Adding template files and updating setup.py

setup.py

@@ -1,57 +1,61 @@
-from setuptools import setup, find_packages
-import os
-
-requirements = [
-    'cobra',
-    'numpy',
-    'scipy',
-    'networkx>=2.1',
-    'python-libsbml',
-]
-
-try:
-    with open('README.rst') as handle:
-        description = handle.read()
-except:
-    description = ''
-datadir = os.path.join('metquest','example','data')
-datafiles = [(d, [os.path.join(d,f) for f in files])
-    for d, folders, files in os.walk(datadir)]
-
-setup(
-    name='metquest',
-    version='0.1.31',
-    packages=find_packages(),
-    project_urls={
-        'Source': 'https://github.com/RamanLab/metquest'
-    },
-
-    install_requires=requirements,
-    setup_requires=[],
-    scripts=['bin/metquest.sh'],
-    author='Aarthi Ravikrishnan',
-    author_email='aarthiravikrishnan@gmail.com',
-    description='MetQuest: Enumerating all possible biosynthetic pathways in metabolic networks ',
-    long_description=description,
-    license='LGPL/GPL v2+',
-    keywords='metabolism biology graph-theory pathways',
-    classifiers=[
-        'Development Status :: 4 - Beta',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: GNU Lesser General Public License v2'
-            ' or later (LGPLv2+)',
-        'License :: OSI Approved :: GNU General Public License v2'
-            ' or later (GPLv2+)',
-        'Operating System :: OS Independent',
-        'Programming Language :: Python :: 3.4',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-        'Topic :: Scientific/Engineering',
-        'Topic :: Scientific/Engineering :: Bio-Informatics'
-    ],
-    platforms='GNU/Linux, Mac OS X >= 10.7, Microsoft Windows >= 7',
-    data_files = datafiles,
-    include_package_data = True
-
-)
-
+from setuptools import setup, find_packages
+import os
+
+requirements = [
+    'cobra',
+    'numpy',
+    'scipy',
+    'networkx>=2.1',
+    'python-libsbml',
+    'seaborn',
+    'matplotlib',
+    'pandas',
+    'pyvis'
+]
+
+try:
+    with open('README.rst') as handle:
+        description = handle.read()
+except:
+    description = ''
+datadir = os.path.join('metquest','example','data')
+datafiles = [(d, [os.path.join(d,f) for f in files])
+    for d, folders, files in os.walk(datadir)]
+
+setup(
+    name='metquest',
+    version='2.0.0',
+    packages=find_packages(),
+    project_urls={
+        'Source': 'https://github.com/dinesh-kumar-k-b/metquest2.0.git'
+    },
+
+    install_requires=requirements,
+    setup_requires=[],
+    scripts=['bin/metquest.sh'],
+    author='Aarthi Ravikrishnan and Dinesh Kumar Kuppa Baskaran',
+    author_email='dineshmine7@gmail.com, aarthiravikrishnan@gmail.com',
+    description='MetQuest: Enumerating all possible biosynthetic pathways in metabolic networks ',
+    long_description=description,
+    license='LGPL/GPL v2+',
+    keywords='metabolism biology graph-theory pathways',
+    classifiers=[
+        'Development Status :: 4 - Beta',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: GNU Lesser General Public License v2'
+            ' or later (LGPLv2+)',
+        'License :: OSI Approved :: GNU General Public License v2'
+            ' or later (GPLv2+)',
+        'Operating System :: OS Independent',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Topic :: Scientific/Engineering',
+        'Topic :: Scientific/Engineering :: Bio-Informatics'
+    ],
+    platforms='GNU/Linux, Mac OS X >= 10.7, Microsoft Windows >= 7',
+    data_files = datafiles,
+    include_package_data = True
+
+)
+

template files/cofactors.txt

@@ -0,0 +1,69 @@
+h
+adp
+atp
+gdp
+gtp
+cdp
+ctp
+tdp
+ttp
+udp
+utp
+pi
+ppi
+mlthf
+ade
+adn
+fad
+fmn
+fadh2
+nad
+nadh
+nadp
+nadph
+dnad
+ca2
+cl
+cobalt2
+coa
+cu2
+cytd
+dcdp
+dcmp
+dctp
+dcyt
+csn
+ctp
+dad_2
+dadp
+datp
+dgdp
+dgtp
+dtdp
+dttp
+dudp
+dutp
+thymd
+fe2
+fe3
+fol
+gua
+gsn
+h2o
+h2co3
+k
+mg2
+mn2
+na1
+nh4
+no3
+no2
+thm
+thym
+ribflv
+ahcys
+amet
+so4
+ura
+uri
+zn2

template files/cofactors_modelseed.txt

@@ -0,0 +1,92 @@
+cpd00008
+cpd00018
+cpd00002
+cpd00052
+cpd00046
+cpd00096
+cpd00533
+cpd00206
+cpd00177
+cpd00115
+cpd00294
+cpd00356
+cpd00295
+cpd00296
+cpd00241
+cpd00358
+cpd00978 
+cpd00299
+cpd00038
+cpd00031
+cpd00126
+cpd00090
+cpd00114
+cpd00068
+cpd00977
+cpd00976
+cpd03704
+cpd00297
+cpd00298
+cpd00357
+cpd00014
+cpd00091
+cpd00062
+cpd00125
+cpd00024
+cpd00022
+cpd11493
+cpd00128
+cpd00182
+cpd00104
+cpd00063
+cpd00099
+cpd00149
+cpd00010
+cpd02083
+cpd00058
+cpd00367
+cpd00307
+cpd00438
+cpd00654
+cpd00277
+cpd00412
+cpd00015
+cpd10515
+cpd10516
+cpd00982
+cpd00050
+cpd00393
+cpd00207
+cpd00311
+cpd00067
+cpd00001
+cpd00242
+cpd00028
+cpd00205
+cpd00254
+cpd00030
+cpd00971
+cpd00003
+cpd00004
+cpd00006
+cpd00005
+cpd19013
+cpd00218
+cpd00355
+cpd00209
+cpd00075
+cpd00009
+cpd00012
+cpd00215
+cpd00220
+cpd00019
+cpd00017
+cpd00048
+cpd00305
+cpd00184
+cpd00151
+cpd15561
+cpd15560
+cpd00092
+cpd00249
+cpd00034

template files/seed_metabolite_file_template.txt

@@ -0,0 +1,6 @@
+metabolite1
+metabolite2
+metabolite3
+metabolite4
+metabolite5
+metabolite6

template files/template_for_cluster_file_homsi.csv

@@ -0,0 +1,6 @@
+Cluster,,,
+1,microbe1,,
+2,microbe2,microbe3,
+3,microbe4,microbe5,microbe6
+4,microbe7,,
+5,microbe8,microbe9,microbe10