Merge branch 'release/1.0.5'

CODE_OF_CONDUCT.md

@@ -14,21 +14,21 @@ appearance, race, religion, or sexual identity and orientation.
 Examples of behavior that contributes to creating a positive environment
 include:
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+  * Using welcoming and inclusive language
+  * Being respectful of differing viewpoints and experiences
+  * Gracefully accepting constructive criticism
+  * Focusing on what is best for the community
+  * Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or
+  * The use of sexualized language or imagery and unwelcome sexual attention or
  advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic
+  * Trolling, insulting/derogatory comments, and personal or political attacks
+  * Public or private harassment
+  * Publishing others' private information, such as a physical or electronic
  address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
+  * Other conduct which could reasonably be considered inappropriate in a
  professional setting
 
 ## Our Responsibilities

Makefile

@@ -206,6 +206,7 @@ release_doc:
 	@ cp  docs/source/example*png docs/build/html/_static
 	@ cp  docs/source/example*pdf docs/build/html/_static
 	@ cp  -r docs/build/html/* docs
+	@ make clean
 	@ git add docs/*
 	@ git commit -m "Updated img in source and source/_static "
 	@ git push

README.rst

@@ -1,8 +1,8 @@
-
 =================         =================
 Pip package               |Pippackage|_
 Platforms                 |platform|_
 License                   |license|_
+Languages                 |lang|_
 Build status              |build|_
 Repository size           |size|_
 Conda                     |conda|_
@@ -15,7 +15,7 @@ Citing                    |citing|_
 Documentation             |documentation|_
 =================         =================
 
-.. |license| image:: https://img.shields.io/github/license/mashape/apistatus.svg
+.. |license| image:: https://img.shields.io/github/license/dputhier/pygtftk.svg
 .. _license: https://github.com/dputhier/pygtftk
 
 .. |pippackage| image:: https://badge.fury.io/py/pygtftk.svg
@@ -51,12 +51,14 @@ Documentation             |documentation|_
 .. |issues| image:: https://img.shields.io/github/issues-raw/dputhier/pygtftk.svg
 .. _issues: https://github.com/dputhier/pygtftk/issues
 
-.. |citing| image:: https://img.shields.io/badge/doi-https%3A%2F%2Fdoi.org%2F10.1093%2Fbioinformatics%2Fbtz116-blue.svg
+.. |citing| image:: https://img.shields.io/badge/pygtftk-https%3A%2F%2Fdoi.org%2F10.1093%2Fbioinformatics%2Fbtz116-blue.svg
 .. _citing: https://doi.org/10.1093/bioinformatics/btz116
 
 .. |documentation| image:: https://img.shields.io/badge/Documentation-https%3A%2F%2Fdputhier.github.io%2Fpygtftk%2F-blue.svg
 .. _documentation: https://dputhier.github.io/pygtftk/
 
+.. |lang| image:: https://img.shields.io/badge/Languages-Python%2C%20Cython%2C%20C-blue.svg
+.. _lang: https://github.com/dputhier/pygtftk
 
 
 Python GTF toolkit (pygtftk)
@@ -77,8 +79,8 @@ Depending on the **size of the GTF file**, pygtftk and gtftk may require lot of
 
 At the moment, the gtftk program has been tested on:
 
-- Linux (Ubuntu 12.04 and 18.04)
-- OSX (Yosemite, El Capitan, Mojave).
+  - Linux (Ubuntu 12.04 and 18.04)
+  - OSX (Yosemite, El Capitan, Mojave).
 
