diff --git a/ariaec/base.py b/ariaec/base.py
index 46748347a79176122da65a5fae5ef5ded53e8e5e..2330b20412fab2df0c073c94de3263795a4b1f22 100644
--- a/ariaec/base.py
+++ b/ariaec/base.py
@@ -10,13 +10,14 @@ import json
import re
import ast
import sys
+import shutil
import numpy as np
import pkg_resources as pkgr
import matplotlib.artist as art
from io import StringIO
-logger = logging.getLogger()
+LOG = logging.getLogger()
def titleprint(outfile, progname='', desc=''):
@@ -121,11 +122,11 @@ def format_str(string):
try:
ev_str = ast.literal_eval(string)
except ValueError:
- logger.error("Don't understand given string %s. Please check "
- "format." % string)
+ LOG.error("Don't understand given string %s. Please check "
+ "format.", string)
return None
except SyntaxError:
- logger.error("Given string %s is not a valid expression" % string)
+ LOG.error("Given string %s is not a valid expression", string)
return None
return ev_str
else:
@@ -251,15 +252,23 @@ class CustomLogging:
:param outdir: path output directory
:return:
"""
- outdir = os.path.join(outdir, "log") if "log" not in outdir else outdir
+ outdir = os.path.join(outdir,
+ "log") if "log" not in outdir else outdir
if not os.path.exists(os.path.abspath(outdir)):
os.makedirs(outdir)
+ else:
+ # Trick to avoid overwriting files with w mode after copy2 call
+ shutil.rmtree(os.path.abspath(outdir))
+ os.makedirs(outdir)
if outdir and "handlers" in self.config:
for hand in self.config["handlers"]:
if "filename" in self.config["handlers"][hand]:
- self.config["handlers"][hand]["filename"] = \
- os.path.join(outdir, os.path.basename(
- self.config["handlers"][hand]["filename"]))
+ oldpath = self.config["handlers"][hand]["filename"]
+ newpath = os.path.abspath(os.path.join(
+ outdir, os.path.basename(
+ self.config["handlers"][hand]["filename"])))
+ self.config["handlers"][hand]["filename"] = newpath
+ shutil.copy2(oldpath, newpath)
logging.config.dictConfig(self.config)
def welcome(self):
@@ -275,6 +284,11 @@ class CustomLogging:
================================================================================
'''.format(self.msg)
print(desc)
+ for hand in self.config.get("handlers"):
+ if "filename" in self.config["handlers"][hand]:
+ with open(self.config["handlers"][hand]["filename"],
+ 'w') as f:
+ f.write(desc)
class Capturing(list):
@@ -293,7 +307,7 @@ class Capturing(list):
"""
:return:
"""
- logger.error("Error during capture [%s]" % str(args))
+ LOG.error("Error during capture [%s]", str(args))
self.extend("\n".join(self._stringio.getvalue().splitlines()))
sys.stdout = self._stdout
@@ -301,6 +315,6 @@ class Capturing(list):
if __name__ == "__main__":
# Test Logger
CustomLogging().set_outdir("../examples/out")
- logger = logging.getLogger("TEST")
- logger.info(dir(logger))
- logger.info("Log test")
+ LOG = logging.getLogger("TEST")
+ LOG.info(dir(LOG))
+ LOG.info("Log test")
diff --git a/ariaec/base.pyc b/ariaec/base.pyc
index 7bf708fc2a352ffa32022e43a46d1585927ecd8c..d7e6811a8be63e072cc464796d4e9212f524b606 100644
Binary files a/ariaec/base.pyc and b/ariaec/base.pyc differ
diff --git a/ariaec/commands.py b/ariaec/commands.py
index bee32d6e00022175300a714cc90ddb7e972f5542..ad37ce5fdb528f7a3d5f265e0e79a177e3e674aa 100644
--- a/ariaec/commands.py
+++ b/ariaec/commands.py
@@ -12,7 +12,8 @@ from .maplot import AriaEcContactMap
from .econverter import AriaEcBbConverter
from .setup import AriaEcSetup
-logger = logging.getLogger(__name__)
+
+LOG = logging.getLogger(__name__)
def check_file(prospective_file):
@@ -62,7 +63,7 @@ class AriaEcCommand:
parser = self._create_argparser()
# parse args
self.args = parser.parse_args()
- # Update logger with outdir
+ # Update LOG with outdir
self._update_logger(custom_logging)
def _update_logger(self, log):
@@ -70,9 +71,9 @@ class AriaEcCommand:
if not self.args.nolog:
# Don't generate log files
# TODO: get handler list from json file or customlogging object
- logger.removeHandler("info_file_handler")
- logger.removeHandler("error_file_handler")
- logger.removeHandler("debug_file_handler")
+ LOG.removeHandler("info_file_handler")
+ LOG.removeHandler("error_file_handler")
+ LOG.removeHandler("debug_file_handler")
log.set_outdir(self.args.output_directory)
log.update_msg(self.args.command)
log.welcome()
@@ -201,24 +202,24 @@ class AriaEcCommand:
return parser
def create_settings(self):
- logger.debug("Create AriaEcSettings")
+ LOG.debug("Create AriaEcSettings")
settings = AriaEcSettings(self.args.command)
- logger.info("Loading default config file")
+ LOG.info("Loading default config file")
settings.load_config(self.default_confile, pkg=True)
if self.args.conf_file:
- logger.info("Updating settings with conf file")
+ LOG.info("Updating settings with conf file")
settings.load_config(self.args.conf_file)
# Update settings associated to command section
- logger.info("Updating %s settings with args" % self.args.command)
+ LOG.info("Updating %s settings with args", self.args.command)
getattr(settings, self.args.command).args.update(self.args.__dict__)
if self.args.output_directory:
- logger.info("Updating output directory")
+ LOG.info("Updating output directory")
settings.infra = self.args.output_directory
return settings
def run(self):
# call method relative to args.command
- logger.info("Run %s command" % self.args.command)
+ LOG.info("Run %s command", self.args.command)
getattr(self, self.args.command)()
