[med-svn] [Git][med-team/tnseq-transit][master] 6 commits: New upstream version 2.3.4

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / tnseq-transit


Commits:
5393164d by Andreas Tille at 2019-01-30T14:50:36Z
New upstream version 2.3.4
- - - - -
0f0cdb1f by Andreas Tille at 2019-01-30T14:53:15Z
Update upstream source from tag 'upstream/2.3.4'

Update to upstream version '2.3.4'
with Debian dir 73d785446094a7db5206045938456260fa2c4ccd
- - - - -
4fb28f5c by Andreas Tille at 2019-01-30T14:53:15Z
New upstream version

- - - - -
7462ab49 by Andreas Tille at 2019-01-30T14:53:16Z
debhelper 12

- - - - -
98a2d8d5 by Andreas Tille at 2019-01-30T14:54:42Z
Standards-Version: 4.3.0

- - - - -
82f48dec by Andreas Tille at 2019-01-30T14:58:55Z
Upload to unstable

- - - - -


9 changed files:

- .gitignore
- CHANGELOG.md
- README.md
- debian/changelog
- debian/compat
- debian/control
- 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
 
 
 [![Build Status](https://travis-ci.org/mad-lab/transit.svg?branch=master)](https://travis-ci.org/mad-lab/transit)   [![Documentation Status](https://readthedocs.org/projects/transit/badge/?version=latest)](http://transit.readthedocs.io/en/latest/?badge=latest) 


=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+tnseq-transit (2.3.4-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper 12
+  * Standards-Version: 4.3.0
+
+ -- Andreas Tille <tille at debian.org>  Wed, 30 Jan 2019 15:54:42 +0100
+
 tnseq-transit (2.3.3-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/compat
=====================================
@@ -1 +1 @@
-11
+12


=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                dh-python,
                python-dev,
                python-setuptools,
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
                python-matplotlib,
                python-statsmodels,
                bwa
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/tnseq-transit
 Vcs-Git: https://salsa.debian.org/med-team/tnseq-transit.git
 Homepage: http://saclab.tamu.edu/essentiality/transit/


=====================================
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/compare/5a1ca0994808bbeb565d764dd3b885b70739ba1e...82f48dec3b16d59aeacccc2dd436896cf80a577e

-- 
View it on GitLab: https://salsa.debian.org/med-team/tnseq-transit/compare/5a1ca0994808bbeb565d764dd3b885b70739ba1e...82f48dec3b16d59aeacccc2dd436896cf80a577e
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