 
 Installation

changelog.md

@@ -1,8 +1,30 @@
 # Changelog
 
+This version provides several improvements and bug fix to ologram. The CLI of mk_matrix and join_multi_file have slightly changed. An int ([0-4]) is now mandatory to control verbosity level.
+
+## v1.0.5
+
+### Bug Fixes
+
+  - Fix #76 (issue with chromosomes in ensembl format when using ologram).
+  - Fix #72 (P-values equal to zero when nb_intersections_true and nb_intersections_esperance_shuffled are equal to zero).
+
+### API Changes
+
+### Code changes
+
+  - Improved p-value precision in ologram.
+
+### New Features
+
+  - Added -j/--sort-features to ologram. Controls the feature sorting in barplot diagram. Changed doc accordingly.
+  - The positional argument 'bigwiglist' in mk_matrix has been replaced by -y.
+  - The verbosity argument now must take a value (0-4).
+  - The positional argument in join_multi_file has been replaced by -m.
+
 ## v1.0.4
 
-- Updated changelog
+  - Updated changelog
 
 ### Bug Fixes
 
@@ -14,79 +36,79 @@
 
 ## v1.0.3
 
-- Improved p-value precision in ologram.
+  - Improved p-value precision in ologram.
 
 ### Bug Fixes
 
 ### API Changes
 
 ### Code changes
 
-- Improved p-value precision in ologram.
-- Added mpmath as dependency.
+  - Improved p-value precision in ologram.
+  - Added mpmath as dependency.
 
 ### New Features
 
-- Added tiny_real dataset.
-- Added -q argument (--quiet) to get_example.
+  - Added tiny_real dataset.
+  - Added -q argument (--quiet) to get_example.
 
 ## v1.0.2
 
-- No more using readthedoc as the doc is becoming too long to process.
+  - No more using readthedoc as the doc is becoming too long to process.
 
 ### Bug Fixes
 
 ### API Changes
 
 ### Code changes
 
-- Many typo detected and fixed.
+  - Many typo detected and fixed.
 
 ### New Features
 
-- Added tiny_real dataset.
-- Added -q argument (--quiet) to get_example.
+  - Added tiny_real dataset.
+  - Added -q argument (--quiet) to get_example.
 
 ## v1.0.0
 
 ### Bug Fixes
 
-- Fix --no-strandness in divergent.
+  - Fix --no-strandness in divergent.
 
 ### API Changes
 
 ### Code changes
 
-- Many typo detected and fixed.
+  - Many typo detected and fixed.
 
 ### New Features
 
-- This version now integrates ologram (OverLap Of Genomic Regions Analysis using Monte Carlo). Ologram annotates peaks (in BED format) with region sets/features extracted from (i) GTF file features (e.g promoter, tts, gene body, UTR...) (ii) GTF file keys (e.g. gene_biotype, user defined keys...) (iii) or from a BED file.
+  - This version now integrates ologram (OverLap Of Genomic Regions Analysis using Monte Carlo). Ologram annotates peaks (in BED format) with region sets/features extracted from (i) GTF file features (e.g promoter, tts, gene body, UTR...) (ii) GTF file keys (e.g. gene_biotype, user defined keys...) (iii) or from a BED file.
 
-- The user can now use --chrom-info to provide the command with a file or a string. The string should be one of 'mm8', 'mm9', 'mm10', 'hg19', 'hg38', 'rn3' or 'rn4'. When a genome version is requested as a string, the conventional chromosomes are used (chrM is discarded together with alternative haplotypes, unlocalized regions...).
+  - The user can now use --chrom-info to provide the command with a file or a string. The string should be one of 'mm8', 'mm9', 'mm10', 'hg19', 'hg38', 'rn3' or 'rn4'. When a genome version is requested as a string, the conventional chromosomes are used (chrM is discarded together with alternative haplotypes, unlocalized regions...).
 
 
 ## v0.9.10
 
 ### Bug Fixes
 
-- Argparse was part of the dependencies. However, argparse is part of Python 3. Thus, this caused pygtftk to come with an older version of argparse...
-- Fixed gene sorting in tss_dict to ensure reproducible result.
-- Fixed a problem with retrieve() when used from interpreter (#45).
-- The load_gtf() function (C API) no raise an error if a GFF3 is passed with .gtf extension.
+  - Argparse was part of the dependencies. However, argparse is part of Python 3. Thus, this caused pygtftk to come with an older version of argparse...
+  - Fixed gene sorting in tss_dict to ensure reproducible result.
+  - Fixed a problem with retrieve() when used from interpreter (#45).
+  - The load_gtf() function (C API) no raise an error if a GFF3 is passed with .gtf extension.
 
