diff --git a/ariaec/commands.py b/ariaec/commands.py
index ad37ce5fdb528f7a3d5f265e0e79a177e3e674aa..13786b437c9b5f0a776eb42e8b2993e820cabf3b 100644
--- a/ariaec/commands.py
+++ b/ariaec/commands.py
@@ -1,3 +1,4 @@
+# coding=utf-8
"""
Input/Output aria_ec
"""
@@ -17,7 +18,10 @@ LOG = logging.getLogger(__name__)
def check_file(prospective_file):
+ """
+ :param prospective_file:
+ """
if not os.path.exists(prospective_file):
raise argp.ArgumentTypeError("readable_file:'{0}' is not a valid "
"path".format(prospective_file))
@@ -27,6 +31,9 @@ def check_file(prospective_file):
class ReadableFile(argp.Action):
+ """
+ Class used with argparse action to check if a file is readable
+ """
def __init__(self, *args, **kwargs):
super(ReadableFile, self).__init__(*args, **kwargs)
@@ -42,7 +49,7 @@ class ReadableFile(argp.Action):
# TODO: Make parent Command class with _create_argparser, self.args,
# update_logger and run
-class AriaEcCommand:
+class AriaEcCommand(object):
"""
Argparse interface for aria_ec
"""
@@ -84,7 +91,8 @@ class AriaEcCommand:
formatter_class=argp.ArgumentDefaultsHelpFormatter)
parser.add_argument("-o", "--output", dest="output_directory",
type=str, help="Output directory", required=True)
- parser.add_argument("-c", "--conf", action=ReadableFile, dest="conf_file",
+ parser.add_argument("-c", "--conf", action=ReadableFile,
+ dest="conf_file",
default=None, help="configuration file")
parser.add_argument("--nolog", action="store_true",
default=False, help="Don't generate log files")
@@ -100,8 +108,9 @@ class AriaEcCommand:
"""
for index, command in enumerate(self.command_list):
# Create subparser defined in command list
- subcommand = getattr(self, "_" + command + "_parser")(desc=self.desc_list[
- index])
+ subcommand = getattr(self, "_" + command + "_parser")(
+ desc=self.desc_list[
+ index])
parser.add_parser(command, parents=[subcommand])
def _setup_parser(self, desc=None):
@@ -202,6 +211,10 @@ class AriaEcCommand:
return parser
def create_settings(self):
+ """
+ create settings relative to args.command
+ :return:
+ """
LOG.debug("Create AriaEcSettings")
settings = AriaEcSettings(self.args.command)
LOG.info("Loading default config file")
@@ -218,20 +231,30 @@ class AriaEcCommand:
return settings
def run(self):
- # call method relative to args.command
+ """
+ call method relative to args.command
+ """
LOG.info("Run %s command", self.args.command)
getattr(self, self.args.command)()
def setup(self):
+ """
+ Setup call
+ """
setup_inst = AriaEcSetup(self.create_settings())
setup_inst.run()
def bbconv(self):
+ """
+ bbcontacts converter call
+ """
bbconverter = AriaEcBbConverter(self.create_settings())
bbconverter.run()
def contactmap(self):
- # instantiate AriaEcContactmap with AriaSettings
+ """
+ instantiate AriaEcContactmap with AriaSettings
+ """
econtactmap = AriaEcContactMap(self.create_settings())
econtactmap.run()
diff --git a/ariaec/commands.pyc b/ariaec/commands.pyc
index ef3fef48cb02bb406983fb6ace50addcd87a0635..72ed275f274dc4fa8fe10a8ea2813228ec3c804c 100644
Binary files a/ariaec/commands.pyc and b/ariaec/commands.pyc differ
diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc
index c52f60e4c6d1b263e46fdadcf909cb845f93855c..67ea09583d2246c33cd715da1ec61b869bc83e65 100644
Binary files a/ariaec/econverter.pyc and b/ariaec/econverter.pyc differ
diff --git a/ariaec/ecsettings.py b/ariaec/ecsettings.py
index 3ecb943f78b0939aa3dbb52e8d25e21328d43af3..4b0756fbefc89d4ca7087ea2fa81f128c28c3191 100644
--- a/ariaec/ecsettings.py
+++ b/ariaec/ecsettings.py
@@ -1,21 +1,26 @@
+# coding=utf-8
"""
Settings section
"""
from __future__ import absolute_import, division, print_function
-import logging
import os
-from configparser import SafeConfigParser
-import collections
+import logging
import pickle
+import collections
import pkg_resources as pkgr
+# noinspection PyCompatibility
+from ConfigParser import ConfigParser
from .base import format_dict
LOG = logging.getLogger(__name__)
-class Setting:
+class Setting(object):
+ """
+ Main setting object with args and config section
+ """
def __init__(self):
self.config = collections.defaultdict()
@@ -27,6 +32,9 @@ class Setting:
class Settings(object):
+ """
+ Group settings with each section corresponding to a Setting object
+ """
def __init__(self, sections):
self._sections = set(sections)
@@ -46,7 +54,8 @@ class Settings(object):
elif not pkg:
LOG.error("Configuration file not found (%s)", configpath)
return None
- config = SafeConfigParser(allow_no_value=True)
+ # config = SafeConfigParser(allow_no_value=True)
+ config = ConfigParser(allow_no_value=True)
if pkg:
with pkgr.resource_stream(__name__, configpath) as conf:
config.readfp(conf)
@@ -64,9 +73,12 @@ class Settings(object):
LOG.warning("Unknow config section %s", section)
def write_config(self, filename):
- # Ecrit les config de toutes les sections dans un autre fichier
+ """
+ Write config of all sections into another file
+ :param filename:
+ """
LOG.info("Writing .ini file (%s)", filename)
- config = SafeConfigParser(allow_no_value=True)
+ config = ConfigParser(allow_no_value=True)
iniout = open(filename, mode="w")
for section in self._sections:
config.add_section(section)
@@ -81,20 +93,26 @@ class Settings(object):
class AriaEcSettings(Settings):