def setup(self):
@@ -238,5 +239,5 @@ class AriaEcCommand:
if __name__ == "__main__":
# Test AriaEcCommand object
logging.basicConfig(level=logging.DEBUG)
- logger = logging.getLogger("IO")
+ LOG = logging.getLogger("IO")
argparser = AriaEcCommand()
diff --git a/ariaec/conf/logging.json b/ariaec/conf/logging.json
index 1b1cd5dab4eb5c3ec0148ca5a9e86423edee17ae..f4eea3defb2521b08188573539665aad74dece6d 100644
--- a/ariaec/conf/logging.json
+++ b/ariaec/conf/logging.json
@@ -3,10 +3,10 @@
"disable_existing_loggers": false,
"formatters": {
"simple": {
- "format": "%(levelname)-8s --- %(message)s"
+ "format": "%(levelname)-8s %(message)s"
},
"detail": {
- "format": "[%(asctime)s] --- %(levelname)8s --- %(message)s (%(filename)s:%(lineno)s)",
+ "format": "[%(asctime)s] --- %(levelname)-8s --- %(message)s (%(filename)s:%(lineno)s)",
"datefmt": "%m/%d/%Y %I:%M:%S %p"
},
"colored": {
@@ -18,7 +18,7 @@
"handlers": {
"console": {
"class": "logging.StreamHandler",
- "level": "INFO",
+ "level": "DEBUG",
"formatter": "colored",
"stream": "ext://sys.stdout"
},
@@ -26,19 +26,18 @@
"info_file_handler": {
"class": "logging.handlers.RotatingFileHandler",
"level": "INFO",
- "formatter": "detail",
- "filename": "/tmp/aria_ec.log",
- "maxBytes": 10485760,
- "backupCount": 20,
+ "formatter": "simple",
+ "filename": "/tmp/ariaec.log",
+ "mode": "a",
"encoding": "utf8"
},
"debug_file_handler": {
"class": "logging.handlers.RotatingFileHandler",
"level": "DEBUG",
- "formatter": "simple",
- "filename": "/tmp/debug.log",
- "mode": "w",
+ "formatter": "detail",
+ "filename": "/tmp/ariaec.debug",
+ "mode": "a",
"encoding": "utf8"
},
@@ -46,15 +45,14 @@
"class": "logging.handlers.RotatingFileHandler",
"level": "ERROR",
"formatter": "detail",
- "filename": "/tmp/errors.log",
- "maxBytes": 10485760,
- "backupCount": 20,
+ "filename": "/tmp/ariaec.error",
+ "mode": "a",
"encoding": "utf8"
}
},
"root": {
- "level": "DEBUG",
+ "level": "INFO",
"handlers": ["console", "info_file_handler", "error_file_handler",
"debug_file_handler"]
}
diff --git a/ariaec/econverter.py b/ariaec/econverter.py
index 2ff6a606effff8bff1b4ef7decbb6bfc8e2a6e79..42d075d6d7b2c501848dbb2f23e7ab30abd15864 100644
--- a/ariaec/econverter.py
+++ b/ariaec/econverter.py
@@ -25,7 +25,7 @@ from aria.AriaXML import AriaXMLPickler
from aria.conversion import Converter, SequenceList, MoleculeSettings
-logger = logging.getLogger(__name__)
+LOG = logging.getLogger(__name__)
class AriaEcBbConverter(object):
@@ -38,10 +38,10 @@ class AriaEcBbConverter(object):
def run(self):
# Check input
- logger.debug("Settings:\n" + json.dumps(self.settings.setup.config,
- indent=4))
- logger.debug("Args:\n" + json.dumps(self.settings.setup.args,
- indent=4))
+ LOG.debug("Settings:\n" + json.dumps(self.settings.setup.config,
+ indent=4))
+ LOG.debug("Args:\n" + json.dumps(self.settings.setup.args,
+ indent=4))
# TODO: redirect print output to logging ? (low priority)
# ----------------------------- Input -------------------------------- #
self.outprefix = get_filename(self.settings.bbconv.args.get("seq",
@@ -128,7 +128,7 @@ class AriaXMLConverter(Converter, object):
sequence.parse(self._mol_set['input'], self._mol_set['format'],
self._mol_set['naming_convention'])
- # logger.info("\n" + "".join(output))
+ # LOG.info("\n" + "".join(output))
factory = self.create_factory()
@@ -232,7 +232,7 @@ assign (resid {res1} and name o) (resid {res2} and name hn) 1.8 {dminus} {dplus
distmap = hbmap.get("distmap")
if n_hb:
contacts = contacts[:n_hb]
- logger.debug(contacts)
+ LOG.debug(contacts)
donors = []
acces = []
for contact in contacts:
@@ -265,15 +265,15 @@ assign (resid {res1} and name o) (resid {res2} and name hn) 1.8 {dminus} {dplus
raise NotImplementedError
else:
if hb_type != "main":
- logger.error("Wrong longrange hbond type given. Default "
+ LOG.error("Wrong longrange hbond type given. Default "
"option used (main)")
# First residue = donor for a backbone hydrogen bond (N-H...O=C)
outfile.write('''\
assign (resid {res1} and name o) (resid {res2} and name n) 2.8 {dminus} {dplus}
assign (resid {res1} and name o) (resid {res2} and name hn) 1.8 {dminus} {dplus}
'''.format(res1=res1, res2=res2, dminus=dminus, dplus=dplus, dist=dist))
- logger.info("Writing %d hbonds from hbmap in %s" % (len(donors),
- outfile.name))
+ LOG.info("Writing %d hbonds from hbmap in %s", len(donors),
+ outfile.name)
def write_hb_tbl(self, protein, outfile, hbmap=None, dminus=0.0,
dplus=0.5, n_hb=None, lr_type='main'):
@@ -428,7 +428,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
elif prod_type == "all":
return list(itertools.product(atms1, atms2))
else:
- logger.error("Wrong pair_list option. Pair_list set to min")
+ LOG.error("Wrong pair_list option. Pair_list set to min")
return min_atms(res1, res2, list(itertools.product(atms1, atms2)))
def targetdistmap(self, distype, sequence, distfile=None, groupby=None):
@@ -514,7 +514,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
nb_c)
# Initial contact list start at 0
# pair_list = [(int(x[0]) + 1, int(x[1]) + 1) for x in pair_list]
- logger.info("Selecting %d contacts:\n%s" % (nb_c, pair_list))
+ LOG.info("Selecting %d contacts:\n%s", nb_c, pair_list)
if self.settings.setup.config['evfold_weight'] and scoremap is not None:
weight_list = list(float(10.0 / (x + 1)) for x, v in enumerate(
@@ -544,7 +544,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