 
 ### API Changes
 
-- Input BED file in bed3 format are now converted to bed6 automatically.
-- The select_by_numeric() function has been renamed eval_numeric()
-- It is now possible to use numpy array of booleans to index the GTF (i.e. using the indexing function).	
-- the prepare_gffutils_db() function allows one to create a db for gffutils while selecting features and attributes.
+  - Input BED file in bed3 format are now converted to bed6 automatically.
+  - The select_by_numeric() function has been renamed eval_numeric()
+  - It is now possible to use numpy array of booleans to index the GTF (i.e. using the indexing function).	
+  - the prepare_gffutils_db() function allows one to create a db for gffutils while selecting features and attributes.
 
 ### Code changes
 
-- The argformatter module was refactored. Development of FormattedFile(argparse.FileType) that test for file extension and content (at least for bed).
-- The BED conversion is now performed using the print_bed() C function .
+  - The argformatter module was refactored. Development of FormattedFile(argparse.FileType) that test for file extension and content (at least for bed).
+  - The BED conversion is now performed using the print_bed() C function .
 
 ### New Features
 
@@ -96,68 +118,65 @@
 
 ### Bug Fixes
 
-- Fix a critical bug in get_sequence that affected get_feat_seq and get_tx_seq.
-- Select_by_key now throw an error when no key/val are available.
-- No more function with mutable objects as default arguments.
-- Fix temporary file deletion. 
+  - Fix a critical bug in get_sequence that affected get_feat_seq and get_tx_seq.
+  - Select_by_key now throw an error when no key/val are available.
+  - No more function with mutable objects as default arguments.
+  - Fix temporary file deletion. 
 
 ### API Changes
 
-- Refactored arg_formatter by  creating a single type (ranged_num) to test for numeric inputs.
-- Refactored all plugins so that there is no more reference to unused arguments (tmp_dir, verbosity...).
+  - Refactored arg_formatter by  creating a single type (ranged_num) to test for numeric inputs.
+  - Refactored all plugins so that there is no more reference to unused arguments (tmp_dir, verbosity...).
 
 
 ### Code changes
 
-- No more reference to PY2.
-- Added several test to get_tx_seq and get_feat_seq.
-- Added several script to manipulate fasta files (see 'tools' folder). For pygtftk dev.
-- Added 'extra_require' slot in setup().
-- The get-feature-seq program now relies on bedtools (not on internal C code). This may change in the future asa a more flexible C interface is available.
+  - No more reference to PY2.
+  - Added several test to get_tx_seq and get_feat_seq.
+  - Added several script to manipulate fasta files (see 'tools' folder). For pygtftk dev.
+  - Added 'extra_require' slot in setup().
+  - The get-feature-seq program now relies on bedtools (not on internal C code). This may change in the future asa a more flexible C interface is available.
 
 ### New Features
 
-- Added --list-bigwigs to profile (to display the content of a coverage file).
-- Added a novel dataset	(mini_real_10M) derived from mini_real and containing 10 Mb of chr1.
-- The configuration directory now supports several subdirectories named based on a hash string computed from path to the gtftk program.
+  - Added --list-bigwigs to profile (to display the content of a coverage file).
+  - Added a novel dataset	(mini_real_10M) derived from mini_real and containing 10 Mb of chr1.
+  - The configuration directory now supports several subdirectories named based on a hash string computed from path to the gtftk program.
 
 
 ## v0.9.8
 
 ### Bug Fixes
 
-- Convergent and divergent return coordinate (e.g. dist_to_divergent) in integer not float...
+  - Convergent and divergent return coordinate (e.g. dist_to_divergent) in integer not float...
 
