Published November 17, 2017
| Version v0.3.1
Software
Open
CGATOxford/cgat: Bugfixes for Python 3
Authors/Creators
- 1. MRC
- 2. CGAT
- 3. University of Sheffield
- 4. Kennedy Institute of Rheumatology, University of Oxford
- 5. University of Oxford
Description
- 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; https://github.com/CGATOxford/cgat/pull/343
- update test_style.py to reflect new repository structure; https://github.com/CGATOxford/cgat/pull/345
- update test_import.py to reflect new repository structure; https://github.com/CGATOxford/cgat/commit/decc5ec0e93b4d2c05b6fa3793b5a73caf1fa8b9
- added script to perform Gene Set Enrichment Analysis; https://github.com/CGATOxford/cgat/pull/344
- updated scripts to work with Python 3.6; https://github.com/CGATOxford/cgat/pull/346
- bugfix bed2bed script; https://github.com/CGATOxford/cgat/pull/349; https://github.com/CGATOxford/cgat/issues/347
- bugfix GTF.py module file; https://github.com/CGATOxford/cgat/issues/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; https://github.com/CGATOxford/cgat/pull/348
- refactor CGAT/PipelineGWAS.py to CGAT/GWAS.py; https://github.com/CGATOxford/cgat/pull/354
- removed unused imports with autoflakes; https://github.com/CGATOxford/cgat/pull/355
- removed basestr, use str instead in Python 3; https://github.com/CGATOxford/cgat/pull/359
- added test for csv2db; https://github.com/CGATOxford/cgat/pull/360
- fixed rename_transcripts test for gtf2gtf.py; https://github.com/CGATOxford/cgat/pull/361
- updated installation; https://github.com/CGATOxford/cgat/pull/364 ; https://github.com/CGATOxford/cgat/pull/373
- updated documentation; https://github.com/CGATOxford/cgat/pull/365 ; https://github.com/CGATOxford/cgat/pull/367
- replaced bx.bbi.bigwig_file with pyBigWig ; https://github.com/CGATOxford/cgat/pull/369
- updated Expression.py to iterate over pandas dataframe; https://github.com/CGATOxford/cgat/pull/370
- updated Expression.py to work with DESeq2 > 1.16 ; https://github.com/CGATOxford/cgat/pull/371
- moved bed_vs_bed.py to obsolete ; https://github.com/CGATOxford/cgat/pull/372
Files
CGATOxford/cgat-v0.3.1.zip
Files
(205.6 MB)
| Name | Size | Download all |
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md5:a58358ef5343458ffb3305201b6d2dd7
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Additional details
Related works
- Is supplement to
- https://github.com/CGATOxford/cgat/tree/v0.3.1 (URL)