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 [](https://travis-ci.org/mad-lab/transit) [](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 <[email protected]> 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 <[email protected]. Uploaders: Andreas Tille <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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