-
# ss_dist = os.path.join(os.path.dirname(os.path.realpath(__file__)),
# 'conf/ss_dist.txt')
# TODO: move these constant variable in objects which can read these file !!
# TODO: Baseclass inspired from this class and ariabase class. All
# objects in this package should extend the base object
+ """
+ Settings object for ariaec
+ """
ARIAPROJ_TEMPLATE = 'templates/aria_project_v2.3.0.xml'
SS_DIST = 'data/ss_dist.txt'
SCSC_MIN = 'data/scsc_min.p'
TOPO = 'data/topallhdg5.3.pro'
+ COMMANDS = ("main", "setup", "contactmap", "bbconv", "contactdef")
def __init__(self, name):
- super(AriaEcSettings, self).__init__(("main", "setup", "contactmap",
- "bbconv", "contactdef"))
+ """
+ Initiate settings with name related to a command
+ :param name:
+ """
+ super(AriaEcSettings, self).__init__(self.COMMANDS)
self._infra = {}
self._scsc_min = None
self._ssdist = None
@@ -109,6 +127,10 @@ class AriaEcSettings(Settings):
@property
def infra(self):
+ """
+ Infrastructure for a specific command
+ :return:
+ """
if self.name == "setup" and not self._infra:
self._infra = {"xml": "", "tbl": "", "others": ""}
self._up_infra()
@@ -130,6 +152,11 @@ class AriaEcSettings(Settings):
@property
def ssdist(self):
+ """
+ Get distance file for secondary structures in the package or in config
+ file
+ :return:
+ """
if not self._ssdist:
if self.main.config["ss_dist_file"] and \
os.path.exists(self.main.config["ss_dist_file"]):
@@ -140,20 +167,28 @@ class AriaEcSettings(Settings):
@property
def template(self):
+ """
+ Get template files in config file or in the package
+ :return:
+ """
if not self._template:
- templatepath = "templates/aria_project_v%s.xml" % str(self.main.config["ariaproject_template"])
+ templatepath = "templates/aria_project_v%s.xml" % \
+ str(self.main.config["ariaproject_template"])
if os.path.exists(pkgr.resource_filename(__name__, templatepath)):
self._template = pkgr.resource_filename(__name__, templatepath)
else:
LOG.error("Template version for aria project (%s) is not "
- "supported", self.main.config.get("ariaproject_template"))
+ "supported", self.main.config.get("ariaproject_template"))
self._template = pkgr.resource_filename(__name__,
self.ARIAPROJ_TEMPLATE)
return self._template
@property
def scsc_min(self):
- # If scsc_min already computed
+ """
+ Get contact index for side chains in package or config file
+ :return:
+ """
if not self._scsc_min:
try:
# Read scsc_min_file given in aria_ec.ini
@@ -174,6 +209,9 @@ class AriaEcSettings(Settings):
return self._scsc_min
def make_infra(self):
+ """
+ Generate infrastructure
+ """
LOG.info("Making output directories")
for direct in self.infra:
LOG.debug("Create %s directory", self.infra[direct])
@@ -181,4 +219,9 @@ class AriaEcSettings(Settings):
os.makedirs(os.path.abspath(self.infra[direct]))
def load_config(self, configpath, **kwargs):
+ """
+
+ :param configpath:
+ :param kwargs:
+ """
super(AriaEcSettings, self).load_config(configpath, **kwargs)
diff --git a/ariaec/ecsettings.pyc b/ariaec/ecsettings.pyc
index 89155bbf715eea0cb2320e460060a723f1e91474..9b233e5f5eb146a89a6df7661662aa9e6a104fbc 100644
Binary files a/ariaec/ecsettings.pyc and b/ariaec/ecsettings.pyc differ
diff --git a/ariaec/maplot.py b/ariaec/maplot.py
index 127f8d6aa7dfa727c2f8dab6365c6945f59f83fd..38bad0a0f2625a0c5d928c233efcf18a51a14545 100644
--- a/ariaec/maplot.py
+++ b/ariaec/maplot.py
@@ -1,3 +1,4 @@
+# coding=utf-8
"""
Input/Output aria_ec scripts
"""
@@ -15,6 +16,10 @@ LOG = logging.getLogger(__name__)
class AriaEcContactMap(object):
+ """
+ Contact maplot class
+ """
+
def __init__(self, settings):
# TODO: check_type settings (AriaEcSettings)
self.settings = settings
@@ -30,6 +35,9 @@ class AriaEcContactMap(object):
def run(self):
# Check input
+ """
+ Main method
+ """
LOG.debug("Settings:\n" + json.dumps(self.settings.contactmap.config,
indent=4))
LOG.debug("Args:\n" + json.dumps(self.settings.contactmap.args,
@@ -128,7 +136,7 @@ class AriaEcContactMap(object):
prefix = "_".join((mapname, self.refname)).replace(".", "_")
if mapname == self.refname:
- if not self.settings.contactmap.args.get("onlyreport", False):
+ if self.settings.contactmap.args.get("onlyreport", False) is not False:
refmap.write_contacts(mapname,
outdir=outdir,
scoremap=self.refmap.get("scoremap",
diff --git a/ariaec/maplot.pyc b/ariaec/maplot.pyc
index a32ab2f8b4e7ea0bfd7f31d87eeb6a269ebae349..06f6847c6a01277b4a3418504cf61e7b3ce0ee37 100644
Binary files a/ariaec/maplot.pyc and b/ariaec/maplot.pyc differ
diff --git a/ariaec/protmap.py b/ariaec/protmap.py
index d99940d83629e98e23fb69ead7b0189950fb1c0d..fa8da27a092e6e3646432e2daf63f92360b5447d 100644
--- a/ariaec/protmap.py
+++ b/ariaec/protmap.py
@@ -1,3 +1,4 @@
+# coding=utf-8
"""
ARIA Evolutionary Constraints Tools
"""
@@ -42,6 +43,11 @@ class Map(pd.DataFrame):
mtype_choices = {'contact': bool, 'distance': float, "score": float}
def update(self, *args, **kwargs):
+ """
+
+ :param args:
+ :param kwargs:
+ """
super(Map, self).update(*args, **kwargs)
# def _constructor_expanddim(self):
@@ -76,6 +82,11 @@ class Map(pd.DataFrame):
def sortedset(self, human_idx=False):
# Remove duplicate in sort_list
+ """
+
+ :param human_idx:
+ :return:
+ """
n = 1 if human_idx else 0
if hasattr(self, "sort_list"):
if self.sym:
@@ -92,6 +103,11 @@ class Map(pd.DataFrame):
return None
def check_type(self, mtype):
+ """
+
+ :param mtype:
+ :return:
+ """
value = self.mtype_choices.get(mtype)
if value:
return value
@@ -101,6 +117,10 @@ class Map(pd.DataFrame):
return None
def reduce(self):
+ """
+
+ :return:
+ """
columns = ['-'.join(idx) for idx in self.columns]
index = ['-'.join(idx) for idx in self.index]
return getattr(self, '__init__')(self.sequence,
@@ -112,6 +132,10 @@ class Map(pd.DataFrame):
def remove(self, rm_list):
# Reset values at positions in rm_list
+ """
+
+ :param rm_list:
+ """
value = False if self.dtype == bool else 0.0
for contact in rm_list:
idx1, idx2 = self.index[contact[0]], self.index[contact[1]]
@@ -127,6 +151,10 @@ class Map(pd.DataFrame):
def to_series(self):
# Return panda series related to lower triangle
+ """
+
+ :return:
+ """
df = self.copy()
df = df.astype(float)
# remove values from upper triangle
@@ -135,9 +163,15 @@ class Map(pd.DataFrame):
return df.unstack().dropna()
def topmap(self, scoremap, nb_topcontact):
+ """
+
+ :param scoremap:
+ :param nb_topcontact:
+ :return:
+ """
if self.dtype != bool:
LOG.info("Error when retrieving top contact map. The type of "
- "the given map is not a contact type!")