contrib_id = 0
for contactidx, contact in enumerate(pair_list):
- logger.debug("Contact %s" % str(contact))
+ LOG.debug("Contact %s" % str(contact))
# Add neighbors if neigh_flag
resx_idx = range(min_ind(contact[0] - 1),
@@ -616,10 +616,10 @@ class AriaEcXMLConverter(AriaXMLConverter):
# In case missing distance values
target_dist = self.settings.setup.config[
"restraint_distance"]
- logger.warning(
+ LOG.warning(
"Target distance is missing for restraint "
- "%s-%s (%s). Using default distance (%s)"
- % (idx_x + 1, idx_y + 1, atm_pair, target_dist))
+ "%s-%s (%s). Using default distance (%s)",
+ idx_x + 1, idx_y + 1, atm_pair, target_dist)
rest_id += 1
contrib_id = 1
@@ -662,7 +662,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
}
xml_file = self.settings.infra["xml"] + "/" + "_".join((
self.outprefix, listname)) + ".xml"
- logger.info("Write %d xml distance restraints in %s" % (nb_c, xml_file))
+ LOG.info("Write %d xml distance restraints in %s", nb_c, xml_file)
self.write_dist_xml(restraint_dict, xml_file)
return xml_file, pair_list
@@ -670,7 +670,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
out = ([], [])
for maptype in maplist:
- logger.info("Writing %s ARIA XML distance restraints" % maptype)
+ LOG.info("Writing %s ARIA XML distance restraints", maptype)
outfile, pairlist = self.write_map_restraint(
maplist[maptype]['contactmap'], maplist[maptype]["nb_c"],
targetmap, listname=maptype,
@@ -694,16 +694,16 @@ class AriaEcXMLConverter(AriaXMLConverter):
"_hbond.tbl")
ssdist_file = os.path.join(self.settings.infra["tbl"], self.outprefix +
"_ssdist.tbl")
- logger.info(" Dihedral restraints (%s)" % dihed_file)
+ LOG.info(" Dihedral restraints (%s)", dihed_file)
self.write_dihedral_tbl(protein.sec_struct.ss_matrix, dihed_file)
- logger.info(" Helix bond restraints (%s)" % hb_file)
+ LOG.info(" Helix bond restraints (%s)", hb_file)
self.write_hb_tbl(protein, hb_file,
hbmap=hbmap, n_hb=n_hb,
lr_type=self.settings.setup.config['longrange_hbtype'],
dminus=self.settings.setup.config['hb_dminus'],
dplus=self.settings.setup.config['hb_dplus'])
- logger.info(" Secondary structure restraints (%s)" %
- ssdist_file)
+ LOG.info(" Secondary structure restraints (%s)",
+ ssdist_file)
self.write_ssdist_tbl(protein.sec_struct.ss_matrix,
protein.sec_struct.ssdist,
ssdist_file)
@@ -718,7 +718,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
except Exception as msg:
- logger.error("Error writing xml seq file : %s" % msg)
+ LOG.error("Error writing xml seq file : %s", msg)
return self._mol_set['output']
@@ -733,7 +733,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
:param desc:
:return:
"""
- logger.info("Loading aria template file %s" % aria_template)
+ LOG.info("Loading aria template file %s", aria_template)
templatepath = os.path.abspath(aria_template)
ariaproj_template = Template(filename=templatepath,
@@ -741,7 +741,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
try:
t = open(templatepath, 'r')
- except Exception, msg:
+ except Exception as msg:
sys.exit("""Can't open "%s" file. %s""" % (templatepath, msg))
aria_project_template = t.read()
@@ -761,13 +761,13 @@ class AriaEcXMLConverter(AriaXMLConverter):
temp_root = os.path.abspath(aria_project_dict['temp_root'])
if not os.path.exists(work_dir):
- logger.info("Working dir %s doesn't exist." % work_dir)
- logger.info("Create new directory %s" % work_dir)
+ LOG.info("Working dir %s doesn't exist.", work_dir)
+ LOG.info("Create new directory %s", work_dir)
os.makedirs(work_dir)
if not os.path.exists(temp_root):
- logger.info("Temp directory %s doesn't exist." % temp_root)
- logger.info("Create new directory %s" % temp_root)
+ LOG.info("Temp directory %s doesn't exist.", temp_root)
+ LOG.info("Create new directory %s", temp_root)
os.makedirs(temp_root)
aria_project_dict['working_directory'] = work_dir
@@ -834,5 +834,5 @@ class AriaEcXMLConverter(AriaXMLConverter):
proj_file = "%s/ariaproject.xml" % work_dir
with open(proj_file, 'w') as proj_xml:
- logger.info("Writing ARIA project file (%s)" % proj_file)
+ LOG.info("Writing ARIA project file (%s)", proj_file)
proj_xml.write(ariaproj_template.render(**aria_project_dict))
diff --git a/ariaec/ecsettings.py b/ariaec/ecsettings.py
index bebf738e19d8cfe0693e494b1b9b53a747435607..3ecb943f78b0939aa3dbb52e8d25e21328d43af3 100644
--- a/ariaec/ecsettings.py
+++ b/ariaec/ecsettings.py
@@ -12,7 +12,7 @@ import pkg_resources as pkgr
from .base import format_dict
-logger = logging.getLogger(__name__)
+LOG = logging.getLogger(__name__)
class Setting:
@@ -21,6 +21,10 @@ class Setting:
self.config = collections.defaultdict()
self.args = collections.defaultdict()
+ def __repr__(self):
+ return "Setting object\n config: %s\n args : %s" % (self.config,
+ self.args)
+
class Settings(object):
@@ -40,7 +44,7 @@ class Settings(object):
if os.path.exists(configpath):
self.configfile = configpath
elif not pkg:
- logger.error("Configuration file not found (%s)" % configpath)
+ LOG.error("Configuration file not found (%s)", configpath)
return None
config = SafeConfigParser(allow_no_value=True)
if pkg:
@@ -48,20 +52,20 @@ class Settings(object):
config.readfp(conf)
else:
config.read(configpath)
- logger.debug(config)
+ LOG.debug(config)
for section in config.sections():
if hasattr(self, section):
tmp = format_dict(dict(config.items(section)))
getattr(self, section).config.update(tmp)
- logger.debug("%s config updated" % section)
