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Giovanni Marco Dall'Olio committed 6935e21

DOCS: added a description to argparse

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Files changed (3)

logs/upload_pypi.log

 running upload
 Submitting dist/vcf2networks-1.0.8.tar.gz to http://pypi.python.org/pypi
 Server response (200): OK
+/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'entry_points'
+  warnings.warn(msg)
+/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
+  warnings.warn(msg)
+running sdist
+running check
+warning: sdist: manifest template 'MANIFEST.in' does not exist (using default file list)
+
+warning: sdist: standard file not found: should have one of README, README.txt
+
+writing manifest file 'MANIFEST'
+creating vcf2networks-1.0.8b
+creating vcf2networks-1.0.8b/src
+creating vcf2networks-1.0.8b/test
+making hard links in vcf2networks-1.0.8b...
+hard linking README.rst -> vcf2networks-1.0.8b
+hard linking setup.cfg -> vcf2networks-1.0.8b
+hard linking setup.py -> vcf2networks-1.0.8b
+hard linking src/GenotypeNetwork.py -> vcf2networks-1.0.8b/src
+hard linking src/__init__.py -> vcf2networks-1.0.8b/src
+hard linking src/binary_to_network.py -> vcf2networks-1.0.8b/src
+hard linking src/cosi_to_binary.py -> vcf2networks-1.0.8b/src
+hard linking src/custom_exceptions.py -> vcf2networks-1.0.8b/src
+hard linking src/filteredvcf_to_binary.py -> vcf2networks-1.0.8b/src
+hard linking src/generate_network_report.py -> vcf2networks-1.0.8b/src
+hard linking src/get_gene_coords.py -> vcf2networks-1.0.8b/src
+hard linking src/get_genotypes_from_1000Genomes.py -> vcf2networks-1.0.8b/src
+hard linking src/get_simulations_background.py -> vcf2networks-1.0.8b/src
+hard linking src/vcf2networks.py -> vcf2networks-1.0.8b/src
+hard linking test/test_AveragePathLenghtCalculation.py -> vcf2networks-1.0.8b/test
+hard linking test/test_BinaryToNetwork.py -> vcf2networks-1.0.8b/test
+hard linking test/test_CosiToBinary.py -> vcf2networks-1.0.8b/test
+hard linking test/test_GenotypeNetwork.py -> vcf2networks-1.0.8b/test
+hard linking test/test_GenotypeNetworkDistance.py -> vcf2networks-1.0.8b/test
+hard linking test/test_GenotypeNetworkIndividuals.py -> vcf2networks-1.0.8b/test
+hard linking test/test_GetGenotypes.py -> vcf2networks-1.0.8b/test
+hard linking test/test_ReadFromGraphml.py -> vcf2networks-1.0.8b/test
+hard linking test/test_Report.py -> vcf2networks-1.0.8b/test
+hard linking test/test_ReportAdvancedFeatures.py -> vcf2networks-1.0.8b/test
+hard linking test/test_ReportByNode.py -> vcf2networks-1.0.8b/test
+hard linking test/test_ReportWindows.py -> vcf2networks-1.0.8b/test
+hard linking test/test_SimulationsBackground.py -> vcf2networks-1.0.8b/test
+hard linking test/test_SubgraphByPop.py -> vcf2networks-1.0.8b/test
+hard linking test/test_SubgraphByPopFromFile.py -> vcf2networks-1.0.8b/test
+hard linking test/test_ValuesByNodeReport.py -> vcf2networks-1.0.8b/test
+hard linking test/test_Vcf2Binary.py -> vcf2networks-1.0.8b/test
+hard linking test/test_commandline_options.py -> vcf2networks-1.0.8b/test
+Creating tar archive
+removing 'vcf2networks-1.0.8b' (and everything under it)
+running upload
+Submitting dist/vcf2networks-1.0.8b.tar.gz to http://pypi.python.org/pypi
+Upload failed (400): A file named "vcf2networks-1.0.8b.tar.gz" already exists for  vcf2networks-1.0.8b. To fix problems with that file you should create a new release.
+/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'entry_points'
+  warnings.warn(msg)
+/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
+  warnings.warn(msg)
+running sdist
+running check
+warning: sdist: manifest template 'MANIFEST.in' does not exist (using default file list)
+
+warning: sdist: standard file not found: should have one of README, README.txt
+
+writing manifest file 'MANIFEST'
+creating vcf2networks-1.0.8c
+creating vcf2networks-1.0.8c/src
+creating vcf2networks-1.0.8c/test
+making hard links in vcf2networks-1.0.8c...
+hard linking README.rst -> vcf2networks-1.0.8c
+hard linking setup.cfg -> vcf2networks-1.0.8c
+hard linking setup.py -> vcf2networks-1.0.8c
+hard linking src/GenotypeNetwork.py -> vcf2networks-1.0.8c/src
+hard linking src/__init__.py -> vcf2networks-1.0.8c/src
+hard linking src/binary_to_network.py -> vcf2networks-1.0.8c/src
+hard linking src/cosi_to_binary.py -> vcf2networks-1.0.8c/src
+hard linking src/custom_exceptions.py -> vcf2networks-1.0.8c/src
+hard linking src/filteredvcf_to_binary.py -> vcf2networks-1.0.8c/src
+hard linking src/generate_network_report.py -> vcf2networks-1.0.8c/src
+hard linking src/get_gene_coords.py -> vcf2networks-1.0.8c/src
+hard linking src/get_genotypes_from_1000Genomes.py -> vcf2networks-1.0.8c/src
+hard linking src/get_simulations_background.py -> vcf2networks-1.0.8c/src
+hard linking src/vcf2networks.py -> vcf2networks-1.0.8c/src
+hard linking test/test_AveragePathLenghtCalculation.py -> vcf2networks-1.0.8c/test
+hard linking test/test_BinaryToNetwork.py -> vcf2networks-1.0.8c/test
+hard linking test/test_CosiToBinary.py -> vcf2networks-1.0.8c/test
+hard linking test/test_GenotypeNetwork.py -> vcf2networks-1.0.8c/test
+hard linking test/test_GenotypeNetworkDistance.py -> vcf2networks-1.0.8c/test
+hard linking test/test_GenotypeNetworkIndividuals.py -> vcf2networks-1.0.8c/test
+hard linking test/test_GetGenotypes.py -> vcf2networks-1.0.8c/test
+hard linking test/test_ReadFromGraphml.py -> vcf2networks-1.0.8c/test
+hard linking test/test_Report.py -> vcf2networks-1.0.8c/test
+hard linking test/test_ReportAdvancedFeatures.py -> vcf2networks-1.0.8c/test
+hard linking test/test_ReportByNode.py -> vcf2networks-1.0.8c/test
+hard linking test/test_ReportWindows.py -> vcf2networks-1.0.8c/test
+hard linking test/test_SimulationsBackground.py -> vcf2networks-1.0.8c/test
+hard linking test/test_SubgraphByPop.py -> vcf2networks-1.0.8c/test
+hard linking test/test_SubgraphByPopFromFile.py -> vcf2networks-1.0.8c/test
+hard linking test/test_ValuesByNodeReport.py -> vcf2networks-1.0.8c/test
+hard linking test/test_Vcf2Binary.py -> vcf2networks-1.0.8c/test
+hard linking test/test_commandline_options.py -> vcf2networks-1.0.8c/test
+Creating tar archive
+removing 'vcf2networks-1.0.8c' (and everything under it)
+running upload
+Submitting dist/vcf2networks-1.0.8c.tar.gz to http://pypi.python.org/pypi
+Server response (200): OK
 