+ "the given map is not a contact type!")
return self
self[:] = False
if self.shape == scoremap.shape:
@@ -165,14 +199,24 @@ class Map(pd.DataFrame):
self.loc[idx, idx] = pairdict[idxval]
def set_value(self, index, col, value, **kwargs):
+ """
+
+ :param index:
+ :param col:
+ :param value:
+ :param kwargs:
+ """
super(Map, self).set_value(index, col, value, **kwargs)
if self.sym:
super(Map, self).set_value(col, index, value, **kwargs)
class ProteinMap(Map):
-
# TODO: Matrices PosAaAtmMap, AaAtmMap, AtmMap
+ """
+ Protein contact map object
+ """
+
def __init__(self, sequence, flaglist=None, seqidx=None, index=None,
columns=None, **kwargs):
idx, col = self.create_index(sequence, seqidx=seqidx, idxnames=index,
@@ -188,9 +232,15 @@ class ProteinMap(Map):
@property
def sequence(self):
+ """
+ aa sequence
+ """
raise NotImplementedError
def plotflush(self):
+ """
+ Flush contact map plot
+ """
plt.clf()
plt.cla()
plt.close()
@@ -198,6 +248,10 @@ class ProteinMap(Map):
@property
def maplot(self):
+ """
+ Contact map plot
+ :return:
+ """
# Contact map Plot
if not self._maplot:
# Flush matplot
@@ -215,12 +269,19 @@ class ProteinMap(Map):
def saveplot(self, outdir='', outprefix="protein", size_fig=10,
plot_ext="pdf", plot_dpi=200):
+ """
+ Save plot
+ :param outdir:
+ :param outprefix:
+ :param size_fig:
+ :param plot_ext:
+ :param plot_dpi:
+ """
plotpath = os.path.join(outdir, "%s.contactmap.%s" % (
outprefix, plot_ext))
LOG.info("Generate contact map plot (%s)", plotpath)
f, ax = plt.subplots(figsize=(12, 9))
- tickrot(self.maplot.axes, self.maplot.figure,
- rotype='horizontal')
+ tickrot(self.maplot.axes, self.maplot.figure)
self.maplot.figure.set_size_inches(size_fig, size_fig)
map_title = "%s contacts map" % outprefix
self.maplot.set_title(map_title)
@@ -230,7 +291,11 @@ class ProteinMap(Map):
self.maplot.figure.savefig(plotpath, dpi=plot_dpi)
def contactset(self, human_idx=False):
- # Remove duplicate in contact_list
+ """
+ Remove duplicate in contact_list
+ :param human_idx:
+ :return:
+ """
if self.contact_list():
return sorted(set((tuple(sorted((x, y)))
for x, y in self.contact_list(human_idx))))
@@ -238,7 +303,11 @@ class ProteinMap(Map):
return None
def contact_list(self, human_idx=False):
- # Return contact list
+ """
+ Return contact list
+ :param human_idx:
+ :return:
+ """
contact_list = []
n = 1 if human_idx else 0
if self.dtype is bool:
@@ -251,9 +320,18 @@ class ProteinMap(Map):
return None
def create_heatmap(self):
+ """
+ Generate heatmap
+ :return:
+ """
raise NotImplementedError
def contact_map(self, contactdef, scsc_min=None):
+ """
+ Generate contact map
+ :param contactdef:
+ :param scsc_min:
+ """
raise NotImplementedError
def create_index(self, sequence, seqidx=None, idxnames=None, colnames=None):
@@ -268,6 +346,14 @@ class ProteinMap(Map):
raise NotImplementedError
def compareplot(self, protmap, save_fig=True, alpha=None, **kwargs):
+ """
+ Compare 2 contact map and plot differences
+ :param protmap:
+ :param save_fig:
+ :param alpha:
+ :param kwargs:
+ :return:
+ """
self.plotflush()
# Contact map plot
if getattr(protmap, "shape") and self.shape != protmap.shape:
@@ -315,6 +401,16 @@ class ProteinMap(Map):
def report(self, cmpmap, scoremap=None, outprefix="", outdir="", plotdir="",
plot_ext="pdf", plotag=True):
+ """
+ Generate report file
+ :param cmpmap:
+ :param scoremap:
+ :param outprefix:
+ :param outdir:
+ :param plotdir:
+ :param plot_ext:
+ :param plotag:
+ """
filename = ".".join((outprefix, "mapreport")) if outprefix else \
"mapreport"
reportpath = "%s/%s" % (outdir, filename)
@@ -333,6 +429,15 @@ class ProteinMap(Map):
allrec = None
prthresholds = None
aver_prec = None
+ acc = None
+ prec = None
+ recall = None
+ mcc = None
+ f1s = None
+ f2s = None
+ f05s = None
+ hamm = None
+ hin = None
if scoremap is not None:
# If prediction scores given, compute roc and precall curves
@@ -347,6 +452,20 @@ class ProteinMap(Map):
y_true, y_scores)
aver_prec = skm.average_precision_score(y_true, y_scores)
+ if 1 in y_pred and 1 in y_true:
+ # If one map is empty, we do not compute analysis
+ acc = skm.accuracy_score(y_true, y_pred)
+ prec = skm.precision_score(y_true, y_pred)
+ recall = skm.recall_score(y_true, y_pred)
+ mcc = skm.matthews_corrcoef(y_true, y_pred)
+ f1s = skm.f1_score(y_true, y_pred)
+ f2s = skm.fbeta_score(y_true, y_pred, 2)
+ f05s = skm.fbeta_score(y_true, y_pred, 0.5)
+ hamm = skm.hamming_loss(y_true, y_pred)
+ hin = skm.hinge_loss(y_true, y_pred)
+ else:
+ LOG.error("Can't analyze empty map(s).")