- logger.debug("%s.%s : %s" % (self.__class__.__name__, section,
- getattr(self, section)))
+ LOG.debug("%s config updated", section)
+ LOG.debug("%s.%s : %s", self.__class__.__name__, section,
+ getattr(self, section))
else:
- logger.warning("Unknow config section %s" % section)
+ LOG.warning("Unknow config section %s", section)
def write_config(self, filename):
# Ecrit les config de toutes les sections dans un autre fichier
- logger.info("Writing .ini file (%s)" % filename)
+ LOG.info("Writing .ini file (%s)", filename)
config = SafeConfigParser(allow_no_value=True)
iniout = open(filename, mode="w")
for section in self._sections:
@@ -72,6 +76,9 @@ class Settings(object):
str(getattr(self, section).config.get(opt)))
config.write(iniout)
+ def __repr__(self):
+ return "<Settings object>\n sections: %s" % self._sections
+
class AriaEcSettings(Settings):
@@ -97,7 +104,7 @@ class AriaEcSettings(Settings):
def _up_infra(self):
for d in self.infra:
- logger.debug("set %s dir: %s" % (d, os.path.join(self.outdir, d)))
+ LOG.debug("set %s dir: %s", d, os.path.join(self.outdir, d))
self._infra[d] = os.path.join(self.outdir, d)
@property
@@ -138,8 +145,8 @@ class AriaEcSettings(Settings):
if os.path.exists(pkgr.resource_filename(__name__, templatepath)):
self._template = pkgr.resource_filename(__name__, templatepath)
else:
- logger.error("Template version for aria project (%s) is not "
- "supported" % self.main.config.get("ariaproject_template"))
+ LOG.error("Template version for aria project (%s) is not "
+ "supported", self.main.config.get("ariaproject_template"))
self._template = pkgr.resource_filename(__name__,
self.ARIAPROJ_TEMPLATE)
return self._template
@@ -167,9 +174,9 @@ class AriaEcSettings(Settings):
return self._scsc_min
def make_infra(self):
- logger.info("Making output directories")
+ LOG.info("Making output directories")
for direct in self.infra:
- logger.debug("Create %s directory" % self.infra[direct])
+ LOG.debug("Create %s directory", self.infra[direct])
if not os.path.exists(self.infra[direct]):
os.makedirs(os.path.abspath(self.infra[direct]))
diff --git a/ariaec/ecsettings.pyc b/ariaec/ecsettings.pyc
index e9698ea485d18bb65619b3c4df6e8879e8beef31..7de756ad69f384c7d04df4932dde27ffa396fab4 100644
Binary files a/ariaec/ecsettings.pyc and b/ariaec/ecsettings.pyc differ
diff --git a/ariaec/maplot.py b/ariaec/maplot.py
index a5e0e61f1f690205cfd35bbe4bdc6dcdc5acdd5f..127f8d6aa7dfa727c2f8dab6365c6945f59f83fd 100644
--- a/ariaec/maplot.py
+++ b/ariaec/maplot.py
@@ -11,7 +11,7 @@ from .reader import ProtFileListReader
from .protmap import MapFilter
from .protein import Protein
-logger = logging.getLogger(__name__)
+LOG = logging.getLogger(__name__)
class AriaEcContactMap(object):
@@ -30,10 +30,10 @@ class AriaEcContactMap(object):
def run(self):
# Check input
- logger.debug("Settings:\n" + json.dumps(self.settings.contactmap.config,
- indent=4))
- logger.debug("Args:\n" + json.dumps(self.settings.contactmap.args,
- indent=4))
+ LOG.debug("Settings:\n" + json.dumps(self.settings.contactmap.config,
+ indent=4))
+ LOG.debug("Args:\n" + json.dumps(self.settings.contactmap.args,
+ indent=4))
if not self.settings.contactmap.args.get("onlyreport", False):
self.settings.make_infra()
# ----------------------------- Input -------------------------------- #
@@ -65,7 +65,7 @@ class AriaEcContactMap(object):
# TODO: filter pour toutes les map de mapdict !! (fonction remove
# s'applique sur l'humanidx contenant les residus)
if idx == 0:
- logger.info("%s map set as reference" % fo.filetype.capitalize())
+ LOG.info("%s map set as reference", fo.filetype.capitalize())
self.refmap = fo.mapdict
self.reftype = fo.filetype
self.refname = fo.filename if type(self.outprefix) != list \
@@ -89,7 +89,7 @@ class AriaEcContactMap(object):
try:
refmap = self.refmap["contactmap"]
except TypeError:
- logger.error("First contact map should be a valid file")
+ LOG.error("First contact map should be a valid file")
sys.exit(1)
# nb_c = int(len(self.protein.aa_sequence.sequence) *
@@ -115,8 +115,8 @@ class AriaEcContactMap(object):
for mapname, mapt in self.allresmap.keys():
if mapt != self.reftype:
# TODO: DON'T WORK !!!!
- logger.info("Merging %s with %s map" % (
- mergetype, mapt))
+ LOG.info("Merging %s with %s map",
+ mergetype, mapt)
up_map = self.allresmap[mapt]["contactmap"]
up_map[:] = up_map[:] + mergecontactmap[:]
mergekey = "%s_%s" % (mapt, mergetype)
@@ -150,8 +150,8 @@ class AriaEcContactMap(object):
cmplist = self.allresmap[(mapname, mapt, mapath)][
'contactmap'].contact_list(human_idx=True)
# else:
- # logger.warning("%s map doesn't have any score related. Can't "
- # "define top list related to this map" % mapt)
+ # LOG.warning("%s map doesn't have any score related. Can't "
+ # "define top list related to this map", mapt)
# continue
# TODO: only one function for output files
@@ -183,5 +183,5 @@ class AriaEcContactMap(object):
**plotparams)
# Contingency table
# print(cmpmap.to_series())
- # logger.info(pd.crosstab(cmpmap.values, refmap.values,
+ # LOG.info(pd.crosstab(cmpmap.values, refmap.values,
# rownames=[mapt], colnames=[self.reftype]))
diff --git a/ariaec/protein.py b/ariaec/protein.py
index e060ae1cf9c1abb8a63f66abb4803811642c2c76..feb8a87bee2ce17a8ec88f11c37cb82a2b8bd016 100644
--- a/ariaec/protein.py
+++ b/ariaec/protein.py
@@ -17,7 +17,7 @@ from .base import (reg_load, ppdict)
