1.5.0 (#36)

* Created setup.py and MANIFEST.in

* Now setup.py and scoary --test work from anywhere

* Version 1.5.0

-Scoary is now installable by pip: pip install git+https://github.com/AdmiralenOla/Scoary.git
-This installs scoary as an executable in your PATH. scoary.py is deprecated

* 1.5.0

* Give a warning message that scoary.py is deprecated when ran directly.

* Fixed indentation

* Change version

* Added filtration options output

* 1.5.0 changes

MANIFEST.in

@@ -0,0 +1 @@
+graft scoary/exampledata

README.md

@@ -24,6 +24,10 @@ Scoary is designed to take the gene_presence_absence.csv file from [Roary] (http
 - [Contact] (#contact)
 
 ## What's new?
+v1.5.0 (13th Sep 2016)
+- Scoary is now installable via pip! (Thanks go to Anders Goncalves da Silva). The scoary.py script will now be deprecated, but is still available for legacy use. See [Installation] (#installation)
+- The program now also prints out the filtration options being used for the current analysis.
+
 v1.4.2 (13th Sep 2016)
 - Fixed a bug that would cause Scoary to crash if ran without any -c options.
 
@@ -113,6 +117,20 @@ v1.1 (29th Mar 2016)
 
 ## Installation
 
+The easiest way to install Scoary is through the pip package manager:
+
+    pip install git+https://github.com/AdmiralenOla/Scoary.git
+
+OR, if you need a local (user) installation:
+
+    pip install --user git+https://github.com/AdmiralenOla/Scoary.git
+
+Finally, to specify a local directory in your user installation:
+
+    pip install --user --install-option="--install-scripts=$HOME/bin" git+https://github.com/AdmiralenOla/Scoary.git
+
+##### Legacy installation
+
 Scoary is a standalone python script and does not require any installation. Simply download and extract the zip archive or clone the git repository:
 
     git clone https://github.com/AdmiralenOla/Scoary
@@ -125,7 +143,11 @@ If you want to add it to your $PATH variable:
 
 ## Usage
 
-    scoary.py -g gene_presence_absence.csv -t traits.csv
+    scoary -g <gene_presence_absence.csv> -t <traits.csv>
+
+##### Legacy usage
+
+    scoary.py -g <gene_presence_absence.csv> -t <traits.csv>
 
 ## Input
 Scoary requires two input files: The gene_presence_absence.csv file from [Roary] (https://sanger-pathogens.github.io/Roary/) and a list of traits to test associations to. 
@@ -346,6 +368,7 @@ Please feel free to suggest improvements, point out bugs or methods that could b
 
 ## Acknowledgements
 - Marco Galardini cleaned my code and made many nifty improvements.
+- Anders Goncalves da Silva made Scoary installable by pip
 - The QuadTree and UPGMA implementation was heavily based on code by Christian Storm Pedersen.
 - Inês Mendes pointed out a number of bugs related adjusted p-values and isolate restriction.
 - Eric Deveaud added versioning.

scoary.py

@@ -19,4 +19,7 @@
 from scoary import methods
 
 if __name__ == '__main__':
+    print("Warning. Since 1.5.0 scoary.py is deprecated. " \
+    "Install Scoary using 'pip install git+https://github.com/AdmiralenOla/" \
+    "Scoary.git' instead")
     methods.main()

scoary/__init__.py

@@ -1 +1 @@
-__version__ = '1.4.2'
+__version__ = '1.5.0'

scoary/methods.py

@@ -18,6 +18,9 @@
 from .classes import PhyloTree
 import scoary
 
+import os
+from pkg_resources import resource_string, resource_filename
+
 SCOARY_VERSION = scoary.__version__
 
 # Python 2/3 annoyances
@@ -139,12 +142,12 @@ def main():
     if args.test:
         args.correction = ['I','EPW']
         args.delimiter = ','
-        args.genes = './exampledata/Gene_presence_absence.csv'
+        args.genes = os.path.join(resource_filename(__name__, 'exampledata'), 'Gene_presence_absence.csv')
         args.max_hits = None
         args.p_value_cutoff = [0.05]
         args.restrict_to = None
         args.start_col = 15
-        args.traits = './exampledata/Tetracycline_resistance.csv'
+        args.traits = os.path.join(resource_filename(__name__, 'exampledata'), 'Tetracycline_resistance.csv')
         args.upgma_tree = True
         args.write_reduced = False
         args.no_time = False
@@ -203,6 +206,7 @@ def main():
         traitsdic = Csv_to_dic(traits, args.delimiter, allowed_isolates)
 
         print("Finished loading files into memory.")
+        print(filtrationoptions(cutoffs))
         print("Tallying genes and performing statistical analyses")
 
         RES_and_GTC = Setup_results(genedic, traitsdic)
@@ -726,6 +730,12 @@ def StoreUPGMAtreeToFile(upgmatree, no_time=False):
         Tree = Tree.replace("]", ")")
         treefile.write(Tree)
         print("Wrote the UPGMA tree to file: %s" % treefilename)
+
+def filtrationoptions(cutoffs):
+    translation = {"I": "Individual (Naive)", "B": "Bonferroni", "BH":"Benjamini-Hochberg",
+                   "PW":"Pairwise comparison (Best)", "EPW": "Pairwise comparison (Entire range)"}
+    filters = [str(translation[k]) + ":    " + str(v) for k,v in cutoffs.items()] 
+    return "Filtration options: \n" + "\n".join(filters)
 
 if __name__ == '__main__':
     pass

setup.py

@@ -0,0 +1,38 @@
+
+from setuptools import setup
+
+
+def readme():
+    with open('README.md') as f:
+        return f.read()
+
+
+setup(name='Scoary',
+      version='1.5.0',
+      description='Microbial pan-GWAS using the output from Roary',
+      long_description=readme(),
+      classifiers=[
+        'Development Status :: 4 - Beta',
+        'License :: OSI Approved :: GPLv3',
+        'Programming Language :: Python :: 2.7',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering :: Medical Science Apps.',
+        'Intended Audience :: Science/Research',
+      ],
+      keywords='microbial genomics GWAS Roary',
+      url='https://github.com/AdmiralenOla/Scoary',
+      author='Ola Brynildsrud',
+      author_email='[email protected]',
+      license='GPLv3',
+      packages=['scoary'],
+      install_requires=[
+          'scipy>=0.16',
+          'argparse'
+      ],
+      test_suite='nose.collector',
+      tests_require=[],
+      entry_points={
+          'console_scripts': ['scoary=scoary.methods:main'],
+      },
+      include_package_data=True,
+      zip_safe=False)