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BUG: Change taxa in compute_taxonomy_ratios.py

This list of taxa now refers to the paper's Figure 2. Previous list
referred to a different grouping of taxa.
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1 parent 3c23a00 commit f9b4da6647b2c049b9d57e8007e60a5bbf7344ce @ElDeveloper ElDeveloper committed Dec 8, 2015
Showing with 13 additions and 5 deletions.
  1. +1 −0 ChangeLog.md
  2. +12 −5 scripts/compute_taxonomy_ratios.py
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@@ -4,6 +4,7 @@ QIIME 1.9.1-dev (changes since 1.9.1 go here)
Bug fixes
---------
+* **Critical**: Fix incorrect list of taxa in ``compute_taxonomy_ratios.py``. **This was a serious bug that was encountered when users would call ``compute_taxonomy_ratios.py`` using the MD-index, custom ratios did not suffer from this bug. Any computations of the MD-index previously generated with that command should be re-run.**.
* Add ``--read_arguments_from_file`` to ``split_libraries_fastq.py``, thus preventing ``multiple_split_libraries_fastq.py`` from failing with an `Argument list too long error` when the number of input files is large, see [#2069](https://github.com/biocore/qiime/issues/2069).
* Fixed bug in start_parallel_jobs_slurm.py, which would cause jobs to not run if ``slurm_memory`` was specified in ``qiime_config``.
@@ -21,16 +21,23 @@
known_indices = {
'md': {'name': 'Microbial dysbiosis index',
'source': 'http://www.ncbi.nlm.nih.gov/pubmed/24629344',
- 'decreased': set(['g__Akkermansia',
+ 'decreased': set(['g__Dialister',
'g__Faecalibacterium',
'g__Ruminococcus',
+ 'g__Sutterella',
+ 'g__Rikenellaceae',
+ 'g__Parabacteroides',
'g__Bacteroides',
- 'g__Parabacteroides']),
+ 'g__Lachnospiraceae',
+ 'g__Coprococcus',
+ 'g__Erysipelotrichaceae',
+ 'g__Dorea',
+ 'g__Ruminococcaceae',
+ 'g__Oscillospira',
+ 'g__Bilophila']),
'increased': set(['g__Escherichia',
- 'g__Fusobacterium',
'g__Haemophilus',
- 'g__Aggregatibacter',
- 'g__Sutterella',
+ 'g__Fusobacterium',
'g__Veillonella'])}}
script_info = {}

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