 | from os.path import exists, abspath, split, join
15 | import logging
16 | from collections import Counter
17 | import pickle
18 | from .common import load_pickle, dump_pickle
19 | from .fasta import parse_fasta_dictionary
20 |
21 |
22 | logger = logging.getLogger(__name__)
23 |
24 |
25 | class SequenceData(object):
26 | """
27 | Container for reference nucleotide and amino acid sequenes.
28 | """
29 |
30 | def __init__(self, fasta_paths, cache_directory_path=None):
31 | if type(fasta_paths) is str:
32 | fasta_paths = [fasta_paths]
33 |
34 | self.fasta_paths = [abspath(path) for path in fasta_paths]
35 | self.fasta_directory_paths = [split(path)[0] for path in self.fasta_paths]
36 | self.fasta_filenames = [split(path)[1] for path in self.fasta_paths]
37 | if cache_directory_path:
38 | self.cache_directory_paths = [cache_directory_path] * len(self.fasta_paths)
39 | else:
40 | self.cache_directory_paths = self.fasta_directory_paths
41 | for path in self.fasta_paths:
42 | if not exists(path):
43 | raise ValueError("Couldn't find FASTA file %s" % (path,))
44 | self.fasta_dictionary_filenames = [
45 | filename + ".pickle" for filename in self.fasta_filenames
46 | ]
47 | self.fasta_dictionary_pickle_paths = [
48 | join(cache_path, filename)
49 | for cache_path, filename in zip(
50 | self.cache_directory_paths, self.fasta_dictionary_filenames
51 | )
52 | ]
53 | self._init_lazy_fields()
54 |
55 | def _init_lazy_fields(self):
56 | self._fasta_dictionary = None
57 | self._fasta_keys = None
58 |
59 | def clear_cache(self):
60 | self._init_lazy_fields()
61 | for path in self.fasta_dictionary_pickle_paths:
62 | if exists(path):
63 | remove(path)
64 |
65 | def __str__(self):
66 | return "SequenceData(fasta_paths=%s)" % (self.fasta_paths,)
67 |
68 | def __repr__(self):
69 | return str(self)
70 |
71 | def __contains__(self, sequence_id):
72 | if self._fasta_keys is None:
73 | self._fasta_keys = set(self.fasta_dictionary.keys())
74 | return sequence_id in self._fasta_keys
75 |
76 | def __eq__(self, other):
77 | # test to see if self.fasta_paths and other.fasta_paths contain
78 | # the same list of paths, regardless of order
79 | return (other.__class__ is SequenceData) and Counter(
80 | self.fasta_paths
81 | ) == Counter(other.fasta_paths)
82 |
83 | def __hash__(self):
84 | return hash(self.fasta_paths)
85 |
86 | def _add_to_fasta_dictionary(self, fasta_dictionary_tmp):
87 | for identifier, sequence in fasta_dictionary_tmp.items():
88 | if identifier in self._fasta_dictionary:
89 | logger.warn(
90 | "Sequence identifier %s is duplicated in your FASTA files!"