 ### API Changes
 
-- pygtftk is no more compatible with python 2. This decision aims at integrating last plotnine versions (starting from 0.5.1) that depends on matplotlib 3.0.0 which strictly depends on py3k.
+  - pygtftk is no more compatible with python 2. This decision aims at integrating last plotnine versions (starting from 0.5.1) that depends on matplotlib 3.0.0 which strictly depends on py3k.
 
 ### New Features
 
-- Added an example for col_from_tab in presentation.rst
-- Added a dataset mini_real_coding_pot.tab.
-- Working on travis now.
-- gtftk configuration directory now contains several subdirectories whose names are computed based on gtftk program location.
-- Added a -d argument to gtftk program. This argument returns gtftk configuration directory. 
-- All tests should be independent of the directory.
-- Added test to count_key_values.
+  - Added an example for col_from_tab in presentation.rst
+  - Added a dataset mini_real_coding_pot.tab.
+  - Working on travis now.
+  - gtftk configuration directory now contains several subdirectories whose names are computed based on gtftk program location.
+  - Added a -d argument to gtftk program. This argument returns gtftk configuration directory. 
+  - All tests should be independent of the directory.
+  - Added test to count_key_values.
 
 ## v0.9.7
 
 ### Bug Fixes
 
-- Fixed a bug in add_attr_from_file. The arg has_header led to empty result.
-- Fixed a bug in select_by_reg_exp. The match method was used instead of search method...
-- Fixed an error in count_key_values. 
+  - Fixed a bug in add_attr_from_file. The arg has_header led to empty result.
+  - Fixed a bug in select_by_reg_exp. The match method was used instead of search method...
+  - Fixed an error in count_key_values. 
 
 ### API Changes
 
 ### New Features
 
-- Several changes in doc to make it compliant with readthedoc.
-
-
-# Changelog
+  - Several changes in doc to make it compliant with readthedoc.
 
 ## v0.9.6
 
@@ -167,7 +186,7 @@
 
 ### New Features
 
-- Several changes in setup.py and requirements_develops.txt to makes it compliant with Pypi and buildable with manylinux.
+  - Several changes in setup.py and requirements_develops.txt to makes it compliant with Pypi and buildable with manylinux.
 
 
 ## v0.9.5
@@ -178,28 +197,28 @@
 
 ### New Features
 
-- Several changes in setup.py and requirements_develops.txt to makes it compliant with Pypi and buildable with manylinux.
+  - Several changes in setup.py and requirements_develops.txt to makes it compliant with Pypi and buildable with manylinux.
 
 ## v0.9.3
 
 ### Bug Fixes
 
-- User-defined colors are now applied when calling profile command (bug in 0.9.2).
-- Fixed test issues when using md5sum under Linux.
-- Lots of typo fixed (their must be lot remaining unfortunatly...).
+  - User-defined colors are now applied when calling profile command (bug in 0.9.2).
+  - Fixed test issues when using md5sum under Linux.
+  - Lots of typo fixed (their must be lot remaining unfortunatly...).
 
 ### API Changes
 
 
 ### New Features
 
-- pygtftk is now compatible with both python 2.7 and >=3.5.
-- libstdcxx is no more required in env.yaml.
-- 'Makefile clean' also reset version.py and conf.py to repository version.
-- Improved parser loading.
-- 5p_3p_coord has been renamed get_5p_3p_coords.
-- Added a pip requirement.txt file for developers.
-- Added a specific conda environment file for py2k.
-- The default conda environment targets Python 3.6.
-- Improve garbage collector behavior upon exit.
-- Added --system-info argument to gtftk.
+  - pygtftk is now compatible with both python 2.7 and >=3.5.
+  - libstdcxx is no more required in env.yaml.
+  - 'Makefile clean' also reset version.py and conf.py to repository version.
+  - Improved parser loading.
+  - 5p_3p_coord has been renamed get_5p_3p_coords.
+  - Added a pip requirement.txt file for developers.
+  - Added a specific conda environment file for py2k.
+  - The default conda environment targets Python 3.6.
+  - Improve garbage collector behavior upon exit.
+  - Added --system-info argument to gtftk.