From 33e5bb559dce68463381552590fa0e6f3f0656d8 Mon Sep 17 00:00:00 2001 From: Your Name Date: Tue, 19 Mar 2019 11:17:23 +0100 Subject: [PATCH 01/10] updated changelog --- changelog.md | 18 ++++++++++++++++++ pygtftk/plugins/ologram.py | 11 ++++++----- 2 files changed, 24 insertions(+), 5 deletions(-) diff --git a/changelog.md b/changelog.md index d440c87f..9346f31d 100644 --- a/changelog.md +++ b/changelog.md @@ -1,5 +1,23 @@ # Changelog +## v1.0.0 + +### Bug Fixes + + + +### API Changes + + +### Code changes + +- Many typo detected. + +### 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. + + ## v0.9.10 ### Bug Fixes diff --git a/pygtftk/plugins/ologram.py b/pygtftk/plugins/ologram.py index 76b1837b..89684903 100644 --- a/pygtftk/plugins/ologram.py +++ b/pygtftk/plugins/ologram.py @@ -34,13 +34,14 @@ OLOGRAM -- OverLap Of Genomic Regions Analysis using Monte Carlo - Annotate peaks (in bed format) with region sets/features computed on the - fly from a GTF file (e.g promoter, tts, gene body, UTR...). Custom features - are supported. + Ologram annotate peaks (in bed format) with (i) genomic features extracted + from a GTF file (e.g promoter, tts, gene body, UTR...) (ii) genomic regions tagged with + particular keys/values in a GTF file (e.g. gene_biotype "protein_coding", + gene_biotype "LncRNA"...) or (iii) from a BED file (e.g. user-defined regions). - Each couple peak file/feature is randomly shuffled across the genome (inter-region + Each couple peak file/region is randomly shuffled across the genome (inter-region lengths are considered). Then the probability of intersection under the null - hypothesis (the peaks and this feature are independant) is deduced thanks to + hypothesis (the peaks and this feature are independent) is deduced thanks to this Monte Carlo approach. The program will return statistics for both the number of intersections and the From 091334aafe994f1770711aeaaaec5996d8987d6f Mon Sep 17 00:00:00 2001 From: Your Name Date: Tue, 19 Mar 2019 11:17:47 +0100 Subject: [PATCH 02/10] Change help in ologram.py --- pygtftk/plugins/ologram.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/pygtftk/plugins/ologram.py b/pygtftk/plugins/ologram.py index 89684903..faa7ffcc 100644 --- a/pygtftk/plugins/ologram.py +++ b/pygtftk/plugins/ologram.py @@ -32,9 +32,8 @@ __updated__ = "2019-03-18" __doc__ = """ - OLOGRAM -- OverLap Of Genomic Regions Analysis using Monte Carlo - - Ologram annotate peaks (in bed format) with (i) genomic features extracted + OLOGRAM -- OverLap Of Genomic Regions Analysis using Monte Carlo. Ologram + annotates peaks (in bed format) using (i) genomic features extracted from a GTF file (e.g promoter, tts, gene body, UTR...) (ii) genomic regions tagged with particular keys/values in a GTF file (e.g. gene_biotype "protein_coding", gene_biotype "LncRNA"...) or (iii) from a BED file (e.g. user-defined regions). @@ -47,7 +46,7 @@ The program will return statistics for both the number of intersections and the total lengths (in basepairs) of all intersections. - Authors : Quentin Ferré and Denis Puthier + Authors : Quentin Ferré and Denis Puthier . """ __notes__ = """ From 169fab3803fdc7817c20f520ee7f2c0ab3af2ffa Mon Sep 17 00:00:00 2001 From: Your Name Date: Tue, 19 Mar 2019 11:26:52 +0100 Subject: [PATCH 03/10] Increase the