91 | % identifier
92 | )
93 | continue
94 | self._fasta_dictionary[identifier] = sequence
95 |
96 | def _load_or_create_fasta_dictionary_pickle(self):
97 | self._fasta_dictionary = dict()
98 | for fasta_path, pickle_path in zip(
99 | self.fasta_paths, self.fasta_dictionary_pickle_paths
100 | ):
101 | if exists(pickle_path):
102 | # try loading the cached file
103 | # but we'll fall back on recreating it if loading fails
104 | try:
105 | fasta_dictionary_tmp = load_pickle(pickle_path)
106 | self._add_to_fasta_dictionary(fasta_dictionary_tmp)
107 | logger.info("Loaded sequence dictionary from %s", pickle_path)
108 | continue
109 | except (pickle.UnpicklingError, AttributeError):
110 | # catch either an UnpicklingError or an AttributeError
111 | # resulting from pickled objects refering to classes
112 | # that no longer exists
113 | logger.warn(
114 | "Failed to load %s, attempting to read FASTA directly",
115 | pickle_path,
116 | )
117 | logger.info("Parsing sequences from FASTA file at %s", fasta_path)
118 |
119 | fasta_dictionary_tmp = parse_fasta_dictionary(fasta_path)
120 | self._add_to_fasta_dictionary(fasta_dictionary_tmp)
121 | logger.info("Saving sequence dictionary to %s", pickle_path)
122 | dump_pickle(fasta_dictionary_tmp, pickle_path)
123 |
124 | def index(self, overwrite=False):
125 | if overwrite:
126 | self.clear_cache()
127 | self._load_or_create_fasta_dictionary_pickle()
128 |
129 | @property
130 | def fasta_dictionary(self):
131 | if not self._fasta_dictionary:
132 | self._load_or_create_fasta_dictionary_pickle()
133 | return self._fasta_dictionary
134 |
135 | def get(self, sequence_id):
136 | """Get sequence associated with given ID or return None if missing"""
137 | return self.fasta_dictionary.get(sequence_id)
138 |
--------------------------------------------------------------------------------
/pyensembl/shell.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | """
14 | Manipulate pyensembl's local cache.
15 |
16 | %(prog)s {install, delete, delete-sequence-cache} [--release XXX --species human...]
17 |
18 | To install particular Ensembl human release(s):
19 | %(prog)s install --release 75 77
20 |
21 | To install particular Ensembl mouse release(s):
22 | %(prog)s install --release 75 77 --species mouse
23 |
24 | To delete all downloaded and cached data for a particular Ensembl release:
25 | %(prog)s delete-all-files --release 75 --species human
26 |
27 | To delete only cached data related to transcript and protein sequences:
28 | %(prog)s delete-index-files --release 75
29 |
30 | To list all installed genomes:
31 | %(prog)s list
32 |
33 | To install a genome from source files:
34 | %(prog)s install \
35 | --reference-name "GRCh38" \
36 | --gtf URL_OR_PATH \
37 | --transcript-fasta URL_OR_PATH \
38 | --protein-fasta URL_OR_PATH
39 | """
40 |
41 | import argparse
42 | import logging.config
43 | import pkg_resources
44 | import os
45 |
46 | from .ensembl_release import EnsemblRelease
47 | from .ensembl_versions import MAX_ENSEMBL_RELEASE
48 | from .genome import Genome
49 | from .species import Species
50 | from .version import __version__
51 |
52 | logging.config.fileConfig(pkg_resources.resource_filename(__name__, "logging.conf"))
53 | logger = logging.getLogger(__name__)
54 |
55 |
56 | parser = argparse.ArgumentParser(usage=__doc__)
57 |
58 | parser.add_argument(
59 | "--version",
60 | action="version",
61 | version='%(prog)s {version}'.format(version=__version__)
62 | )
63 |
64 | parser.add_argument(
65 | "--overwrite",
66 | default=False,
67 | action="store_true",
68 | help="Force download and indexing even if files already exist locally",
69 | )
70 |
71 |
72 | root_group = parser.add_mutually_exclusive_group()
73 |
74 | release_group = root_group.add_argument_group()
75 | release_group.add_argument(
76 | "--release",
77 | type=int,
78 | nargs="+",
79 | default=[],
80 | help="Ensembl release version(s) (default=%d)" % MAX_ENSEMBL_RELEASE,
81 | )
82 |
83 | release_group.add_argument(
84 | "--species",
85 | default=[],
86 | nargs="+",
87 | help="Which species to download Ensembl data for (default=human)",
88 | )
89 |
90 | release_group.add_argument(
91 | "--custom-mirror",
