Merge branch 'master' into release/1.0.1

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 "#-----------------------------------------------#"
@@ -202,15 +205,15 @@ release_doc:
 	@ git push
 
 
-release_pip_unix:
+release_pip_unix: 
 	@ echo "#-----------------------------------------------#"
 	@ echo "# Creating manylinux compliant package (pip)    #"
 	@ echo "#-----------------------------------------------#"
 	@rm -rf /tmp/tmp                                            ; \
  	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

changelog.md

@@ -1,5 +1,24 @@
 # Changelog
 
+## v1.0.0
+
+### Bug Fixes
+
+- Fix --no-strandness in divergent.
+
+### API Changes
+
+### Code changes
+
+- 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
 
 ### Bug Fixes

conda/env_read_the_doc.yaml

@@ -1,19 +1,15 @@
 name: pygtftk
 
 channels:
-#    - conda-forge
-    - defaults
     - bioconda
     - auto
-    
+
 dependencies:
     - bedtools ==2.27.1
-    - python ==3.5
     - pyBigWig >=0.3.12
     - pybedtools >=0.7.8
     - sphinx_bootstrap_theme >=0.4.9
     - sphinxcontrib-programoutput >=0.8
- #   - pyproj
     - pyyaml
     - nose
     - numpy >=1.10.0

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
 

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.

pygtftk/plugins/ologram.py

@@ -32,21 +32,21 @@
 __updated__ = "2019-03-18"
 __doc__ = """
 
- OLOGRAM -- OverLap Of Genomic Regions Analysis using Monte Carlo
+ 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).
 
- 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.
-
- 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
  total lengths (in basepairs) of all intersections.
 
- Authors : Quentin Ferré <[email protected]> and Denis Puthier <[email protected]>
+ Authors : Quentin Ferré <[email protected]> and Denis Puthier <[email protected]>.
  """
 
 __notes__ = """

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'

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.
 

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 = [email protected]