default number of cpus for sphinx --- docs/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Makefile b/docs/Makefile index cb225f86..e12304f1 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line. SPHINXOPTS = -SPHINXBUILD = sphinx-build -j 3 +SPHINXBUILD = sphinx-build -j 8 PAPER = BUILDDIR = build From 4ab99e916af2e4aebf81aec22909b9d3e59188a2 Mon Sep 17 00:00:00 2001 From: Your Name Date: Tue, 19 Mar 2019 11:47:34 +0100 Subject: [PATCH 04/10] Trying to fix error 247 from rtfd (as usual). --- conda/env_read_the_doc.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/conda/env_read_the_doc.yaml b/conda/env_read_the_doc.yaml index 47408913..f9f45a63 100644 --- a/conda/env_read_the_doc.yaml +++ b/conda/env_read_the_doc.yaml @@ -1,8 +1,6 @@ name: pygtftk channels: -# - conda-forge - - defaults - bioconda - auto @@ -13,7 +11,6 @@ dependencies: - pybedtools >=0.7.8 - sphinx_bootstrap_theme >=0.4.9 - sphinxcontrib-programoutput >=0.8 - # - pyproj - pyyaml - nose - numpy >=1.10.0 From 7b073fa5855f89e52e5c1169e8918aa8ae190cea Mon Sep 17 00:00:00 2001 From: Your Name Date: Tue, 19 Mar 2019 11:52:33 +0100 Subject: [PATCH 05/10] Trying to fix error 247 from rtfd (as usual). --- conda/env_read_the_doc.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda/env_read_the_doc.yaml b/conda/env_read_the_doc.yaml index f9f45a63..6ff42a30 100644 --- a/conda/env_read_the_doc.yaml +++ b/conda/env_read_the_doc.yaml @@ -6,7 +6,7 @@ channels: dependencies: - bedtools ==2.27.1 - - python ==3.5 + - python ==3.6 - pyBigWig >=0.3.12 - pybedtools >=0.7.8 - sphinx_bootstrap_theme >=0.4.9 From 7839475fb6cc015b703abb64b78b19d9955a5dab Mon Sep 17 00:00:00 2001 From: Your Name Date: Tue, 19 Mar 2019 12:09:58 +0100 Subject: [PATCH 06/10] Trying to fix error 247 from rtfd (as usual). --- conda/env_read_the_doc.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/conda/env_read_the_doc.yaml b/conda/env_read_the_doc.yaml index 6ff42a30..91912678 100644 --- a/conda/env_read_the_doc.yaml +++ b/conda/env_read_the_doc.yaml @@ -3,10 +3,9 @@ name: pygtftk channels: - bioconda - auto - + dependencies: - bedtools ==2.27.1 - - python ==3.6 - pyBigWig >=0.3.12 - pybedtools >=0.7.8 - sphinx_bootstrap_theme >=0.4.9 From 8b44d4b5ac2c928e77dbad5dd808f7c8fa088561 Mon Sep 17 00:00:00 2001 From: Your Name Date: Tue, 19 Mar 2019 14:02:18 +0100 Subject: [PATCH 07/10] Updated Roadmap --- roadmap.md | 1 - 1 file changed, 1 deletion(-) diff --git a/roadmap.md b/roadmap.md index 0142a872..2fa27752 100644 --- a/roadmap.md +++ b/roadmap.md @@ -5,5 +5,4 @@ Below are the short-mid term objectives of the next release. - Integrate blast to gtf (already available in libgtftk). - Resurrect heatmap that was abandonned due to limits of matplot 2k layout. -- Ressurect ologram that was part of the original program but is currently being improved regarding statistical tests. From a77e78ad19e8264afd69cc99570f30e6597904a1 Mon Sep 17 00:00:00 2001 From: Your Name Date: Tue, 19 Mar 2019 14:51:36 +0100 Subject: [PATCH 08/10] updated changelog --- changelog.