[med-svn] [Git][med-team/tnseq-transit][upstream] New upstream version 2.3.3
Andreas Tille
gitlab at salsa.debian.org
Tue Dec 18 16:53:32 GMT 2018
Andreas Tille pushed to branch upstream at Debian Med / tnseq-transit
Commits:
2707cb28 by Andreas Tille at 2018-12-18T15:54:26Z
New upstream version 2.3.3
- - - - -
12 changed files:
- CHANGELOG.md
- README.md
- setup.py
- src/pytransit/__init__.py
- src/pytransit/analysis/hmm.py
- src/pytransit/analysis/normalize.py
- src/pytransit/analysis/tnseq_stats.py
- src/pytransit/doc/source/tpp.rst
- src/pytransit/doc/source/transit_methods.rst
- src/pytransit/doc/source/transit_overview.rst
- src/pytransit/export/combined_wig.py
- src/pytransit/tnseq_tools.py
Changes:
=====================================
CHANGELOG.md
=====================================
@@ -1,6 +1,10 @@
# Change log
All notable changes to this project will be documented in this file.
+## Version 2.3.3 2018-12-06
+- TRANSIT:
+ - Minor bug fixes related to flags in HMM
+
## Version 2.3.2 2018-11-09
- TRANSIT:
- Minor bug fixes related to changing parameters in TPP GUI
=====================================
README.md
=====================================
@@ -1,12 +1,17 @@
-# TRANSIT 2.3.2
+# TRANSIT 2.3.3
[](https://travis-ci.org/mad-lab/transit) [](http://transit.readthedocs.io/en/latest/?badge=latest)
-Welcome! This is the distribution for the TRANSIT and TPP tools developed by the Ioerger Lab.
+Welcome! This is the distribution for the TRANSIT and TPP tools developed by the Ioerger Lab at Texas A&M University.
-TRANSIT is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.
+TRANSIT is a tool for processing and statistical analysis of Tn-Seq data.
+It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.
+
+TRANSIT Home page: http://saclab.tamu.edu/essentiality/transit/index.html
+
+TRANSIT Documentation: https://transit.readthedocs.io/en/latest/transit_overview.html
[Changelog](https://github.com/mad-lab/transit/blob/master/CHANGELOG.md)
@@ -42,7 +47,7 @@ For any questions or comments, please contact Dr. Thomas Ioerger, ioerger at cs.tam
For full instructions on how to install and run TRANSIT (and the optional pre-processor, TPP), please see the documentation included in this distribution ("src/pytransit/doc" folder) or visit the following web page:
-http://saclab.tamu.edu/essentiality/transit/transit.html
+https://transit.readthedocs.io/en/latest/
## Datasets
=====================================
setup.py
=====================================
@@ -6,10 +6,13 @@ https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
-from setuptools import setup, find_packages
+from setuptools import setup, find_packages, Command
# To use a consistent encoding
from codecs import open
from os import path
+from shutil import rmtree
+
+import os
here = path.abspath(path.dirname(__file__))
@@ -22,7 +25,68 @@ with open(path.join(here, 'README.md'), encoding='utf-8') as f:
import sys
sys.path.insert(1, "src/")
import pytransit
-version = pytransit.__version__[1:] #"2.0.3"
+version = pytransit.__version__[1:]
+
+class UploadCommand(Command):
+ """Support setup.py upload."""
+
+ description = 'Build and publish the package.'
+ user_options = []
+
+ @staticmethod
+ def status(s):
+ """Prints things in bold."""
+ print('\033[1m{0}\033[0m'.format(s))
+
+ def initialize_options(self):
+ pass
+
+ def finalize_options(self):
+ pass
+
+ def yes_or_no(self, question):
+ while True:
+ reply = str(raw_input(question +' (y/n): ')).lower().strip()
+ if reply == 'y':
+ return True
+ return False
+
+ def run(self):
+ try:
+ self.status('Removing previous builds...')
+ rmtree(os.path.join(here, 'dist'))
+ except OSError:
+ pass
+
+ if not self.yes_or_no("Have you done the following? \n" +
+ "- Updated README/Documentation?\n"
+ "- Have you updated CHANGELOG?\n"
+ "- Have you updated Transit Essentiality page?\n"
+ "- Is version v{0} correct".format(version)):
+ self.status("Exiting...")
+ sys.exit()
+
+ self.status('Building Source and Wheel (universal) distribution...')
+ os.system('{0} setup.py sdist bdist_wheel'.format(sys.executable))
+
+ if self.yes_or_no("Add tag and push to public github? tag:v{0}".format(version)):
+ self.status('Adding and pushing git tags to origin and public...')
+ os.system('git tag v{0}'.format(version))
+ os.system('git push origin --tags')
+ os.system('git push https://github.com/mad-lab/transit')
+ os.system('git push https://github.com/mad-lab/transit --tags')
+ else:
+ self.status("Exiting...")
