Bugfixes for Python 3
·
33 commits
to master
since this release
- bugfix cgat CLI
- added scripts to help find R and Python dependencies: scripts/cgat_deps_R.sh, scripts/cgat_deps_python.sh
- modified install script to use conda environment files instead of conda meta-packages; #343
- update test_style.py to reflect new repository structure; #345
- update test_import.py to reflect new repository structure; decc5ec
- added script to perform Gene Set Enrichment Analysis; #344
- updated scripts to work with Python 3.6; #346
- bugfix bed2bed script; #349; #347
- bugfix GTF.py module file; #350
- various bugfixes for Python 3 problems when running pipeline_annotations in python 3, plus a modification of the new "assembly report" section to allow genomes without a standard assembly report (e.g. yeast) to be processed; #348
- refactor CGAT/PipelineGWAS.py to CGAT/GWAS.py; #354
- removed unused imports with autoflakes; #355
- removed basestr, use str instead in Python 3; #359
- added test for csv2db; #360
- fixed rename_transcripts test for gtf2gtf.py; #361
- updated installation; #364 ; #373
- updated documentation; #365 ; #367
- replaced bx.bbi.bigwig_file with pyBigWig ; #369
- updated Expression.py to iterate over pandas dataframe; #370
- updated Expression.py to work with DESeq2 > 1.16 ; #371
- moved bed_vs_bed.py to obsolete ; #372