[med-svn] [Git][med-team/tnseq-transit][upstream] New upstream version 2.3.4
Andreas Tille
gitlab at salsa.debian.org
Wed Jan 30 15:10:23 GMT 2019
Andreas Tille pushed to branch upstream at Debian Med / tnseq-transit
Commits:
5393164d by Andreas Tille at 2019-01-30T14:50:36Z
New upstream version 2.3.4
- - - - -
6 changed files:
- .gitignore
- CHANGELOG.md
- README.md
- src/pytransit/__init__.py
- src/pytransit/analysis/hmm.py
- src/pytransit/analysis/resampling.py
Changes:
=====================================
.gitignore
=====================================
@@ -1,3 +1,7 @@
+# # Mac
+.DS_STORE
+.env
+
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
=====================================
CHANGELOG.md
=====================================
@@ -1,6 +1,10 @@
# Change log
All notable changes to this project will be documented in this file.
+## Version 2.3.4 2019-01-14
+- TRANSIT:
+ - Minor bug fixes related to flags in Resampling and HMM
+
## Version 2.3.3 2018-12-06
- TRANSIT:
- Minor bug fixes related to flags in HMM
=====================================
README.md
=====================================
@@ -1,4 +1,4 @@
-# TRANSIT 2.3.3
+# TRANSIT 2.3.4
[](https://travis-ci.org/mad-lab/transit) [](http://transit.readthedocs.io/en/latest/?badge=latest)
=====================================
src/pytransit/__init__.py
=====================================
@@ -2,6 +2,6 @@
__all__ = ["transit_tools", "tnseq_tools", "norm_tools", "stat_tools"]
-__version__ = "v2.3.3"
+__version__ = "v2.3.4"
prefix = "[TRANSIT]"
=====================================
src/pytransit/analysis/hmm.py
=====================================
@@ -226,6 +226,7 @@ class HMMMethod(base.SingleConditionMethod):
normalization = wxobj.hmmNormChoice.GetString(wxobj.hmmNormChoice.GetCurrentSelection())
LOESS = False
+ LOESS = wxobj.hmmLoessCheck.GetValue()
#Get output path
name = transit_tools.basename(ctrldata[0])
@@ -377,6 +378,8 @@ class HMMMethod(base.SingleConditionMethod):
self.output.write("# \n")
self.output.write("# Mean:\t%2.2f\n" % (numpy.average(reads_nz)))
self.output.write("# Median:\t%2.2f\n" % numpy.median(reads_nz))
+ self.output.write("# Normalization:\t%s\n" % self.normalization)
+ self.output.write("# LOESS Correction:\t%s\n" % str(self.LOESS))
self.output.write("# pins (obs):\t%f\n" % pins_obs)
self.output.write("# pins (est):\t%f\n" % pins)
self.output.write("# Run length (r):\t%d\n" % r)
=====================================
src/pytransit/analysis/resampling.py
=====================================
@@ -219,6 +219,7 @@ class ResamplingMethod(base.DualConditionMethod):
base.DualConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, ctrldata, expdata, annotation_path, output_file, normalization=normalization, replicates=replicates, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+ self.Z = False
self.samples = samples
self.adaptive = adaptive
self.doHistogram = doHistogram
@@ -316,7 +317,6 @@ class ResamplingMethod(base.DualConditionMethod):
includeZeros = not excludeZeros
pseudocount = float(kwargs.get("pc", 0.00))
- self.Z = False
if "Z" in kwargs: self.Z = True
LOESS = kwargs.get("l", False)
View it on GitLab: https://salsa.debian.org/med-team/tnseq-transit/commit/5393164db100874de45ce4f503825be59a3c251e
--
View it on GitLab: https://salsa.debian.org/med-team/tnseq-transit/commit/5393164db100874de45ce4f503825be59a3c251e
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