92 | default=None,
93 | help="URL and directory to use instead of the default Ensembl FTP server",
94 | )
95 |
96 | path_group = root_group.add_argument_group()
97 |
98 | path_group.add_argument(
99 | "--reference-name",
100 | type=str,
101 | default=None,
102 | help="Name of the reference, e.g. GRCh38",
103 | )
104 |
105 | path_group.add_argument(
106 | "--annotation-name", default=None, help="Name of annotation source (e.g. refseq)"
107 | )
108 |
109 | path_group.add_argument(
110 | "--annotation-version", default=None, help="Version of annotation database"
111 | )
112 |
113 | path_group.add_argument(
114 | "--gtf",
115 | type=str,
116 | default=None,
117 | help="URL or local path to a GTF file containing annotations.",
118 | )
119 |
120 | path_group.add_argument(
121 | "--transcript-fasta",
122 | type=str,
123 | action="append",
124 | default=[],
125 | help="URL or local path to a FASTA files containing the transcript "
126 | "data. This option can be specified multiple times for multiple "
127 | "FASTA files.",
128 | )
129 |
130 | path_group.add_argument(
131 | "--protein-fasta",
132 | type=str,
133 | default=[],
134 | action="append",
135 | help="URL or local path to a FASTA file containing protein data.",
136 | )
137 |
138 | path_group.add_argument(
139 | "--shared-prefix",
140 | default="",
141 | help="Add this prefix to URLs or paths specified by --gtf, --transcript-fasta, --protein-fasta",
142 | )
143 |
144 | parser.add_argument(
145 | "action",
146 | type=lambda arg: arg.lower().strip(),
147 | choices=(
148 | "install",
149 | "delete-all-files",
150 | "delete-index-files",
151 | "list",
152 | ),
153 | help=(
154 | '"install" will download and index any data that is not '
155 | 'currently downloaded or indexed. "delete-all-files" will delete all data '
156 | 'associated with a genome annotation. "delete-index-files" deletes '
157 | "all files other than the original GTF and FASTA files for a genome. "
158 | '"list" will show you all installed Ensembl genomes.'
159 | ),
160 | )
161 |
162 |
163 | def collect_all_installed_ensembl_releases():
164 | genomes = []
165 | for species, release in Species.all_species_release_pairs():
166 | genome = EnsemblRelease(release, species=species)
167 | if genome.required_local_files_exist():
168 | genomes.append(genome)
169 | return sorted(genomes, key=lambda g: (g.species.latin_name, g.release))
170 |
171 |
172 | def all_combinations_of_ensembl_genomes(args):
173 | """
174 | Use all combinations of species and release versions specified by the
175 | commandline arguments to return a list of EnsemblRelease or Genome objects.
176 | The results will typically be of type EnsemblRelease unless the
177 | --custom-mirror argument was given.
178 | """
179 | species_list = args.species if args.species else ["human"]
180 | release_list = args.release if args.release else [MAX_ENSEMBL_RELEASE]
181 | genomes = []
182 | for species in species_list:
183 | # Otherwise, use Ensembl release information
184 | for version in release_list:
185 | ensembl_release = EnsemblRelease(version, species=species)
186 |
187 | if not args.custom_mirror:
188 | genomes.append(ensembl_release)
189 | else:
190 | # if we're using a custom mirror then we expect the provided
191 | # URL to be a directory with all the same filenames as
192 | # would be provided by Ensembl
193 | gtf_url = os.path.join(
194 | args.custom_mirror, os.path.basename(ensembl_release.gtf_url)
195 | )
196 | transcript_fasta_urls = [
197 | os.path.join(
198 | args.custom_mirror, os.path.basename(transcript_fasta_url)
199 | )
200 | for transcript_fasta_url in ensembl_release.transcript_fasta_urls
201 | ]
202 | protein_fasta_urls = [
203 | os.path.join(
204 | args.custom_mirror, os.path.basename(protein_fasta_url)
205 | )
206 | for protein_fasta_url in ensembl_release.protein_fasta_urls
207 | ]
208 | reference_name = ensembl_release.reference_name
209 | genome = Genome(
210 | reference_name=reference_name,
211 | annotation_name="ensembl",
212 | annotation_version=version,
213 | gtf_path_or_url=gtf_url,
214 | transcript_fasta_paths_or_urls=transcript_fasta_urls,
215 | protein_fasta_paths_or_urls=protein_fasta_urls,
216 | )
217 | genomes.append(genome)
