Mercurial > repos > vimalkumarvelayudhan > riboplot
changeset 7:096c6bbf4a04
Bugfix: (ribocounts) Read length was sent as rnafile argument in check_optional_arguments
| author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
|---|---|
| date | Thu, 13 Aug 2015 15:03:20 +0100 |
| parents | 2ffa8172dce1 |
| children | 844eb8c36f32 |
| files | AUTHORS.rst CONTRIBUTING.rst HISTORY.rst Makefile README.rst docs/authors.rst docs/conf.py docs/contributing.rst docs/history.rst docs/index.rst docs/readme.rst docs/usage.rst riboplot.egg-info/PKG-INFO riboplot.egg-info/SOURCES.txt riboplot/ribocore.py riboplot/ribocount.py riboplot/riboplot.py run_ribocount_sample.sh runtests.sh tests/test_riboplot.py |
| diffstat | 20 files changed, 225 insertions(+), 185 deletions(-) [+] |
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--- a/AUTHORS.rst Wed Aug 12 16:28:43 2015 +0100 +++ b/AUTHORS.rst Thu Aug 13 15:03:20 2015 +0100 @@ -1,13 +1,1 @@ -======= -Credits -======= - -Development Lead ----------------- - -* Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> - -Contributors ------------- - -None yet. Why not be the first? \ No newline at end of file +docs/authors.rst \ No newline at end of file
--- a/CONTRIBUTING.rst Wed Aug 12 16:28:43 2015 +0100 +++ b/CONTRIBUTING.rst Thu Aug 13 15:03:20 2015 +0100 @@ -1,111 +1,1 @@ -============ -Contributing -============ - -Contributions are welcome, and they are greatly appreciated! Every -little bit helps, and credit will always be given. - -You can contribute in many ways: - -Types of Contributions ----------------------- - -Report Bugs -~~~~~~~~~~~ - -Report bugs at https://github.com/vimalkumarvelayudhan/riboplot/issues. - -If you are reporting a bug, please include: - -* Your operating system name and version. -* Any details about your local setup that might be helpful in troubleshooting. -* Detailed steps to reproduce the bug. - -Fix Bugs -~~~~~~~~ - -Look through the GitHub issues for bugs. Anything tagged with "bug" -is open to whoever wants to implement it. - -Implement Features -~~~~~~~~~~~~~~~~~~ - -Look through the GitHub issues for features. Anything tagged with "feature" -is open to whoever wants to implement it. - -Write Documentation -~~~~~~~~~~~~~~~~~~~ - -RiboPlot could always use more documentation, whether as part of the -official RiboPlot docs, in docstrings, or even on the web in blog posts, -articles, and such. - -Submit Feedback -~~~~~~~~~~~~~~~ - -The best way to send feedback is to file an issue at https://github.com/vimalkumarvelayudhan/riboplot/issues. - -If you are proposing a feature: - -* Explain in detail how it would work. -* Keep the scope as narrow as possible, to make it easier to implement. -* Remember that this is a volunteer-driven project, and that contributions - are welcome :) - -Get Started! ------------- - -Ready to contribute? Here's how to set up `riboplot` for local development. - -1. Fork the `riboplot` repo on GitHub. -2. Clone your fork locally:: - - $ git clone git@github.com:your_name_here/riboplot.git - -3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:: - - $ mkvirtualenv riboplot - $ cd riboplot/ - $ python setup.py develop - -4. Create a branch for local development:: - - $ git checkout -b name-of-your-bugfix-or-feature - - Now you can make your changes locally. - -5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:: - - $ flake8 riboplot tests - $ python setup.py test - $ tox - - To get flake8 and tox, just pip install them into your virtualenv. - -6. Commit your changes and push your branch to GitHub:: - - $ git add . - $ git commit -m "Your detailed