+
msg = """\
## Report {map1name} vs. {map2name}
##
@@ -402,22 +521,16 @@ class ProteinMap(Map):
## False Positive Rate (1 - Specificity) values:
## {allfpr}
## Score tresholds ({map2name}):
-## {rocthres}""".format(map1name=map1name, map2name=map2name,
- map1path=self.path, map2path=cmpmap.path,
- seq=self.sequence, protlen=len(self.sequence),
- date=datetime.date.today().strftime("%A %d. %B %Y"),
- outdir=outdir, accuracy=skm.accuracy_score(y_true, y_pred),
- precision=skm.precision_score(y_true, y_pred),
- recall=skm.recall_score(y_true, y_pred),
- mcc=skm.matthews_corrcoef(y_true, y_pred),
- f1s=skm.f1_score(y_true, y_pred),
- f2s=skm.fbeta_score(y_true, y_pred, 2),
- f05s=skm.fbeta_score(y_true, y_pred, 0.5),
- hamm=skm.hamming_loss(y_true, y_pred),
- hin=skm.hinge_loss(y_true, y_pred), aver_prec=aver_prec,
- roc_auc=roc_auc, allprec=allprec, allrec=allrec,
- prthres=prthresholds, alltpr=alltpr, allfpr=allfpr,
- rocthres=rocthresholds)
+## {rocthres}""".format(
+ map1name=map1name, map2name=map2name, map1path=self.path,
+ map2path=cmpmap.path, seq=self.sequence,
+ protlen=len(self.sequence),
+ date=datetime.date.today().strftime("%A %d. %B %Y"),
+ outdir=outdir, accuracy=acc, precision=prec, recall=recall,
+ mcc=mcc, f1s=f1s, f2s=f2s, f05s=f05s, hamm=hamm, hin=hin,
+ aver_prec=aver_prec, roc_auc=roc_auc, allprec=allprec,
+ allrec=allrec, prthres=prthresholds, alltpr=alltpr,
+ allfpr=allfpr, rocthres=rocthresholds)
LOG.debug("\n" + msg)
reportf.write(msg)
@@ -468,6 +581,16 @@ class ProteinMap(Map):
def compare_contactmap(self, cmpmap, contactlist, outprefix,
outdir="", distmap=None, human_idx=True):
+ """
+ Compare 2 contact map and plot differences
+ :param cmpmap:
+ :param contactlist:
+ :param outprefix:
+ :param outdir:
+ :param distmap:
+ :param human_idx:
+ :return:
+ """
# CSV file giving TP/FP contacts
outpath = "%s/%s.contactcmp.csv" % (outdir, outprefix)
LOG.info("Generate stat file (%s)", outpath)
@@ -499,6 +622,14 @@ class ProteinMap(Map):
def write_contacts(self, filename, outdir="", human_idx=True,
scoremap=None):
+ """
+
+ :param filename:
+ :param outdir:
+ :param human_idx:
+ :param scoremap:
+ :return:
+ """
filepath = "%s/%s.contact.txt" % (outdir, filename)
LOG.info("Generate contact file (%s)", filepath)
with open(filepath, 'w') as outfile:
@@ -551,12 +682,24 @@ class ResAtmMap(ProteinMap):
@property
def sequence(self):
- # Amino Acid sequence string in humanidx
+ """
+ Amino Acid sequence string in humanidx
+ :return:
+ """
return "".join(AminoAcid.AminoAcid(_.split("-")[1])[0] for _ in
self.index.levels[0])
def create_index(self, sequence, seq_pos=True, seqidx=None,
idxnames=None, colnames=None):
+ """
+
+ :param sequence:
+ :param seq_pos:
+ :param seqidx:
+ :param idxnames:
+ :param colnames:
+ :return:
+ """
LOG.info("Indexing res - res dataframe")
# Atom table for residues (keys are in 3L code)
seqidx = seqidx if seqidx and len(seqidx) == len(sequence) else None
@@ -600,6 +743,10 @@ class ResAtmMap(ProteinMap):
return index, columns
def create_heatmap(self):
+ """
+
+ :return:
+ """
unidf = self.reduce()
if unidf.isnull().values.sum() == 0:
# If there's no nan values
@@ -607,6 +754,11 @@ class ResAtmMap(ProteinMap):
return None
def reduce(self, groupby="min"):
+ """
+
+ :param groupby:
+ :return:
+ """
if self.index.nlevels == 1 or not groupby:
return self
newmap = ResMap(self.sequence, dtype=self.dtype, desc=self.desc,
@@ -623,6 +775,7 @@ class ResAtmMap(ProteinMap):
"""
Contact map generator from all atoms distance map. There's a contact
with 2 residues iff dist between 2 atoms are below the given treshold
+ :param def_cut:
:param scsc_min:
:param contactdef:
for all atom pair
@@ -660,7 +813,7 @@ class ResAtmMap(ProteinMap):
treshold = contactdef[pair]
else:
LOG.warning("Treshold for %s ignored (lower than "
- "the default cutoff)", str(pair))
+ "the default cutoff)", str(pair))
LOG.info(
"Filtering values in matrix related to %s (%s)",
str(pair), str(treshold) if treshold else def_cutoff)
@@ -696,7 +849,7 @@ class ResAtmMap(ProteinMap):
contact_map.update(tmp)
else:
LOG.error("Missing values in contact definition section. Add "
- "at least a default_cutoff value.")
+ "at least a default_cutoff value.")