# TODO: interface skbio ??
-logger = logging.getLogger(__name__)
+LOG = logging.getLogger(__name__)
class SsList:
@@ -77,17 +77,16 @@ class SsList:
:return:
"""
self.check_filetype(filename)
- logger.info("Reading secondary structure file %s [%s]" % (
- filename,
- self.filetype))
+ LOG.info("Reading secondary structure file %s [%s]",
+ filename, self.filetype)
# TODO: better read with getattr
if self.filetype == "indextableplus":
self.read_indextableplus(filename)
else:
self.read_psipred(filename)
- logger.debug("Secondary structure matrix:\n%s\n"
- "Secondary structure dict:\n%s" % (self.ss_matrix,
- self.ssdict))
+ LOG.debug("Secondary structure matrix:\n%s\n"
+ "Secondary structure dict:\n%s", self.ss_matrix,
+ self.ssdict)
if sequence:
self.seq_sublist(sequence)
@@ -175,7 +174,7 @@ class SsList:
:param filename:
:return:
"""
- logger.info("Reading distance file {0}".format(filename))
+ LOG.info("Reading distance file {0}".format(filename))
c = 0
atom_list = []
for line in infile:
@@ -208,14 +207,14 @@ class SsList:
"""
filename = os.path.abspath(ssdistpath) if ssdistpath else None
- logger.info("Loading ss dist file")
+ LOG.info("Loading ss dist file")
try:
with open(filename) as f:
self._read_ssdist(f, filename=filename)
except Exception as message:
- logger.error("%s" % message)
- logger.error("Can't load given ss dist file...")
- logger.error("Loading default ss dist file")
+ LOG.error("%s", message)
+ LOG.error("Can't load given ss dist file...")
+ LOG.error("Loading default ss dist file")
with pkgr.resource_stream(__name__, self.settings.SS_DIST) as f:
self._read_ssdist(f, filename=self.settings.SS_DIST)
@@ -238,8 +237,8 @@ class SsList:
sys.exit('Missing residues in indextableplus file')
self.ss_matrix = self.ss_matrix[imin:imax]
- logger.debug("Secondary structure matrix relative to given "
- "sequence:\n%s" % self.ss_matrix)
+ LOG.debug("Secondary structure matrix relative to given "
+ "sequence:\n%s", self.ss_matrix)
# TODO: read_dssp
@@ -365,7 +364,7 @@ class AminoAcidSequence(SequenceList.SequenceList, object):
# Add dict
topo[resname][regid].append(match.groupdict())
break
- logger.debug("Topology used:\n%s" % ppdict(topo))
+ LOG.debug("Topology used:\n%s", ppdict(topo))
return topo
def read(self, filename):
@@ -378,11 +377,11 @@ class AminoAcidSequence(SequenceList.SequenceList, object):
# TODO: capturing has some troubles with unicode ...
# with Capturing() as output:
self.ReadFasta(text_type(filename))
- # logger.info(''.join(output))
+ # LOG.info(''.join(output))
self.sequence = "".join((AmnAcd.AminoAcid(str(_))[0] for _ in
self.aalist))
- logger.info("Amino acid sequence:\t%s" % self.sequence)
+ LOG.info("Amino acid sequence:\t%s", self.sequence)
class Protein:
@@ -441,7 +440,7 @@ class Protein:
if self.sec_struct.ss_matrix:
self.sec_struct.seq_sublist(self.aa_sequence.sequence)
if ssidx:
- logger.info("Using secondary structure index for amino acid "
+ LOG.info("Using secondary structure index for amino acid "
"sequence")
self.index = self.sync_index(self.aa_sequence.humanidx,
self.sec_struct.index)
@@ -462,15 +461,15 @@ class Protein:
# Read secondary distance matrix
self.sec_struct.read_ssdist(ssdist_filename)
else:
- logger.error("No secondary structure distance file found. Please "
+ LOG.error("No secondary structure distance file found. Please "
"check configuration file")
if self.aa_sequence.sequence:
# Synchronise sec structure sequence with aa sequence
- logger.info("Align secondary structure sequence with protein "
+ LOG.info("Align secondary structure sequence with protein "
"sequence")
self.sec_struct.seq_sublist(self.aa_sequence.sequence)
if ssidx:
- logger.info("Using secondary structure index for amino acid "
+ LOG.info("Using secondary structure index for amino acid "
"sequence")
self.index = self.sync_index(self.aa_sequence.humanidx,
self.sec_struct.index)
@@ -484,7 +483,7 @@ class Protein:
# TODO: same as above, trouble with unicode calls inside capturing
# with Capturing() as output:
self.aa_sequence.WriteSeq(text_type(outfile))
- # logger.info(''.join(output))
+ # LOG.info(''.join(output))
self.seqfile_path = outfile
@@ -493,4 +492,4 @@ if __name__ == "__main__":
settings = AriaEcSettings("setup")
prot = Protein(settings)
prot.set_aa_sequence("../examples/data/BPT1_BOVIN.fa")
- logger.info(prot.aa_sequence)
+ LOG.info(prot.aa_sequence)
diff --git a/ariaec/protmap.py b/ariaec/protmap.py
index 266156bf3d6baf09d044bb54b22daade6cce8076..d99940d83629e98e23fb69ead7b0189950fb1c0d 100644
--- a/ariaec/protmap.py
+++ b/ariaec/protmap.py
@@ -27,7 +27,7 @@ from .base import (tickmin, tickrot, titleprint)
import sklearn.metrics as skm
-logger = logging.getLogger(__name__)
+LOG = logging.getLogger(__name__)
# TODO: check dataframe symmetry or always use unstack
@@ -96,8 +96,8 @@ class Map(pd.DataFrame):
if value:
return value
else:
- logger.error("Map type should be in list %s" %
- self.mtype_choices.keys())
+ LOG.error("Map type should be in list %s",
+ self.mtype_choices.keys())
return None
def reduce(self):
@@ -136,7 +136,7 @@ class Map(pd.DataFrame):
def topmap(self, scoremap, nb_topcontact):
if self.dtype != bool:
- logger.info("Error when retrieving top contact map. The type of "
+ LOG.info("Error when retrieving top contact map. The type of "
"the given map is not a contact type!")
return self
self[:] = False
@@ -147,7 +147,7 @@ class Map(pd.DataFrame):
self.iat[(contact[0], contact[1])] = True
return self
else:
- logger.error("Given scoremap has not the same dimension !")