218 | return genomes
219 |
220 |
221 | def collect_selected_genomes(args):
222 | # If specific genome source URLs are provided, use those
223 | if args.gtf or args.transcript_fasta or args.protein_fasta:
224 | if args.release:
225 | raise ValueError(
226 | "An Ensembl release cannot be specified if "
227 | "specific paths are also given"
228 | )
229 | if not args.reference_name:
230 | raise ValueError("Must specify a reference name")
231 | if not args.annotation_name:
232 | raise ValueError("Must specify the name of the annotation source")
233 |
234 | return [
235 | Genome(
236 | reference_name=args.reference_name,
237 | annotation_name=args.annotation_name,
238 | annotation_version=args.annotation_version,
239 | gtf_path_or_url=os.path.join(args.shared_prefix, args.gtf),
240 | transcript_fasta_paths_or_urls=[
241 | os.path.join(args.shared_prefix, transcript_fasta)
242 | for transcript_fasta in args.transcript_fasta
243 | ],
244 | protein_fasta_paths_or_urls=[
245 | os.path.join(args.shared_prefix, protein_fasta)
246 | for protein_fasta in args.protein_fasta
247 | ],
248 | )
249 | ]
250 | else:
251 | return all_combinations_of_ensembl_genomes(args)
252 |
253 |
254 | def run():
255 | args = parser.parse_args()
256 | if args.action == "list":
257 | # TODO: how do we also identify which non-Ensembl genomes are
258 | # installed?
259 | genomes = collect_all_installed_ensembl_releases()
260 | for genome in genomes:
261 | # print every directory in which downloaded files are located
262 | # in most case this will be only one directory
263 | filepaths = genome.required_local_files()
264 | directories = {os.path.split(path)[0] for path in filepaths}
265 | print("-- %s: %s" % (genome, ", ".join(directories)))
266 | else:
267 | genomes = collect_selected_genomes(args)
268 |
269 | if len(genomes) == 0:
270 | logger.error("ERROR: No genomes selected!")
271 | parser.print_help()
272 |
273 | for genome in genomes:
274 | logger.info("Running '%s' for %s", args.action, genome)
275 | if args.action == "delete-all-files":
276 | genome.download_cache.delete_cache_directory()
277 | elif args.action == "delete-index-files":
278 | genome.delete_index_files()
279 | elif args.action == "install":
280 | genome.download(overwrite=args.overwrite)
281 | genome.index(overwrite=args.overwrite)
282 | else:
283 | raise ValueError("Invalid action: %s" % args.action)
284 |
--------------------------------------------------------------------------------
/pyensembl/version.py:
--------------------------------------------------------------------------------
1 | __version__ = "2.3.13"
2 |
3 | def print_version():
4 | print(f"v{__version__}")
5 |
6 | if __name__ == "__main__":
7 | print_version()
8 |
--------------------------------------------------------------------------------
/pylintrc:
--------------------------------------------------------------------------------
1 | [TYPECHECK]
2 | # Without ignoring this, we get errors like:
3 | # E:249,20: Module 'numpy' has no 'nan' member (no-member)
4 | ignored-modules = numpy
5 |
6 |
--------------------------------------------------------------------------------
/requirements.txt:
--------------------------------------------------------------------------------
1 | typechecks>=0.0.2,<1.0.0
2 | datacache>=1.4.0,<2.0.0
3 | memoized-property>=1.0.2
4 | tinytimer>=0.0.0,<1.0.0
5 | gtfparse>=2.5.0,<3.0.0
6 | serializable>=0.2.1,<1.0.0
7 | pylint>=2.17.2,<3.0.0
8 |
--------------------------------------------------------------------------------
/setup.py:
--------------------------------------------------------------------------------
1 | # Licensed under the Apache License, Version 2.0 (the "License");
2 | # you may not use this file except in compliance with the License.
3 | # You may obtain a copy of the License at
4 | #
5 | # http://www.apache.org/licenses/LICENSE-2.0
6 | #
7 | # Unless required by applicable law or agreed to in writing, software
8 | # distributed under the License is distributed on an "AS IS" BASIS,
9 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10 | # See the License for the specific language governing permissions and
11 | # limitations under the License.