LOG.debug("Contact map\n%s", contact_map.head())
return contact_map
@@ -714,13 +867,24 @@ class ResMap(ResAtmMap):
@property
def sequence(self):
- # Amino Acid sequence string in humanidx
+ """
+ Amino Acid sequence string in humanidx
+ :return:
+ """
return "".join(AminoAcid.AminoAcid(aa.split("-")[1])[0] for aa in
self.index)
def create_index(self, sequence, seqidx=None, idxnames=None,
colnames=None, **kwargs):
- # Index correspondant a la liste de residus
+ """
+ Index related to residue list
+ :param sequence:
+ :param seqidx:
+ :param idxnames:
+ :param colnames:
+ :param kwargs:
+ :return:
+ """
seq = [AminoAcid.AminoAcid(aa)[1] for aa in sequence]
seqidx = seqidx if seqidx and len(seqidx) == len(sequence) else None
if seqidx:
@@ -734,16 +898,31 @@ class ResMap(ResAtmMap):
return index, col
def create_heatmap(self):
+ """
+
+ :return:
+ """
if self.as_matrix().isnull().values.sum() == 0:
# If there's no nan values
return sns.heatmap(self.as_matrix())
return None
def contact_map(self, contactdef, **kwargs):
+ """
+
+ :param contactdef:
+ :param kwargs:
+ :return:
+ """
contact_map = ResMap(self.sequence, mtype="contact", desc=self.desc,
sym=self.sym)
def treshconv(x):
+ """
+
+ :param x:
+ :return:
+ """
return x <= treshold
# Applique treshold sur la matrice ssi c'est une matrice de distance
@@ -772,6 +951,10 @@ class AaMap(Map):
@staticmethod
def create_index():
+ """
+
+ :return:
+ """
res_list = ConversionTable.ConversionTable().table['AMINO_ACID'][
'iupac'].keys()
index = pd.Index(res_list, name="residuex")
@@ -791,10 +974,17 @@ class AtmMap(Map):
super(AtmMap, self).__init__(*args, **kwargs)
def create_index(self):
- pass
+ """
+
+ :return:
+ """
+ raise NotImplementedError
-class ProtMapCollection:
+class ProtMapCollection(object):
+ """
+ Group all protein maps
+ """
def __init__(self, settings):
self._alldistmap = None
@@ -865,6 +1055,10 @@ class ProtMapCollection:
@property
def distmap(self):
+ """
+
+ :return:
+ """
if self._alldistmap:
return self._alldistmap.reduce(groupby=self.settings[
"groupby_method"])
@@ -876,7 +1070,7 @@ class ProtMapCollection:
self._distmap = resmap
-class MapFilter:
+class MapFilter(object):
"""
Filter contactmap/distancemap
nd : Network deconvolution
@@ -905,6 +1099,11 @@ class MapFilter:
def nd_filter(self, mapdict):
# TODO: build ROC curve with number of top contacts as the parameter
+ """
+
+ :param mapdict:
+ :return:
+ """
LOG.info("...Network deconvolution filter (alpha=%.2f, beta=%.2f)",
self.settings["nd_beta"], self.settings["nd_alpha"])
scoremap = mapdict["scoremap"]
@@ -938,6 +1137,12 @@ class MapFilter:
def cons_filter(self, mapdict, **kwargs):
# Liste les contacts aves des residus fortement conserves
+ """
+
+ :param mapdict:
+ :param kwargs:
+ :return:
+ """
LOG.info("...Conservation filter")
sec_struct = kwargs.get("sec_struct")
clash_list = kwargs.get("clash_list")
@@ -947,7 +1152,7 @@ class MapFilter:
if sec_struct.filetype != "indextableplus":
LOG.warning("Conservation filter only works with indextableplus "
- "files !")
+ "files !")
return {'clash': None, 'desc': None}
# parcours la liste de paires dans la matrice struct secondaire
@@ -970,6 +1175,12 @@ class MapFilter:
# Si scoremap existe, selectionner les contacts cys-cys qui ont les
# meilleurs scores, fournit une liste des contacts disulfures qui
# possedent des scores plus faibles
+ """
+
+ :param mapdict:
+ :param kwargs:
+ :return:
+ """
LOG.info("...Disulfure bridge unicity filter")
clash_list = kwargs.get("clash_list")
unidisbridge_list = [] # Liste les ponts disulfures uniques
@@ -1024,7 +1235,19 @@ class MapFilter:
@staticmethod
def ssclash_filter(mapdict, **kwargs):
+ """
+
+ :param mapdict:
+ :param kwargs:
+ :return:
+ """
+
def hum_contact(xy):
+ """
+
+ :param xy:
+ :return:
+ """
return xy[0] + 1, xy[1] + 1
# TODO: better add clash list and sec_struct as object attribute
@@ -1157,15 +1380,15 @@ class MapFilter:
# Allow contact to the fifth residue in the
# helix
LOG.debug("Found (H-2, H) for contact %s clash "
- "but contact with fifth residue is "
- "actually allowed",
+ "but contact with fifth residue is "
+ "actually allowed",
outcontact)
ssclash = None
elif ssclash in ("H-3,H", "H+3,H") \
and abs(resi - resj) < 12:
LOG.debug("Found (H-3, H) for contact %s clash "
- "but contact between 3rd and 10th "
- "residues are actually allowed",
+ "but contact between 3rd and 10th "
+ "residues are actually allowed",
outcontact)
# Allow contact between 3rd residue and 10th
ssclash = None
@@ -1187,8 +1410,8 @@ class MapFilter:
end = ss_start_end[strand][0]
if abs(start - end + 1) <= 5:
LOG.debug("Found (E-2, E+2) for contact "
- "%s clash but strand "
- "is < 5 residues", outcontact)
+ "%s clash but strand "
+ "is < 5 residues", outcontact)
# Allow contact if strand < 5 residues (gap <8)
ssclash = None
elif ssclash in ("E-3,E+3", "E+3,E-3"):
@@ -1200,8 +1423,8 @@ class MapFilter:
elif ssclash in ("E-4,E", "E+4,E") \
and abs(resi - resj) < 8:
LOG.debug("Found (E-4, E) for contact %s clash "
- "but contacts below 4th residue are "
- "actually allowed", outcontact)
+ "but contacts below 4th residue are "
+ "actually allowed", outcontact)
ssclash = None
if ssclash:
LOG.debug(
@@ -1296,6 +1519,16 @@ class MapFilter:
def write_filtout(clash_dict, desc_dict, contactlist, outdir="",
outprefix="protein", clashlist=None, human_idx=True):
# TODO: utiliser self.clash_dict au lieu de meta_clash
+ """
+
+ :param clash_dict:
+ :param desc_dict:
+ :param contactlist:
+ :param outdir:
+ :param outprefix:
+ :param clashlist:
+ :param human_idx:
+ """
meta_clash = {
"cons": {
"flag": 888, "msg": "", "warn": "",
diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc
index adcbcfc0577822efdbee59aae4830d90257bacd6..6919d03072f4c46b59bc6fc6602a553761e8b7e9 100644
Binary files a/ariaec/protmap.pyc and b/ariaec/protmap.pyc differ
diff --git a/ariaec/reader.py b/ariaec/reader.py
index 7b27c166b3c0620d0fe0283178cdff51b2fd4668..fec18b7b783e4405730651caed7d8bd272484365 100644
--- a/ariaec/reader.py
+++ b/ariaec/reader.py
@@ -1,3 +1,4 @@
+# coding=utf-8
"""
Reader objects
"""
@@ -17,6 +18,10 @@ Atom = collections.namedtuple("Atom", ["name", "coords"])
class RegexFile(object):
+ """
+ File which can be parsed with a regex
+ """
+
def __init__(self, filepath, filetype='', regex='', sort=''):
self.regex = regex
self.sort = sort
@@ -52,6 +57,9 @@ class MapFile(RegexFile):