+ LOG.error("Given scoremap has not the same dimension !")
return None
def subfill(self, pairdict, level=0):
@@ -201,7 +201,7 @@ class ProteinMap(Map):
# Contact map Plot
if not self._maplot:
# Flush matplot
- logger.debug("Build maplot")
+ LOG.debug("Build maplot")
minticks = tickmin(self, shift=1) # Nb graduations
self._maplot = sns.heatmap(self, square=True, cbar=False,
@@ -217,7 +217,7 @@ class ProteinMap(Map):
plot_ext="pdf", plot_dpi=200):
plotpath = os.path.join(outdir, "%s.contactmap.%s" % (
outprefix, plot_ext))
- logger.info("Generate contact map plot (%s)" % plotpath)
+ LOG.info("Generate contact map plot (%s)", plotpath)
f, ax = plt.subplots(figsize=(12, 9))
tickrot(self.maplot.axes, self.maplot.figure,
rotype='horizontal')
@@ -296,13 +296,13 @@ class ProteinMap(Map):
linewidths=0.1, alpha=alpha,
marker=mark)
else:
- logger.info("Contact list: %s" % cmplist)
+ LOG.info("Contact list: %s", cmplist)
xind = [x - .5 for x in
zip(*cmplist)[0] + zip(*cmplist)[1]]
yind = [ymax - y + 1.5 for y in
zip(*cmplist)[1] + zip(*cmplist)[0]]
- logger.debug("Xind: %s" % xind)
- logger.debug("Yind: %s" % yind)
+ LOG.debug("Xind: %s", xind)
+ LOG.debug("Yind: %s", yind)
color = "red"
# width = [0.3 for _ in xind]
# for x, y, h in zip(xind, yind, width):
@@ -318,7 +318,7 @@ class ProteinMap(Map):
filename = ".".join((outprefix, "mapreport")) if outprefix else \
"mapreport"
reportpath = "%s/%s" % (outdir, filename)
- logger.info("Generate map report file (%s)" % reportpath)
+ LOG.info("Generate map report file (%s)", reportpath)
with open(reportpath, 'w') as reportf:
y_true = list(self.values.astype(int).flat)
y_pred = list(cmpmap.values.astype(int).flat)
@@ -418,12 +418,12 @@ class ProteinMap(Map):
roc_auc=roc_auc, allprec=allprec, allrec=allrec,
prthres=prthresholds, alltpr=alltpr, allfpr=allfpr,
rocthres=rocthresholds)
- logger.debug("\n" + msg)
+ LOG.debug("\n" + msg)
reportf.write(msg)
if plotag and scoremap is not None:
csv_roc = os.path.join(plotdir, "%s.roc.csv" % outprefix)
- logger.info("Generate roc file (%s)" % csv_roc)
+ LOG.info("Generate roc file (%s)", csv_roc)
with open(csv_roc, "w") as f:
f.write("TPR,FPR,Treshold\n")
writer = csv.writer(f)
@@ -431,7 +431,7 @@ class ProteinMap(Map):
plotpath = os.path.join(plotdir, "%s.roc.%s" % (outprefix,
plot_ext))
- logger.info("Generate roc plot (%s)" % plotpath)
+ LOG.info("Generate roc plot (%s)", plotpath)
plt.figure()
plt.plot(allfpr, alltpr, label='ROC curve (area = %0.2f)' % roc_auc)
plt.plot([0, 1], [0, 1], 'k--')
@@ -445,7 +445,7 @@ class ProteinMap(Map):
plt.savefig(plotpath)
csv_precall = os.path.join(plotdir, "%s.roc.csv" % outprefix)
- logger.info("Generate precall file (%s)" % csv_precall)
+ LOG.info("Generate precall file (%s)", csv_precall)
with open(csv_precall, "w") as f:
f.write("Precision,Recall,Treshold\n")
writer = csv.writer(f)
@@ -453,7 +453,7 @@ class ProteinMap(Map):
plotpath = os.path.join(plotdir, "%s.precall.%s" % (outprefix,
plot_ext))
- logger.info("Generate precall plot (%s)" % plotpath)
+ LOG.info("Generate precall plot (%s)", plotpath)
# Precision recall curve
plt.clf()
plt.plot(allrec, allprec, label='Precision-Recall curve')
@@ -470,7 +470,7 @@ class ProteinMap(Map):
outdir="", distmap=None, human_idx=True):
# CSV file giving TP/FP contacts
outpath = "%s/%s.contactcmp.csv" % (outdir, outprefix)
- logger.info("Generate stat file (%s)" % outpath)
+ LOG.info("Generate stat file (%s)", outpath)
with open(outpath, 'w') as outfile:
offset = 1 if human_idx else 0
extra_header = "" if distmap is None else ",dmin"
@@ -500,7 +500,7 @@ class ProteinMap(Map):
def write_contacts(self, filename, outdir="", human_idx=True,
scoremap=None):
filepath = "%s/%s.contact.txt" % (outdir, filename)
- logger.info("Generate contact file (%s)" % filepath)
+ LOG.info("Generate contact file (%s)", filepath)
with open(filepath, 'w') as outfile:
offset = 1 if human_idx else 0
# contacts = [sorted(contact) for contact in self.contactset()]
@@ -557,7 +557,7 @@ class ResAtmMap(ProteinMap):
def create_index(self, sequence, seq_pos=True, seqidx=None,
idxnames=None, colnames=None):
- logger.info("Indexing res - res dataframe")
+ 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
iupac_aa = ConversionTable.ConversionTable().table['AMINO_ACID'][
@@ -584,8 +584,8 @@ class ResAtmMap(ProteinMap):
atm_list = [atm for aa in seq for atm in filter(self.heavy_reg.match,
iupac_aa[aa].keys())]
if len(atm_list) != len(res_list):
- logger.error("Index lists aren't the same size\n%s\n%s" % (
- res_list, atm_list))
+ LOG.error("Index lists aren't the same size\n%s\n%s",
+ res_list, atm_list)
idxnames = idxnames if idxnames and len(idxnames) == 2 else [
"residuex", "atomx"]
@@ -596,7 +596,7 @@ class ResAtmMap(ProteinMap):
columns = pd.MultiIndex.from_tuples(list(zip(*[res_list,
atm_list])),
names=colnames)
- logger.debug("Index:\n%s" % index)
+ LOG.debug("Index:\n%s", index)
return index, columns
def create_heatmap(self):
@@ -632,8 +632,8 @@ class ResAtmMap(ProteinMap):