description of your changes." - $ git push origin name-of-your-bugfix-or-feature - -7. Submit a pull request through the GitHub website. - -Pull Request Guidelines ------------------------ - -Before you submit a pull request, check that it meets these guidelines: - -1. The pull request should include tests. -2. If the pull request adds functionality, the docs should be updated. Put - your new functionality into a function with a docstring, and add the - feature to the list in README.rst. -3. The pull request should work for Python 2.6, 2.7, 3.3, and 3.4, and for PyPy. Check - https://travis-ci.org/vimalkumarvelayudhan/riboplot/pull_requests - and make sure that the tests pass for all supported Python versions. - -Tips ----- - -To run a subset of tests:: - - $ python -m unittest tests.test_riboplot \ No newline at end of file +docs/contributing.rst \ No newline at end of file
--- a/HISTORY.rst Wed Aug 12 16:28:43 2015 +0100 +++ b/HISTORY.rst Thu Aug 13 15:03:20 2015 +0100 @@ -1,9 +1,1 @@ -.. :changelog: - -History -------- - -0.1.0 (2015-08-05) ---------------------- - -* First release on PyPI. \ No newline at end of file +docs/history.rst \ No newline at end of file
--- a/Makefile Wed Aug 12 16:28:43 2015 +0100 +++ b/Makefile Thu Aug 13 15:03:20 2015 +0100 @@ -55,7 +55,6 @@ sphinx-apidoc -o docs/ riboplot $(MAKE) -C docs clean $(MAKE) -C docs html - open docs/_build/html/index.html release: clean python setup.py sdist upload @@ -67,4 +66,4 @@ ls -l dist install: clean - python setup.py install \ No newline at end of file + python setup.py install
--- a/README.rst Wed Aug 12 16:28:43 2015 +0100 +++ b/README.rst Thu Aug 13 15:03:20 2015 +0100 @@ -1,20 +1,1 @@ -=============================== -RiboPlot -=============================== - -.. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg - :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot - -.. image:: https://img.shields.io/pypi/v/riboplot.svg - :target: https://pypi.python.org/pypi/riboplot - - -Plot read counts of RiboSeq data from BAM format alignment files - -* Free software: BSD license -* Documentation: https://riboplot.readthedocs.org. - -Features --------- - -* TODO \ No newline at end of file +docs/readme.rst \ No newline at end of file
--- a/docs/authors.rst Wed Aug 12 16:28:43 2015 +0100 +++ b/docs/authors.rst Thu Aug 13 15:03:20 2015 +0100 @@ -1,1 +1,13 @@ -../AUTHORS.rst \ No newline at end of file +======= +Credits +======= + +Development Lead +---------------- + +* Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> + +Contributors +------------ + +None yet. Why not be the first? \ No newline at end of file
--- a/docs/conf.py Wed Aug 12 16:28:43 2015 +0100 +++ b/docs/conf.py Thu Aug 13 15:03:20 2015 +0100 @@ -111,12 +111,20 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = 'default' +html_theme = 'alabaster' # Theme options are theme-specific and customize the look and feel of a # theme further. For a list of options available for each theme, see the # documentation. #html_theme_options = {} +html_theme_options = { + 'font_family': '"Open Sans", Ubuntu, sans-serif', + 'head_font_family': '"Open Sans", Ubuntu, sans-serif', + 'code_font_family': '"Source Code Pro", "Ubuntu Mono", monospace', + 'code_font_size': '0.8em', + 'pre_bg': '#f9f9f9', 'note_bg': '#e6f7ff', 'note_border': '#ccefff', + 'sidebar_list': '#777777', 'body_text': '#515151', 'show_powered_by': False} + # Add any paths that contain custom themes here, relative to this directory. #html_theme_path = [] @@ -272,4 +280,4 @@ #texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False \ No newline at end of file +#texinfo_no_detailmenu = False