+ sys.exit()
+
+ if self.yes_or_no("Proceed with publish to PyPI? version: v{0}, tag:v{0}".format(version)):
+ self.status('Uploading the package to PyPI via Twine...')
+ os.system('twine upload dist/*')
+ else:
+ self.status("Exiting...")
+ sys.exit()
+
+ sys.exit()
setup(
name='tnseq-transit',
@@ -117,5 +181,8 @@ setup(
'tpp=pytpp.__main__:run_main',
],
},
+ cmdclass={
+ 'upload': UploadCommand,
+ },
)
=====================================
src/pytransit/__init__.py
=====================================
@@ -2,6 +2,6 @@
__all__ = ["transit_tools", "tnseq_tools", "norm_tools", "stat_tools"]
-__version__ = "v2.3.2"
+__version__ = "v2.3.3"
prefix = "[TRANSIT]"
=====================================
src/pytransit/analysis/hmm.py
=====================================
@@ -257,7 +257,7 @@ class HMMMethod(base.SingleConditionMethod):
output_file = open(outpath, "w")
replicates = kwargs.get("r", "Mean")
- normalization = kwargs.get("r", "TTR")
+ normalization = kwargs.get("n", "TTR")
LOESS = kwargs.get("l", False)
ignoreCodon = True
NTerminus = float(kwargs.get("iN", 0.0))
@@ -430,6 +430,7 @@ class HMMMethod(base.SingleConditionMethod):
Optional Arguments:
-r <string> := How to handle replicates. Sum, Mean. Default: -r Mean
+ -n <string> := Normalization method. Default: -n TTR
-l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Off.
-iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0
-iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0
=====================================
src/pytransit/analysis/normalize.py
=====================================
@@ -101,6 +101,7 @@ class NormalizeMethod(base.SingleConditionMethod):
self.infile = args[0] # only 1 input wig file
self.outfile = args[1] # if no arg give, could print to screen
self.normalization = kwargs.get("n", "TTR") # check if it is a legal method name
+ self.combined_wig = kwargs.get("c",False)
return self(self.infile,self.outfile,self.normalization)
@@ -117,15 +118,20 @@ class NormalizeMethod(base.SingleConditionMethod):
for line in open(infile):
if line.startswith("variableStep"): line2 = line.rstrip(); break
- (data, sites) = tnseq_tools.get_data(self.ctrldata)
+ if self.combined_wig==True: (sites,data,files) = tnseq_tools.read_combined_wig(self.ctrldata[0])
+ else: (data, sites) = tnseq_tools.get_data(self.ctrldata)
(data,factors) = norm_tools.normalize_data(data,self.normalization)
print "writing",outputPath
file = open(outputPath,"w")
file.write("# %s normalization of %s\n" % (self.normalization,infile))
- file.write(line2+"\n")
- for j in range(len(sites)):
- file.write("%s %s\n" % (sites[j],int(data[0,j])))
+ if self.combined_wig==True:
+ for f in files: file.write("#File: %s\n" % f)
+ for i in range(len(sites)): file.write('\t'.join([str(sites[i])]+["%0.1f" % x for x in list(data[...,i])])+"\n")
+ else:
+ file.write(line2+"\n")
+ for j in range(len(sites)):
+ file.write("%s %s\n" % (sites[j],int(data[0,j])))
file.close()
self.finish()
@@ -134,9 +140,10 @@ class NormalizeMethod(base.SingleConditionMethod):
@classmethod
def usage_string(self):
return """
-python %s normalize <input.wig> <output.wig> [-n TTR|betageom]
+python %s normalize <input.wig> <output.wig> [-c] [-n TTR|betageom]
Optional Arguments:
+ -c := the input file is a combined_wig file
-n <string> := Normalization method. Default: -n TTR
""" % (sys.argv[0])
=====================================
src/pytransit/analysis/tnseq_stats.py
=====================================
@@ -122,7 +122,7 @@ class TnseqStatsMethod(base.SingleConditionMethod):
for i in range(data.shape[0]):
density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis = tnseq_tools.get_data_stats(data[i,:])
nzmedianrd = int(nzmedianrd) if numpy.isnan(nzmedianrd)==False else 0
- vals = [datasets[i], "%0.2f" % density, "%0.1f" % meanrd, "%0.1f" % nzmeanrd, "%d" % nzmedianrd, maxrd, totalrd, "%0.1f" % skew, "%0.1f" % kurtosis]
+ vals = [datasets[i], "%0.2f" % density, "%0.1f" % meanrd, "%0.1f" % nzmeanrd, "%d" % nzmedianrd, maxrd, int(totalrd), "%0.1f" % skew, "%0.1f" % kurtosis]
file.write('\t'.join([str(x) for x in vals])+'\n')
if self.outfile!=None: file.close()
=====================================
src/pytransit/doc/source/tpp.rst
=====================================
@@ -1,7 +1,7 @@
-Overview
-========
+TPP Overview
+============
TPP is a software tool for processing raw reads (e.g. .fastq files,
*untrimmed*) from an Tn-Seq experiment, extracting counts of transposon
=====================================
src/pytransit/doc/source/transit_methods.rst
=====================================
@@ -868,12 +868,15 @@ Example
> python src/transit.py normalize --help
- usage: python src/transit.py normalize <input.wig> <output.wig> [-n TTR|betageom]
+ usage: python src/transit.py normalize <input.wig> <output.wig> [-c] [-n TTR|betageom]
> python src/transit.py normalize Rv_1_H37RvRef.wig Rv_1_H37RvRef_TTR.wig -n TTR
> python src/transit.py normalize Rv_1_H37RvRef.wig Rv_1_H37RvRef_BG.wig -n betageom
+The normalize command now also works on combined_wig files too.