12 |
13 | from __future__ import print_function
14 | import os
15 | import re
16 |
17 | # TODO: replace setup.py with pyproject.toml
18 | from setuptools import setup
19 |
20 | package_name = "pyensembl"
21 | current_directory = os.path.dirname(__file__)
22 | readme_filename = "README.md"
23 | readme_path = os.path.join(current_directory, readme_filename)
24 | github_url = "https://github.com/openvax/%s" % package_name
25 |
26 | try:
27 | with open(readme_path, "r") as f:
28 | readme_markdown = f.read()
29 | except IOError as e:
30 | print(e)
31 | print("Failed to open %s" % readme_path)
32 | readme_markdown = ""
33 |
34 |
35 | with open("%s/version.py" % package_name, "r") as f:
36 | version = re.search(
37 | r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]', f.read(), re.MULTILINE
38 | ).group(1)
39 |
40 | if not version:
41 | raise RuntimeError("Cannot find version information")
42 |
43 | if __name__ == "__main__":
44 | with open("requirements.txt") as f:
45 | requirements = [l.strip() for l in f]
46 |
47 | setup(
48 | name=package_name,
49 | version=version,
50 | description="Python interface to Ensembl reference genome metadata",
51 | author="Alex Rubinsteyn",
52 | author_email="alex.rubinsteyn@unc.edu",
53 | url=github_url,
54 | license="http://www.apache.org/licenses/LICENSE-2.0.html",
55 | entry_points={
56 | "console_scripts": ["pyensembl = %s.shell:run" % package_name],
57 | },
58 | classifiers=[
59 | "Development Status :: 4 - Beta",
60 | "Environment :: Console",
61 | "Operating System :: OS Independent",
62 | "Intended Audience :: Science/Research",
63 | "License :: OSI Approved :: Apache Software License",
64 | "Programming Language :: Python",
65 | "Topic :: Scientific/Engineering :: Bio-Informatics",
66 | ],
67 | install_requires=requirements,
68 | long_description=readme_markdown,
69 | long_description_content_type="text/markdown",
70 | packages=[package_name],
71 | package_data={
72 | package_name: ["logging.conf", "../requirements.txt"],
73 | },
74 | )
75 |
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/test.sh:
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1 | pytest --cov=pyensembl/ --cov-report=term-missing tests
2 |
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/tests/__init__.py:
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https://raw.githubusercontent.com/openvax/pyensembl/d292b1749875904b380a209f4ff44b7d75dafdc3/tests/__init__.py
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/tests/common.py:
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1 | import functools
2 |
3 | from pyensembl import genome_for_reference_name, cached_release
4 |
5 | import pytest
6 |
7 |
8 | grch37 = genome_for_reference_name("GRCh37")
9 | grch38 = genome_for_reference_name("GRCh38")
10 |
11 | major_releases = [grch37, grch38]
12 |
13 | contigs = [str(c) for c in range(1, 23)] + ["X", "Y", "M"]
14 |
15 |
16 | def run_multiple_genomes(*versions):
17 | if len(versions) == 1 and callable(versions[0]):
18 | return pytest.mark.parametrize("genome", major_releases)(versions[0])
19 | if not versions:
20 | genomes = major_releases
21 | else:
22 | genomes = [cached_release(v) for v in versions]
23 | return lambda fn: pytest.mark.parametrize("genome", genomes)(fn)
24 |
25 |
26 | # TemporaryDirectory only got added to Python in version 3.2
27 | try:
28 | # pylint: disable=no-name-in-module
29 | from tempfile import TemporaryDirectory
30 |
31 | except ImportError:
32 | # only added in Python 3.2
33 | from tempfile import mkdtemp
34 | from shutil import rmtree
35 |