--- a/docs/contributing.rst Wed Aug 12 16:28:43 2015 +0100 +++ b/docs/contributing.rst Thu Aug 13 15:03:20 2015 +0100 @@ -1,1 +1,111 @@ -../CONTRIBUTING.rst \ No newline at end of file +============ +Contributing +============ + +Contributions are welcome, and they are greatly appreciated! Every +little bit helps, and credit will always be given. + +You can contribute in many ways: + +Types of Contributions +---------------------- + +Report Bugs +~~~~~~~~~~~ + +Report bugs at https://github.com/vimalkumarvelayudhan/riboplot/issues. + +If you are reporting a bug, please include: + +* Your operating system name and version. +* Any details about your local setup that might be helpful in troubleshooting. +* Detailed steps to reproduce the bug. + +Fix Bugs +~~~~~~~~ + +Look through the GitHub issues for bugs. Anything tagged with "bug" +is open to whoever wants to implement it. + +Implement Features +~~~~~~~~~~~~~~~~~~ + +Look through the GitHub issues for features. Anything tagged with "feature" +is open to whoever wants to implement it. + +Write Documentation +~~~~~~~~~~~~~~~~~~~ + +RiboPlot could always use more documentation, whether as part of the +official RiboPlot docs, in docstrings, or even on the web in blog posts, +articles, and such. + +Submit Feedback +~~~~~~~~~~~~~~~ + +The best way to send feedback is to file an issue at https://github.com/vimalkumarvelayudhan/riboplot/issues. + +If you are proposing a feature: + +* Explain in detail how it would work. +* Keep the scope as narrow as possible, to make it easier to implement. +* Remember that this is a volunteer-driven project, and that contributions + are welcome :) + +Get Started! +------------ + +Ready to contribute? Here's how to set up `riboplot` for local development. + +1. Fork the `riboplot` repo on GitHub. +2. Clone your fork locally:: + + $ git clone git@github.com:your_name_here/riboplot.git + +3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:: + + $ mkvirtualenv riboplot + $ cd riboplot/ + $ python setup.py develop + +4. Create a branch for local development:: + + $ git checkout -b name-of-your-bugfix-or-feature + + Now you can make your changes locally. + +5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:: + + $ flake8 riboplot tests + $ python setup.py test + $ tox + + To get flake8 and tox, just pip install them into your virtualenv. + +6. Commit your changes and push your branch to GitHub:: + + $ git add . + $ git commit -m "Your detailed description of your changes." + $ git push origin name-of-your-bugfix-or-feature + +7. Submit a pull request through the GitHub website. + +Pull Request Guidelines +----------------------- + +Before you submit a pull request, check that it meets these guidelines: + +1. The pull request should include tests. +2. If the pull request adds functionality, the docs should be updated. Put + your new functionality into a function with a docstring, and add the + feature to the list in README.rst. +3. The pull request should work for Python 2.6, 2.7, 3.3, and 3.4, and for PyPy. Check + https://travis-ci.org/vimalkumarvelayudhan/riboplot/pull_requests + and make sure that the tests pass for all supported Python versions. + +Tips +---- + +To run a subset of tests:: + + $ python -m unittest tests.test_riboplot \ No newline at end of file
--- a/docs/history.rst Wed Aug 12 16:28:43 2015 +0100 +++ b/docs/history.rst Thu Aug 13 15:03:20 2015 +0100 @@ -1,1 +1,9 @@ -../HISTORY.rst \ No newline at end of file +.. :changelog: + +History +======= + +0.1.0 (2015-08-05) +--------------------- + +* First release on PyPI.