+If the input file is a combined_wig file, add the '-c' flag at the end.
+
.. _combined_wig:
Combined wig files
=====================================
src/pytransit/doc/source/transit_overview.rst
=====================================
@@ -2,8 +2,8 @@
-Overview
-========
+TRANSIT Overview
+================
+ This is a software that can be used to analyze Tn-Seq datasets. It includes various statistical calculations of essentiality of genes or genomic regions (including conditional essentiality between 2 conditions). These methods were developed and tested as a collaboration between the Sassetti lab (UMass) and the Ioerger lab (Texas A&M) [DeJesus2015TRANSIT]_.
@@ -108,14 +108,15 @@ own primer sequences, if they use a different sample prep protocol.
Developers
----------
-================== ============ ==============================================================================
- Name Time Active Contact Information
-================== ============ ==============================================================================
-Michael A. DeJesus 2015-Present `http://mad-lab.org <http://mad-lab.org>`_
-Thomas R. Ioerger 2015-Present `http://faculty.cs.tamu.edu/ioerger/ <http://faculty.cs.tamu.edu/ioerger/>`_
-Chaitra Ambadipudi 2015
-Eric Nelson 2016
-================== ============ ==============================================================================
+======================= ============ ==============================================================================
+ Name Time Active Contact Information
+======================= ============ ==============================================================================
+Thomas R. Ioerger 2015-Present `http://faculty.cs.tamu.edu/ioerger/ <http://faculty.cs.tamu.edu/ioerger/>`_
+Michael A. DeJesus 2015-2018 `http://mad-lab.org <http://mad-lab.org>`_
+Chaitra Ambadipudi 2015
+Eric Nelson 2016
+Siddharth Subramaniyam 2018
+======================= ============ ==============================================================================
=====================================
src/pytransit/export/combined_wig.py
=====================================
@@ -195,7 +195,7 @@ class CombinedWigMethod(base.SingleConditionMethod):
@classmethod
def usage_string(self):
- return """python %s export combined_wig <comma-separated .wig files> <annotation .prot_table> <output file>""" % (sys.argv[0])
+ return """python %s export combined_wig <comma-separated .wig files> <annotation .prot_table> <output file> [-n normalization_method]\ndefault normalization_method=TTR""" % (sys.argv[0])
if __name__ == "__main__":
=====================================
src/pytransit/tnseq_tools.py
=====================================
@@ -28,23 +28,30 @@ def rv_siteindexes_map(genes, TASiteindexMap):
RvSiteindexesMap[gene["rv"]] = siteindexes
return RvSiteindexesMap
+# format:
+# header lines (prefixed by '#'), followed by lines with counts
+# counts lines contain the following columns: TA coord, counts, other info like gene/annotation
+# for each column of counts, there must be a header line prefixed by "#File: " and then an id or filename
+
def read_combined_wig(fname):
"""
Read the combined wig-file generated by Transit
- :: Filename -> Tuple([Site], [[WigData]])
- Site :: [Integer]
+ :: Filename -> Tuple([Site], [WigData], [Filename])
+ Site :: Integer
WigData :: [Integer]
+ Filename :: String
"""
sites,countsByWig,files = [],[],[]
with open(fname) as f:
lines = f.readlines()
for line in lines:
- if line.startswith("#File:"):
+ if line.startswith("#File: "):
files.append(line.split()[1])
countsByWig = [[] for _ in files]
for line in lines:
if line[0]=='#': continue
- cols = line.split("\t")[0:-1]
+ cols = line.split("\t")[0:1+len(files)]
+ cols = cols[:1+len(files)] # additional columns at end could contain gene info
# Read in position as int, and readcounts as float
cols = map(lambda (i, v): int(v) if i == 0 else float(v), enumerate(cols))
position, wigCounts = cols[0], cols[1:]
View it on GitLab: https://salsa.debian.org/med-team/tnseq-transit/commit/2707cb289c1324ea6c6786942cce9079927fbcb5
--
View it on GitLab: https://salsa.debian.org/med-team/tnseq-transit/commit/2707cb289c1324ea6c6786942cce9079927fbcb5
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