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/changelog.md b/changelog.md index 9346f31d..823b4ac1 100644 --- a/changelog.md +++ b/changelog.md @@ -4,19 +4,20 @@ ### Bug Fixes - +- Fix --no-strandness in divergent. ### API Changes - ### Code changes -- Many typo detected. +- 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. +- 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 From b71fbb955bf60bea98620c0c32540eb63c5fcb14 Mon Sep 17 00:00:00 2001 From: Your Name Date: Tue, 19 Mar 2019 14:54:15 +0100 Subject: [PATCH 09/10] Bumped version 1.0.1 --- docs/source/conf.py | 4 ++-- pygtftk/version.py | 4 ++-- setup.cfg | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index e776f22f..09f2b5e8 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -55,10 +55,10 @@ # built documents. # # The short X.Y version. -version = u'1.0.0' +version = u'1.0.1' # The full version, including alpha/beta/rc tags. -release = u'1.0.0' +release = u'1.0.1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/pygtftk/version.py b/pygtftk/version.py index 72541b12..7c6ec2ed 100644 --- a/pygtftk/version.py +++ b/pygtftk/version.py @@ -1,2 +1,2 @@ -__base_version__='1.0.0' -__version__='1.0.0' +__base_version__='1.0.1' +__version__='1.0.1' diff --git a/setup.cfg b/setup.cfg index 7c319e61..f7c57a42 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = pygtftk -version = 1.0.0 +version = 1.0.1 author = D. Puthier and F. Lopez author-email = denis.puthier@univ-amu.fr From 9aa331370e04f63a597edaed5e0793dc48f57b2b Mon Sep 17 00:00:00 2001 From: Your Name Date: Tue, 19 Mar 2019 15:11:40 +0100 Subject: [PATCH 10/10] Updated Makefile --- Makefile | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/Makefile b/Makefile index 1ef0a8ea..729790de 100644 --- a/Makefile +++ b/Makefile @@ -52,6 +52,7 @@ doc: @cd docs/; make html -j 4; cd ../..; @echo ">>>> Docs is available in: docs/build/html/index.html" + pylint: @find . -name "*.py" -exec pylint $(PYLINT_ARGS) {} \; @@ -142,8 +143,10 @@ nb_test: # Creating a release #------------------------------------------------------------------ +__check_defined_VER: + @[ "$(VER)" ] || ( echo ">> VER is not set"; exit 1 ) -release: +release: __check_defined_VER @ echo "#-----------------------------------------------#" @ echo "# Starting the release $(VER) #" @ echo "#-----------------------------------------------#" @@ -202,7 +205,7 @@ release_doc: @ git push -release_pip_unix: +release_pip_unix: @ echo "#-----------------------------------------------#" @ echo "# Creating manylinux compliant package (pip) #" @ echo "#-----------------------------------------------#" @@ -210,7 +213,7 @@ release_pip_unix: rm -f manylinux/pygtftk-*whl ; \ cd manylinux ; \ docker rmi -f manylinux ; \ - docker stop imanylinux || true && docker rm -f imanylinux || true ; \ ;\ + docker rm -f imanylinux || true ; \ ;\ docker build -t manylinux . ; \ docker create -t --name imanylinux manylinux /bin/bash ; \ docker cp imanylinux:/tmp/ /tmp ; \ @@ -221,13 +224,13 @@ release_pip_unix: echo "Manylinux wheels should be in wheels folder." ; \ echo "Have a look at log in wheels/log and upload user twine if OK." -release_pip_osx: +release_pip_osx: release_bump @ echo "#-----------------------------------------------#" @ echo "# Creating osx compliant package (pip) #" @ echo "#-----------------------------------------------#" + @ mkdir -p wheels @rm -rf dist build; python setup.py bdist_wheel ; \ - cd dist ; \ - mv *whl ../wheels ; \ + cp dist/*whl wheels ; \ cd ..; rm -rf dist build release_pip: release_pip_unix release_pip_osx