# If self is already a contact map
return None
# TODO: issue with sc_sc treshold !!!!!
- logger.info("Generate contact map using contact definition %s" %
- contactdef)
+ LOG.info("Generate contact map using contact definition %s",
+ contactdef)
# Initialize contact map to a boolean matrix filled with False
contact_map = ResAtmMap(sequence=self.sequence, mtype="contact",
desc=self.desc, sym=self.sym, path=self.path)
@@ -644,7 +644,7 @@ class ResAtmMap(ProteinMap):
contact_map[:] = self.applymap(lambda x: x < contactdef)
elif sum(x is not None for x in contactdef.values()) == 1 and def_cutoff:
- logger.info("Using default cutoff")
+ LOG.info("Using default cutoff")
contact_map[:] = self.applymap(lambda x: x < contactdef.get("default_cutoff"))
elif sum(x is not None for x in contactdef.values()) > 1:
@@ -659,11 +659,11 @@ class ResAtmMap(ProteinMap):
if contactdef[pair] > def_cutoff:
treshold = contactdef[pair]
else:
- logger.warning("Treshold for %s ignored (lower than "
- "the default cutoff)" % str(pair))
- logger.info(
- "Filtering values in matrix related to %s (%s)" %
- (str(pair), str(treshold) if treshold else def_cutoff))
+ LOG.warning("Treshold for %s ignored (lower than "
+ "the default cutoff)", str(pair))
+ LOG.info(
+ "Filtering values in matrix related to %s (%s)",
+ str(pair), str(treshold) if treshold else def_cutoff)
if pair in (("SC", "SC"), ("sc", "sc")):
# Use scsc_min to apply treshold updateonly for selected atom
# sidechain
@@ -683,11 +683,11 @@ class ResAtmMap(ProteinMap):
mask = ([any(tup) for tup in zip(*idx_list)],
[any(tup) for tup in zip(*col_list)])
elif pair not in atms_list:
- logger.error("Pair %s doesn't exist ..." % str(pair))
+ LOG.error("Pair %s doesn't exist ...", str(pair))
# Already applied a treshold for this pair
continue
else:
- logger.debug("Apply treshold for %s" % str(pair))
+ LOG.debug("Apply treshold for %s", str(pair))
atms_list.discard(pair)
# Selecting rows for each atom
mask = (self.index.get_level_values(1) == pair[0],
@@ -695,9 +695,9 @@ class ResAtmMap(ProteinMap):
tmp = self.loc[mask].apply(lambda x: x < float(treshold))
contact_map.update(tmp)
else:
- logger.error("Missing values in contact definition section. Add "
+ LOG.error("Missing values in contact definition section. Add "
"at least a default_cutoff value.")
- logger.debug("Contact map\n%s" % (contact_map.head()))
+ LOG.debug("Contact map\n%s", contact_map.head())
return contact_map
@@ -905,12 +905,12 @@ class MapFilter:
def nd_filter(self, mapdict):
# TODO: build ROC curve with number of top contacts as the parameter
- logger.info("...Network deconvolution filter (alpha=%.2f, beta=%.2f)" %
- (self.settings["nd_beta"], self.settings["nd_alpha"]))
+ LOG.info("...Network deconvolution filter (alpha=%.2f, beta=%.2f)",
+ self.settings["nd_beta"], self.settings["nd_alpha"])
scoremap = mapdict["scoremap"]
- logger.info(net_deconv(mapdict["scoremap"].as_matrix(),
- beta=self.settings["nd_beta"],
- alpha=self.settings["nd_alpha"]))
+ LOG.info(net_deconv(mapdict["scoremap"].as_matrix(),
+ beta=self.settings["nd_beta"],
+ alpha=self.settings["nd_alpha"]))
# TODO: MAJ score map avec matrice obtenue !!!
# !!!! Verifier que scoremap est bien maj et UTILISEE !!
return scoremap
@@ -924,7 +924,7 @@ class MapFilter:
"""
# Liste les contacts proches
clash_list = kwargs.get("clash_list")
- logger.info("...Position filter")
+ LOG.info("...Position filter")
close_list = []
contact_list = mapdict["contactmap"].contact_list()
@@ -938,7 +938,7 @@ class MapFilter:
def cons_filter(self, mapdict, **kwargs):
# Liste les contacts aves des residus fortement conserves
- logger.info("...Conservation filter")
+ LOG.info("...Conservation filter")
sec_struct = kwargs.get("sec_struct")
clash_list = kwargs.get("clash_list")
cons_pair = []
@@ -946,7 +946,7 @@ class MapFilter:
contact_list = mapdict["contactmap"].contact_list()
if sec_struct.filetype != "indextableplus":
- logger.warning("Conservation filter only works with indextableplus "
+ LOG.warning("Conservation filter only works with indextableplus "
"files !")
return {'clash': None, 'desc': None}
@@ -962,7 +962,7 @@ class MapFilter:
# If this clash already exist
continue
cons_pair.append(contact)
- logger.debug("Highly conserverd residue list: %s" % cons_res)
+ LOG.debug("Highly conserverd residue list: %s", cons_res)
return {'clash': cons_pair, 'desc': None}
@staticmethod
@@ -970,7 +970,7 @@ 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
- logger.info("...Disulfure bridge unicity filter")
+ LOG.info("...Disulfure bridge unicity filter")
clash_list = kwargs.get("clash_list")
unidisbridge_list = [] # Liste les ponts disulfures uniques
clashdisbridge_list = [] # Liste les ponts disulfures incompatibles
@@ -1030,7 +1030,7 @@ class MapFilter:
# TODO: better add clash list and sec_struct as object attribute
sec_struct = kwargs.get("sec_struct")
clash_list = kwargs.get("clash_list")
- logger.info("...Secondary structure clash filter")
+ LOG.info("...Secondary structure clash filter")
ss_matrix = sec_struct.ss_matrix
ss_list = zip(*ss_matrix)[2]