--- a/docs/index.rst Wed Aug 12 16:28:43 2015 +0100 +++ b/docs/index.rst Thu Aug 13 15:03:20 2015 +0100 @@ -3,8 +3,8 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -Welcome to RiboPlot's documentation! -====================================== +RiboPlot documentation +====================== Contents:
--- a/docs/readme.rst Wed Aug 12 16:28:43 2015 +0100 +++ b/docs/readme.rst Thu Aug 13 15:03:20 2015 +0100 @@ -1,1 +1,28 @@ -../README.rst \ No newline at end of file +=============================== +RiboPlot +=============================== + +.. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg + :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot + +.. image:: https://img.shields.io/pypi/v/riboplot.svg + :target: https://pypi.python.org/pypi/riboplot + + +RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format). + +There are two programs in the package: + +**riboplot** + Plot and output read counts (csv) for a single transcript. + +**ribocount** + Output read counts for all transcripts in an alignment. + +For help on using these programs, please refer to :doc:`usage`. + + +Free software: BSD license. + +Documentation: https://riboplot.readthedocs.org. +
--- a/docs/usage.rst Wed Aug 12 16:28:43 2015 +0100 +++ b/docs/usage.rst Thu Aug 13 15:03:20 2015 +0100 @@ -2,6 +2,15 @@ Usage ======== -To use RiboPlot in a project:: +RiboPlot +-------- +Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM). - import riboplot \ No newline at end of file +Parameters +.......... +1. Ribo-Seq alignment file (sorted BAM) + A bowtie 1 + +RiboCount +--------- +
--- a/riboplot.egg-info/PKG-INFO Wed Aug 12 16:28:43 2015 +0100 +++ b/riboplot.egg-info/PKG-INFO Thu Aug 13 15:03:20 2015 +0100 @@ -17,25 +17,35 @@ :target: https://pypi.python.org/pypi/riboplot - Plot read counts of RiboSeq data from BAM format alignment files + RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format). - * Free software: BSD license - * Documentation: https://riboplot.readthedocs.org. + There are two programs in the package: + + **riboplot** + Plot and output read counts (csv) for a single transcript. - Features - -------- + **ribocount** + Output read counts for all transcripts in an alignment. + + For help on using these programs, please refer to :doc:`usage`. + - * TODO + Free software: BSD license. + + Documentation: https://riboplot.readthedocs.org. + + History - ------- + ======= 0.1.0 (2015-08-05) --------------------- * First release on PyPI. + Keywords: riboplot Platform: UNKNOWN Classifier: Development Status :: 2 - Pre-Alpha
--- a/riboplot.egg-info/SOURCES.txt Wed Aug 12 16:28:43 2015 +0100 +++ b/riboplot.egg-info/SOURCES.txt Thu Aug 13 15:03:20 2015 +0100 @@ -14,7 +14,9 @@ docs/index.rst docs/installation.rst docs/make.bat +docs/modules.rst docs/readme.rst +docs/riboplot.rst docs/todo.rst docs/usage.rst riboplot/__init__.py @@ -22,12 +24,12 @@ riboplot/ribocore.py riboplot/ribocount.py riboplot/riboplot.py +riboplot/riboplot_multi.py riboplot.egg-info/PKG-INFO riboplot.egg-info/SOURCES.txt riboplot.egg-info/dependency_links.txt riboplot.egg-info/not-zip-safe riboplot.egg-info/top_level.txt -tests/.test_riboplot.py.swp tests/__init__.py tests/test_riboplot.py tests/data/5hRPF.bam
--- a/riboplot/ribocore.py Wed Aug 12 16:28:43 2015 +0100 +++ b/riboplot/ribocore.py Thu Aug 13 15:03:20 2015 +0100 @@ -162,7 +162,7 @@ if transcript_name not in bam_file.references: raise ArgumentError('Transcript "{}" does not exist in BAM file'.format(transcript_name)) -def check_optional_arguments(ribo_file, rna_file=None, read_length=None, read_offset=None): +def check_optional_arguments(ribo_file, read_length=None, read_offset=None, rna_file=None): """Check all optional arguments.""" if rna_file: try:
--- a/riboplot/ribocount.py Wed Aug 12 16:28:43 2015 +0100 +++ b/riboplot/ribocount.py Thu Aug 13 15:03:20 2015 +0100 @@ -64,11 +64,11 @@ args.ribo_file, args.transcriptome_fasta, args.read_length, args.read_offset, args.output_path) logging.info('Checking if required arguments are valid...') - ribocore.check_required_arguments(ribo_file, transcriptome_fasta) + ribocore.check_required_arguments(ribo_file=ribo_file, transcriptome_fasta=transcriptome_fasta) logging.info('Done') logging.info('Checking if optional arguments are valid...') - ribocore.check_optional_arguments(ribo_file, read_length, read_offset) + ribocore.check_optional_arguments(ribo_file=ribo_file, read_length=read_length, read_offset=read_offset) logging.info('Done') if not os.path.exists(output_path):
--- a/riboplot/riboplot.py Wed Aug 12 16:28:43 2015 +0100 +++ b/riboplot/riboplot.py Thu Aug 13 15:03:20 2015 +0100 @@ -270,10 +270,12 @@ args.read_length, args.read_offset, args.output_path) logging.info('Checking if required arguments are valid...') - ribocore.check_required_arguments(ribo_file, transcriptome_fasta, transcript_name) + ribocore.check_required_arguments(ribo_file=ribo_file, transcriptome_fasta=transcriptome_fasta, + transcript_name=transcript_name) logging.info('Checking if optional arguments are valid...') - ribocore.check_optional_arguments(ribo_file, rna_file, read_length, read_offset) + ribocore.check_optional_arguments(ribo_file=ribo_file, read_length=read_length, read_offset=read_offset, + rna_file=rna_file) logging.info('Get ribo-seq read counts and total reads in Ribo-Seq...') bam_fileobj = pysam.AlignmentFile(ribo_file, 'rb')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_ribocount_sample.sh Thu Aug 13 15:03:20 2015 +0100 @@ -0,0 +1,4 @@ +#!/bin/bash +python riboplot/ribocount.py -b tests/data/5hRPFsorted.bam \ + -f tests/data/zebrafish.fna +
--- a/runtests.sh Wed Aug 12 16:28:43 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -#!/bin/bash -python -m unittest discover --verbose
--- a/tests/test_riboplot.py Wed Aug 12 16:28:43 2015 +0100 +++ b/tests/test_riboplot.py Thu Aug 13 15:03:20 2015 +0100 @@ -27,7 +27,7 @@ ['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', RNA_FILE]) save_path = os.environ['PATH'] os.environ['PATH'] = '' - self.assertRaises(OSError, ribocore.check_optional_arguments, args.ribo_file, args.rna_file) + self.assertRaises(OSError, ribocore.check_optional_arguments, ribo_file=args.ribo_file, rna_file=args.rna_file) os.environ['PATH'] = save_path def test_is_bam_valid(self): @@ -70,19 +70,19 @@ args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-l', '-1']) # invalid read length -1 self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments, - args.ribo_file, None, args.read_length) + ribo_file=args.ribo_file, read_length=args.read_length) args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-l', '100']) # invalid read length 100 self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments, - args.ribo_file, None, args.read_length) + ribo_file=args.ribo_file, read_length=args.read_length) def test_valid_read_offset(self): """Read offset should be positive.""" args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-s', '-1']) # invalid read offset -1 self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments, - args.ribo_file, None, None, args.read_offset) + ribo_file=args.ribo_file, read_offset=args.read_offset) def test_is_fasta_valid(self): """A valid FASTA file can be opened with pysam.FastaFile.""" @@ -116,7 +116,7 @@ # using transcriptome FASTA file as the invalid RNA file for test parser = riboplot.create_parser() args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', TRANSCRIPTOME_FASTA]) - self.assertRaises(ValueError, ribocore.check_optional_arguments, args.ribo_file, args.rna_file) + self.assertRaises(ValueError, ribocore.check_optional_arguments, ribo_file=args.ribo_file, rna_file=args.rna_file) class RiboPlotTestCase(unittest.TestCase):