# sort_field allow sorting lines with values into this field
# TODO: wrong regex for native_full ?
# TODO: smarter dict ...
+ """
+ Map file class
+ """
types = {
"plmdca": {
"regex": re.compile(r"^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+"
@@ -180,6 +188,10 @@ class MapFile(RegexFile):
"regex": re.compile(
r'^\s*(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)\s+'),
"score_field": None
+ },
+ "empty": {
+ "regex": re.compile(r'^\s*$'),
+ "score_field": None
}
}
check_type = True
@@ -231,7 +243,7 @@ class MapFile(RegexFile):
if self.lines[line]['res1_name'] != aa_seq[int(self.lines[line]['res1_nb']) - 1] \
or self.lines[line]['res2_name'] != aa_seq[int(self.lines[line]['res2_nb']) - 1]:
LOG.error("Difference between given sequence and residu "
- "names in contact file at line %d !", line)
+ "names in contact file at line %d !", line)
def update_map(self, resmap):
"""
@@ -247,22 +259,28 @@ class MapFile(RegexFile):
:return:
"""
- LOG.info("Checking format for file %s", self.filepath)
+ LOG.info("Checking if file %s correspond to %s format", self.filepath,
+ self.filetype)
# Check if given type is supported
# TODO: report this check into commands section
+ defaults = ("default_1", "default_2", "default_3", "default_4", "empty")
+ if os.stat(self.filepath).st_size == 0:
+ LOG.warning("File %s is empty !", self.filepath)
+ return [
+ self.types["empty"].get("regex"),
+ self.filetype,
+ self.types["empty"].get("score_field")
+ ]
with open(self.filepath) as infile:
# Check first and second line of file
for index, line in enumerate(infile):
if self.filetype in self.types:
+ LOG.info("Given format (%s) should be supported",
+ self.filetype)
match = self.types[self.filetype].get("regex").match(line)
else:
match = None
LOG.error("Format %s not supported !", self.filetype)
- # TODO: DRY rule !!
- def1match = self.types["default_1"]["regex"].match(line)
- def2match = self.types["default_2"]["regex"].match(line)
- def3match = self.types["default_3"]["regex"].match(line)
- def4match = self.types["default_4"]["regex"].match(line)
if match:
LOG.debug("Format type correct")
return [
@@ -270,37 +288,20 @@ class MapFile(RegexFile):
self.filetype,
self.types[self.filetype].get("score_field")
]
- elif def1match:
- LOG.debug("Format type correct")
- return [
- self.types["default_1"].get("regex"),
- self.filetype,
- self.types["default_1"].get("score_field")
- ]
- elif def2match:
- LOG.debug("Format type correct")
- return [
- self.types["default_2"].get("regex"),
- self.filetype,
- self.types["default_2"].get("score_field")
- ]
- elif def3match:
- LOG.debug("Format type correct")
- return [
- self.types["default_3"].get("regex"),
- self.filetype,
- self.types["default_3"].get("score_field")
- ]
- elif def4match:
- LOG.debug("Format type correct")
- return [
- self.types["default_4"].get("regex"),
- self.filetype,
- self.types["default_4"].get("score_field")
- ]
+ else:
+ LOG.warning("Given type do not correspond, checking default"
+ " format for contactlist or empty file...")
+ for subformat in defaults:
+ if self.types.get(subformat)["regex"].match(line):
+ LOG.debug("Format type correct %s", subformat)
+ return [
+ self.types[subformat].get("regex"),
+ self.filetype,
+ self.types[subformat].get("score_field")
+ ]
if index > 2:
+ # Stop checking after second line
LOG.error("Error reading %s file.", self.filetype)
- # Remove contact file
break
LOG.error("Wrong format type given ...")