-__version__ = '1.0.8'
+__version__ = '1.0.8c'
 
 
 

src/vcf2networks.py

 #!/usr/bin/env python
 """
-This script takes as input a VCF file, and generates a report of the Genotype Network properties from it.
+VCF2Networks is a python script that allows to calculate Genotype Networks from a Variant Call Format (VCF) file.
+
+Read more about it, and follow the tutorial, at https://bitbucket.org/dalloliogm/vcf2networks
 
 
 """
 from __init__ import __version__
 
 def get_options():
-    parser = argparse.ArgumentParser(#            description=__doc__,
+    parser = argparse.ArgumentParser(description=__doc__,
             formatter_class=argparse.ArgumentDefaultsHelpFormatter,
             prog="vcf2networks")
 #    config_group = argparse.OptionGroup(parser, "Configuration options. Required")
             help='File containing the classification of individuals into populations. This must be a tab-separated file, in which the first column is the individual ID, the second is the population, the third is the continental group (or other classification), and the other columns contain classification in phenotypes, one per column. This can also defined in the parameters file (--config). Required.', 
             default="")
     config_group.add_argument('-c', '--config', '--params', dest='params_file', 
-            help='File containing many parameters of the analysis. In particular, the list of network properties that will be included in the output report. Required.', 
+            help='File containing many parameters of the analysis. In particular, the list of network properties that will be included in the output report. This option is not mandatory, but if it is not defined, a warning message will be shown.', 
             default=False)
     config_group.add_argument('-p', '--property', '--phenotype', dest='phenotype', 
             help='Phenotype column used to define the Genotype Networks (e.g. population, disease status, eye color, etc..). When this option is defined, the output will consist of one line for the global population, plus one line for each Genotype Network built using only individuals having the same phenotype.',