36 | class TemporaryDirectory(object):
37 | def __init__(self):
38 | self.name = mkdtemp()
39 |
40 | def __enter__(self, *args, **kwargs):
41 | return self.name
42 |
43 | def __exit__(self, type, value, traceback):
44 | rmtree(self.name)
45 | # don't suppress exceptions
46 | return False
47 |
48 |
49 | def ok_(b):
50 | assert b
51 |
52 |
53 | def eq_(x, y, msg=None):
54 | if msg is None:
55 | assert x == y
56 | else:
57 | assert x == y, msg
58 |
59 |
60 | def neq_(x, y, msg=None):
61 | if msg is None:
62 | assert x != y
63 | else:
64 | assert x != y, msg
65 |
66 |
67 | def gt_(x, y, msg=None):
68 | if msg is None:
69 | assert x > y
70 | else:
71 | assert x > y, msg
72 |
73 |
74 | def gte_(x, y, msg=None):
75 | if msg is None:
76 | assert x >= y
77 | else:
78 | assert x >= y, msg
79 |
80 |
81 | def lt_(x, y, msg=None):
82 | if msg is None:
83 | assert x < y
84 | else:
85 | assert x < y, msg
86 |
87 |
88 | def lte_(x, y, msg=None):
89 | if msg is None:
90 | assert x <= y
91 | else:
92 | assert x <= y, msg
93 |
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/tests/data.py:
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1 | import os
2 | from pyensembl import Locus, Genome
3 |
4 |
5 | def data_path(name):
6 | """
7 | Return the absolute path to a file in the test/data directory.
8 | The name specified should be relative to test/data.
9 | """
10 | return os.path.join(os.path.dirname(__file__), "data", name)
11 |
12 |
13 | # mapping of ensembl releases to transcript IDs for FOXP3-001
14 | FOXP3_001_transcript_id = "ENST00000376207"
15 |
16 | TP53_gene_id = "ENSG00000141510"
17 |
18 | # beta-catenin interacting protein from the negative strand of chromosome 1
19 | # URL: http://useast.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?
20 | # db=core;g=ENSG00000178585;r=1:9848276-9910336;t=ENST00000377256
21 | CTNNBIP1_004_transcript_id = "ENST00000377256"
22 |
23 | # coding sequence for beta-catenin interacting protein (CTNNBIP1-004)
24 | CTNNBIP1_004_CDS = "".join([
25 | "ATG",
26 | "AACCGCGAGGGAGCTCCCGGGAAGAGTCCGGAG",
27 | "GAGATGTACATTCAGCAGAAGGTCCGAGTGCTGCTCATGCTGCGGAAGATGGGATCAAAC",
28 | "CTGACAGCCAGCGAGGAGGAGTTCCTGCGCACCTATGCAGGGGTGGTCAACAGCCAGCTC",
29 | "AGCCAGCTGCCTCCGCACTCCATCGACCAGG",
30 | "GTGCAGAGGACGTGGTGATGGCGTTTTCCAGGTCGGAGACGGAAGACCGGAGGCAG",
31 | "TAG"
32 | ])
33 |
34 | # 5' UTR for beta-catenin interacting protein (CTNNBIP1-004)
35 | CTNNBIP1_004_UTR5 = "".join([
36 | "TGTGGGTGCAGGTTTCCTGGGCTTGCCAGACACACAGGGCGGCACCTTCCTACTTCTGCC",
37 | "CAGCCACAGCCCTCCCCTCACAGTTGAGCACCTGTTTGCCTGAAGTTAATTTCCAGAAGC",
38 | "AGGAGTCCCCAGAGCCAGGCAGGGGG"])
39 |
40 | # 3' UTR for beta-catenin interacting protein (CTNNBIP1-004)
41 | CTNNBIP1_004_UTR3 = \
42 | "CTGCAAAGCCCTTGGAACACCCTGGATGCTGTTGAGGGCCAAGAGATCTGTGTGGCTCC"
43 |
44 | CTNNBIP1_004_locus = Locus("1", 9850659, 9878176, "-")
45 |
46 | # properties of CTNNBIP1-004's exons copied from
47 | # http://useast.ensembl.org/Homo_sapiens/Transcript/Exons?g=ENSG00000178585;
48 | # r=1:9850659-9878176;redirect=no;t=ENST00000377256
49 | CTTNNIP1_004_exon_ids = [
50 | 'ENSE00001473268',
51 | 'ENSE00001643659',
52 | 'ENSE00001600669',
53 | 'ENSE00001267940',
54 | 'ENSE00001473265',
55 | ]
56 |
57 | CTTNNIP1_004_exon_lengths = [
58 | 37,
59 | 85,
60 | 120,
61 | 91,
62 | 118
63 | ]
64 |
65 |
66 | #
67 | # Information for EGFR from Ensembl website
68 | # Date: March 25th, 2015
69 | # Ensembl Release: 79
70 | #
71 | EGFR_001_name = "EGFR-001"
72 | EGFR_001_transcript_id = "ENST00000275493"
73 | EGFR_001_ccds_id = "CCDS5514"
74 | EGFR_001_protein_id = "ENSP00000275493"