return [None] * 3
@@ -368,12 +369,16 @@ class MapFile(RegexFile):
self.lines[contact].get("res2_nb")]
if len(self.contactlist) != len(self.clashlist):
LOG.error("When reading input file, clash list is not "
- "the same length than contactlist")
+ "the same length than contactlist")
LOG.debug(self.clashlist)
class ContactMapFile(MapFile):
# "plmdca", "evfold", "bbcontacts", "pconsc", "gremlin", "metapsicov",
+ """
+ Contact map file
+ """
+
def __init__(self, filepath, filetype):
"""
@@ -384,6 +389,11 @@ class ContactMapFile(MapFile):
super(self.__class__, self).__init__(filepath, filetype)
def update_map(self, resmap):
+ """
+
+ :param resmap:
+ :return:
+ """
# TODO: swap dataframe factory here
raise NotImplementedError
@@ -432,7 +442,7 @@ class ContactMapFile(MapFile):
if (int(residx1.split("-")[0]) != resid1) or \
(resid2 != int(residx2.split("-")[0])):
LOG.error("Wrong resid humanidx (%d, %d) in contact (%d) is "
- "not the same in resmap (%d, %d)",
+ "not the same in resmap (%d, %d)",
resid1, resid2, contact_id,
int(residx1.split("-")[0]),
int(residx2.split("-")[0]))
@@ -454,6 +464,9 @@ class ContactMapFile(MapFile):
class PDBFile(MapFile):
+ """
+ PDB file
+ """
pdbreg = re.compile(r'^(?P<record>ATOM |HETATM)(?P<serial>[\s\w]{5})'
r'\s(?P<name>[\s\w]{4})'
r'(?P<altLoc>[\s\w])'
@@ -475,9 +488,20 @@ class PDBFile(MapFile):
def create_map(self, protein, contactdef, groupby_method="min", scsc=None,
flaglist=None, sym=True, path=""):
+ """
+
+ :param protein:
+ :param contactdef:
+ :param groupby_method:
+ :param scsc:
+ :param flaglist:
+ :param sym:
+ :param path:
+ """
resmap = ResAtmMap(protein.aa_sequence.sequence, mtype='distance',
flaglist=flaglist, path=path,
seqidx=protein.index, desc=self.filetype)
+ # noinspection PyTypeChecker
resmap[:] = self.update_map(resmap, sym=sym)
LOG.debug("pdb distance map:\n%s", resmap)
self.mapdict["alldistmap"] = resmap
@@ -487,6 +511,12 @@ class PDBFile(MapFile):
self.mapdict["contactmap"] = self.mapdict["allcontactmap"].reduce()
def update_map(self, resmap, sym=True):
+ """
+
+ :param resmap:
+ :param sym:
+ :return:
+ """
# Map only on heavy atoms
# TODO: check if same sequence in pdb file
LOG.info("Updating distance map with pdb file")
@@ -537,35 +567,63 @@ class PDBFile(MapFile):
if sym:
newmap.loc[:][idx] = None
LOG.error("Can't update pdb distance map for pos in pdb file "
- "%s with %s", list(error_list), missidx)
+ "%s with %s", list(error_list), missidx)
return newmap
class DistanceMapFile(MapFile):
+ """
+ Distance matrix file
+ """
def __init__(self, filepath, filetype):
super(MapFile).__init__(filepath, filetype)
raise NotImplementedError
def create_map(self, aa_seq, contactdef, **kwargs):
+ """
+
+ :param aa_seq:
+ :param contactdef:
+ :param kwargs:
+ :return:
+ """
pass
# Native dist
def update_map(self, resmap):
+ """
+
+ :param resmap:
+ :return:
+ """
pass
# Construit map avec la liste de residus + infos de distance du fichier
# return DistanceMap
-class ProtFileListReader:
+class ProtFileListReader(object):
+ """
+ List of file object
+ """
def __init__(self, cont_def=5.0):
self.filelist = []
self.contactdef = cont_def
def clear(self):
+ """
+ Initiatise from scratch object
+ :return:
+ """
# TODO: Init supprime bien les fichiers du cache ?
self.__init__(self.contactdef)
def add_file(self, filepathlist, filetypelist=None):
+ """
+
+ :param filepathlist:
+ :param filetypelist:
+ :return:
+ """
filepathlist = [filepathlist] if type(
filepathlist) != list else filepathlist
filetypelist = [filetypelist] if type(
@@ -594,6 +652,15 @@ class ProtFileListReader:
def read(self, filepathlist, filetypelist=None, protein=None, scsc=None,
**kwargs):
+ """
+
+ :param filepathlist:
+ :param filetypelist:
+ :param protein:
+ :param scsc:
+ :param kwargs:
+ :return:
+ """
self.clear()
self.add_file(filepathlist, filetypelist=filetypelist)
for fo in self.filelist:
diff --git a/ariaec/reader.pyc b/ariaec/reader.pyc
index 3164221557912ab2ccdb44d3ba8fd89f3154d085..a7730d5d715b4bb4ee16c4a2946b21f7f9f9d329 100644
Binary files a/ariaec/reader.pyc and b/ariaec/reader.pyc differ
diff --git a/ariaec/setup.py b/ariaec/setup.py
index 2336dcabc4d69f85ea4a878c1b748ea9a9b3af22..18e4890aee0877637fc6c928b9535503ff9094ba 100644
--- a/ariaec/setup.py
+++ b/ariaec/setup.py
@@ -1,11 +1,12 @@
+# coding=utf-8
"""
Input/Output aria_ec scripts
"""
from __future__ import absolute_import, division, print_function
-import logging
-import json
import os
+import json
+import logging
from .protein import Protein
from .reader import ProtFileListReader
@@ -14,15 +15,17 @@ from .protmap import MapFilter
from .econverter import AriaEcXMLConverter
# TODO: S'inspirer de pandas/__init__.py pour les dependances
-# from basictools import *
LOG = logging.getLogger(__name__)
-class AriaEcSetup:
+class AriaEcSetup(object):
+ """
+ Aria Ec Setup protocol
+ """
+
def __init__(self, settings):
"""
-
:param settings:
:return:
"""
@@ -40,7 +43,7 @@ class AriaEcSetup:
def run(self):
"""
-
+ main method
:return:
"""
# Check input
@@ -70,21 +73,24 @@ class AriaEcSetup:
# TODO: change read method in reader to __call__
# -------------------------- contact maps ---------------------------- #
self.reader.read(self.settings.setup.args.get("infiles"),
- filetypelist=self.settings.setup.args.get("contact_types"),
+ filetypelist=self.settings.setup.args.get(
+ "contact_types"),
protein=self.protein,
- groupby_method=self.settings.setup.config['groupby_method'],
+ groupby_method=self.settings.setup.config[
+ 'groupby_method'],
scsc=self.settings.scsc_min)
- for fo in self.reader.filelist:
+ for mapfile in self.reader.filelist:
# fo need a contactmap in order to wite XML dist restraints
# TODO: filter pour toutes les map de mapdict !! (fonction remove
# s'applique sur l'humanidx contenant les residus)
- self.filter(fo.mapdict, fo.filetype, fo.contactlist, self.protein,
- clashlist=fo.clashlist, outprefix=self.outprefix,
+ self.filter(mapfile.mapdict, mapfile.filetype, mapfile.contactlist,
+ self.protein, clashlist=mapfile.clashlist,
+ outprefix=self.outprefix,
outdir=self.settings.infra.get("others", ''))
- self.allresmap[fo.filetype] = fo.mapdict
+ self.allresmap[mapfile.filetype] = mapfile.mapdict
- if fo.filetype != "pdb" and "pdb" in self.allresmap:
- fo.contactmap.compareplot(self.allresmap["pdb"])
+ if mapfile.filetype != "pdb" and "pdb" in self.allresmap:
+ mapfile.contactmap.compareplot(self.allresmap["pdb"])
# ---------------------------- target map ---------------------------- #
if self.settings.setup.args.get("distfile") and \
@@ -138,9 +144,11 @@ class AriaEcSetup:
# ------------------------------ Output ------------------------------ #
# ----------------------------- SEQ file ----------------------------- #
- self.protein.write_seq(os.path.join(self.settings.infra.get("others", ''),
- self.outprefix + ".seq"))
- # Load aria molecule object from generated seq file
+ self.protein.write_seq(
+ os.path.join(self.settings.infra.get("others", ''),
+ self.outprefix + ".seq"))
+ # Load aria molecule object from seq file and convert it into xml format
+ LOG.info("Load molecule file and convert it into xml format")
self.converter.load_molecule(self.protein.seqfile_path)
# --------------------------- TBL restraints ------------------------- #
# Setting contact number limit for hbmap
@@ -152,11 +160,12 @@ class AriaEcSetup:
# --------------------------- XML restraints ------------------------- #
# Setting contact number limit for map restraints (native, ec, ...)
- # nb_c = int(len(self.protein.aa_sequence.sequence) *
- # self.settings.setup.config.get("n_factor"))
- dist_files, pair_lists = self.converter.write_maplist_restraints(
- self.allresmap, self.targetmap)
+ # dist_files, pair_lists = self.converter.write_maplist_restraints(
+ # self.allresmap, self.targetmap)
+
+ dist_files = self.converter.write_maplist_restraints(
+ self.allresmap, self.targetmap)[0]
# --------------------------- XML SEQ file --------------------------- #
xmlseq_file = self.converter.write_xmlseq()
@@ -169,7 +178,7 @@ class AriaEcSetup:
def write_optional_files(self):
"""
-
+ Write filtered contacts & distance maps (.csv)
:return:
"""
# Indextableplus file (submatrix)
@@ -184,16 +193,18 @@ class AriaEcSetup:
"%s/%s.distmap.csv" % (self.settings.infra.get("others"),
maptype))
if self.refmaps:
- self._write_contacts(self.allresmap[maptype].get(
- "filteredlist", None), self.protein.aa_sequence.sequence,
- self.settings.infra.get("others", ''), "_".join((
- self.outprefix, maptype, "filtered")),
+ self._write_contacts(
+ self.allresmap[maptype].get("filteredlist", None),
+ self.protein.aa_sequence.sequence,
+ self.settings.infra.get("others", ''),
+ "_".join((self.outprefix, maptype, "filtered")),
ref=self.refmaps["contactmap"],
distmap=self.refmaps["distmap"])
if self.refmaps:
self.refmaps["alldistmap"].to_csv(
"%s/%s_%s.distmap.csv" % (self.settings.infra.get("others"),
- self.outprefix, self.refmaps.filetype))
+ self.outprefix,
+ self.refmaps.filetype))
def _write_contacts(self, contacts_list, seq, out, prefix, nc=None,
append=False, ref=None, distmap=None):
@@ -209,7 +220,7 @@ class AriaEcSetup:
:return:
"""
mapy = []
- tp = 0
+ tp_count = 0
filemode = 'a' if append else 'w'
dist_desc = '\tTP/FP\tdist%s(ref)' % self.settings.setup.config[
"groupby_method"] if \
@@ -217,10 +228,12 @@ class AriaEcSetup:
else ''
with open("%s/%s.contacts.txt" % (out, prefix), filemode) as outfile:
if not append:
- outfile.write('''# resid1\tresid2\tres1\tres2%s\n''' % dist_desc)
+ outfile.write(
+ '''# resid1\tresid2\tres1\tres2%s\n''' % dist_desc)
- if type(contacts_list) is dict:
- contacts = contacts_list.keys() if not nc else contacts_list.keys()[:nc]
+ if hasattr(contacts_list, 'keys'):
+ contacts = contacts_list.keys() if not nc else \
+ contacts_list.keys()[:nc]
d_type = True
else:
# Check if contacts is 2-tuple
@@ -228,6 +241,7 @@ class AriaEcSetup:
raise TypeError('Contact list must be 2-tuple !')
contacts = contacts_list if not nc else contacts_list[:nc]
d_type = False
+
LOG.debug("Contact list %s", contacts)
for contact in contacts:
@@ -250,7 +264,7 @@ class AriaEcSetup:
if ref is not None:
if ref.ix[(resid1, resid2)]:
asses = 'TP'
- tp += 1
+ tp_count += 1
else:
asses = 'FP'
outfile.write(
@@ -265,12 +279,12 @@ class AriaEcSetup:
seq[resid1],
seq[resid2]))
- ptp = (tp / float(len(contacts))) * 100.0 if ref is not None else \
+ ptp = (tp_count / float(len(contacts))) * 100.0 if ref is not None else \
None
outfile.write('''
# TP number : {tp} ({ptp:.2f} %)
# Number of contacts : {nc}
- '''.format(tp=tp, ptp=ptp, nc=len(contacts)))
+ '''.format(tp=tp_count, ptp=ptp, nc=len(contacts)))
if __name__ == "__main__":
diff --git a/ariaec/setup.pyc b/ariaec/setup.pyc
index b001ed643a5309525fcc71bf8eed70b38cae559a..057ee8b97f13255915fad56e0326949f25f4ae71 100644
Binary files a/ariaec/setup.pyc and b/ariaec/setup.pyc differ
diff --git a/setup.py b/setup.py
index b04abf47acdeb5225b7860e49612f478748a14d3..3d1a52ccda283fcc85ad85bacc418059b2a15a4f 100644
--- a/setup.py
+++ b/setup.py
@@ -1,3 +1,4 @@
+# coding=utf-8
import os
import subprocess
from setuptools import setup, find_packages, Command
@@ -9,7 +10,7 @@ try:
version_git = subprocess.check_output(["git", "describe",
"--tags"]).rstrip()
except subprocess.CalledProcessError:
- with open(version_py, 'r') as fh:
+ with open(version_py) as fh:
version_git = open(version_py).read().strip().split('=')[-1].replace('"',
'')
@@ -26,14 +27,27 @@ class CleanCommand(Command):
"""Custom clean command to tidy up the project root."""
user_options = []
- def initialize_options(self):
+ @staticmethod
+ def initialize_options():
+ """
+
+ :return:
+ """
pass
- def finalize_options(self):
+ @staticmethod
+ def finalize_options():
+ """
+
+ :return:
+ """
pass
@staticmethod
def run():
+ """
+ call clean command
+ """
os.system('rm -vrf ./build ./dist ./*.pyc ./*.tgz ./*.egg '
'./*.egg-info')
@@ -93,6 +107,7 @@ setup(
'matplotlib'],
install_requires=[
+ # 'configparser', # TODO: add this requiirement only if python v2
'docutils>=0.3',
'pandas',
'seaborn',