Commit 5393164d authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.3.4

parent 2707cb28

.gitignore

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# # Mac

.DS_STORE

.env



# Byte-compiled / optimized / DLL files

__pycache__/

*.py[cod]

CHANGELOG.md

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# 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

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# 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)

src/pytransit/__init__.py

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@@ -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

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@@ -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)