75 | EGFR_001_protein_sequence = "".join([
76 | "MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYV",
77 | "QRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNL",
78 | "QEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGEENCQKL",
79 | "TKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVN",
80 | "PEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLS",
81 | "INATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAF",
82 | "ENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKI",
83 | "ISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHP",
84 | "ECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTG",
85 | "PGLEGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPN",
86 | "QALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVD",
87 | "NPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAA",
88 | "RNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTF",
89 | "GSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLV",
90 | "IQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGFFSSPSTSRTPLLSSLSATSNNSTVACI",
91 | "DRNGLQSCPIKEDSFLQRYSSDPTGALTEDSIDDTFLPVPEYINQSVPKRPAGSVQNPVYHNQPLNPAPS"
92 | "RDPHYQDPHSTAVGNPEYLNTVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGS"
93 | "TAENAEYLRVAPQSSEFIGA"
94 | ])
95 |
96 |
97 | # GTF cropped from ftp://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/
98 | # Mus_musculus.GRCm38.81.gtf.gz via:
99 | # grep "ENSMUSG00000017167" Mus_musculus.GRCm38.81.gtf
100 |
101 | # Transcript FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/
102 | # fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz via:
103 | # grep "ENSMUSG00000017167" Mus_musculus.GRCm38.cdna.all.fa -A 50
104 |
105 | # ncRNA FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/
106 | # fasta/mus_musculus/cdna/Mus_musculus.GRCm38.ncrna.fa.gz via:
107 | # grep "ENSMUSG00000088969" Mus_musculus.GRCm38.ncrna.fa -A 2
108 |
109 | # Protein FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/fasta/
110 | # mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz via:
111 | # grep "ENSMUSG00000017167" Mus_musculus.GRCm38.pep.all.fa -A 50
112 |
113 | # Tested against:
114 | # http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000017167
115 |
116 | MOUSE_ENSMUSG00000017167_PATH = data_path(
117 | "mouse.ensembl.81.partial.ENSMUSG00000017167.gtf")
118 | MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH = data_path(
119 | "mouse.ensembl.81.partial.ENSMUSG00000017167.fa")
120 | MOUSE_ENSMUSG00000088969_NCRNA_FASTA_PATH = data_path(
121 | "mouse.ensembl.81.partial.ncrna.ENSMUSG00000017167.fa")
122 | MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH = data_path(
123 | "mouse.ensembl.81.partial.ENSMUSG00000017167.pep")
124 |
125 |
126 | custom_mouse_genome_grcm38_subset = Genome(
127 | reference_name="GRCm38",
128 | annotation_name="_test_mouse_ensembl81_subset",
129 | gtf_path_or_url=MOUSE_ENSMUSG00000017167_PATH,
130 | transcript_fasta_paths_or_urls=[MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH],
131 | protein_fasta_paths_or_urls=[MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH])
132 |
133 |
134 | def setup_init_custom_mouse_genome():
135 | """
136 | If a unit test needs to start from a cleared cache, add this to the test
137 | setup.
138 | """
139 | custom_mouse_genome_grcm38_subset.clear_cache()
140 | custom_mouse_genome_grcm38_subset.index()
141 |
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/tests/data/gencode.ucsc.small.gtf:
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1 | # expected format is
5 |