# contact_list from contact map start at 0 !!
@@ -1075,8 +1075,8 @@ class MapFilter:
# If both residues are in same helix or strand
desc = "%s,%s" % (ssi[0], ssj[0])
desc_dict[contact] = desc
- logger.debug("Ss conflict for contact %d %s (%s)" % (
- icontact, outcontact, desc))
+ LOG.debug("Ss conflict for contact %d %s (%s)",
+ icontact, outcontact, desc)
ssclash_pair.append(contact)
# ELIF encadre H ou E
elif ssi != ssj:
@@ -1150,63 +1150,63 @@ class MapFilter:
break
if ssclash:
- logger.debug("Ss clash for contact %d %s (%s)" % (
- icontact, outcontact, ssclash))
+ LOG.debug("Ss clash for contact %d %s (%s)",
+ icontact, outcontact, ssclash)
if ssclash in ("H-2,H", "H+2,H") \
and abs(resi - resj) == 6:
# Allow contact to the fifth residue in the
# helix
- logger.debug("Found (H-2, H) for contact %s clash "
+ LOG.debug("Found (H-2, H) for contact %s clash "
"but contact with fifth residue is "
- "actually allowed" %
- outcontact)
+ "actually allowed",
+ outcontact)
ssclash = None
elif ssclash in ("H-3,H", "H+3,H") \
and abs(resi - resj) < 12:
- logger.debug("Found (H-3, H) for contact %s clash "
+ LOG.debug("Found (H-3, H) for contact %s clash "
"but contact between 3rd and 10th "
- "residues are actually allowed" %
- outcontact)
+ "residues are actually allowed",
+ outcontact)
# Allow contact between 3rd residue and 10th
ssclash = None
elif ssclash in ("H-4,H", "H+4,H"):
- logger.debug("H-4,H are actually allowed")
+ LOG.debug("H-4,H are actually allowed")
ssclash = None
elif ssclash in ("H-2,H+2", "H+2,H-2"):
- logger.debug("H-2,H+2 are actually allowed")
+ LOG.debug("H-2,H+2 are actually allowed")
ssclash = None
elif ssclash in ("H-3,H+3", "H+3,H-3"):
- logger.debug("H-3,H+3 are actually allowed")
+ LOG.debug("H-3,H+3 are actually allowed")
ssclash = None
elif ssclash in ("H-4,H+4", "H+4,H-4"):
- logger.debug("H-4,H+4 are actually allowed")
+ LOG.debug("H-4,H+4 are actually allowed")
ssclash = None
elif ssclash == "E-2,E+2":
strand = ssj if ssj[0] == "E" else ssi
start = ss_start_end[strand][1]
end = ss_start_end[strand][0]
if abs(start - end + 1) <= 5:
- logger.debug("Found (E-2, E+2) for contact "
+ LOG.debug("Found (E-2, E+2) for contact "
"%s clash but strand "
- "is < 5 residues" % outcontact)
+ "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"):
- logger.debug("E-3,E+3 are actually allowed")
+ LOG.debug("E-3,E+3 are actually allowed")
ssclash = None
elif ssclash in ("E-4,E+4", "E+4,E-4"):
- logger.debug("E-4,E+4 are actually allowed")
+ LOG.debug("E-4,E+4 are actually allowed")
ssclash = None
elif ssclash in ("E-4,E", "E+4,E") \
and abs(resi - resj) < 8:
- logger.debug("Found (E-4, E) for contact %s clash "
+ LOG.debug("Found (E-4, E) for contact %s clash "
"but contacts below 4th residue are "
- "actually allowed" % outcontact)
+ "actually allowed", outcontact)
ssclash = None
if ssclash:
- logger.debug(
- "Ss conflict for contact %d %s (%s)" % (
- icontact, outcontact, ssclash))
+ LOG.debug(
+ "Ss conflict for contact %d %s (%s)",
+ icontact, outcontact, ssclash)
desc_dict[contact] = ssclash
ssclash_pair.append(contact)
break
@@ -1241,7 +1241,7 @@ class MapFilter:
mapfilters = [mapfilters]
if "pos" not in mapfilters:
mapfilters.insert(0, "pos")
- logger.info("Filtering %s contact map" % mtype)
+ LOG.info("Filtering %s contact map", mtype)
for flt in mapfilters:
# /!\ cys unicity filter must be the last filter !
# TODO: contacts_flt.out checking if given clash in coupling
@@ -1253,9 +1253,9 @@ class MapFilter:
if flt_res.get("clash"):
clash_list.extend(flt_res.get("clash"))
hum_list = [(x + 1, y + 1) for x, y in flt_res.get("clash")]
- logger.info(
- "Removed %d contacts:\n%s" % (len(flt_res.get("clash")) / 2,
- hum_list))
+ LOG.info(
+ "Removed %d contacts:\n%s", len(flt_res.get("clash")) / 2,
+ hum_list)
clash_dict[flt] = flt_res.get("clash")
if flt_res.get("desc"):
desc_dict.update(flt_res.get("desc"))
@@ -1266,28 +1266,28 @@ class MapFilter:
# Contactmap always filtered
# TODO: could set a treshold instead of n_factor
- logger.info("Setting contact number with treshold %s" %
- self.settings.get("n_factor"))
+ LOG.info("Setting contact number with treshold %s",
+ self.settings.get("n_factor"))
nb_c = int(len(mapdict["contactmap"].sequence) * float(
self.settings.get("n_factor")))
nb_c = nb_c if nb_c < len(mapdict["contactmap"].contactset()) else len(
mapdict["contactmap"].contactset())
mapdict["nb_c"] = nb_c
- logger.info("Update %s contactmap" % mtype)
+ LOG.info("Update %s contactmap", mtype)
mapdict["contactmap"].remove(clash_list)
if mapdict["scoremap"] is not None:
- logger.info("Update %s scoremap" % mtype)
+ LOG.info("Update %s scoremap", mtype)
mapdict["scoremap"].remove(clash_list)
# Get nb_c top maps
- logger.info("Select top %d contacts according to scoremap" % nb_c)
+ LOG.info("Select top %d contacts according to scoremap", nb_c)
# TODO: deplacer cette partie dans l'appel de contactmap une fois
# la classe mapcollections utilisee
mapdict["contactmap"] = mapdict["contactmap"].topmap(mapdict["scoremap"],
nb_c)
if mapdict["distmap"] is not None:
- logger.info("Update %s distmap" % mtype)
+ LOG.info("Update %s distmap", mtype)
mapdict["distmap"].remove(clash_list)
return mapdict
diff --git a/ariaec/reader.py b/ariaec/reader.py
index 30b7a9c05b59787334883d9fa6aed81eef139c83..7b27c166b3c0620d0fe0283178cdff51b2fd4668 100644
--- a/ariaec/reader.py
+++ b/ariaec/reader.py
@@ -12,7 +12,7 @@ import scipy.spatial.distance as distance
from .base import sort_2dict
from .protmap import (ResMap, ResAtmMap)
-logger = logging.getLogger(__name__)
+LOG = logging.getLogger(__name__)
Atom = collections.namedtuple("Atom", ["name", "coords"])
@@ -33,7 +33,7 @@ class RegexFile(object):
lines_dict = {}
if not self.regex:
- logger.error("Can't parse file %s" % self.filepath)
+ LOG.error("Can't parse file %s", self.filepath)
with open(self.filepath) as f:
for index, line in enumerate(f):
@@ -226,12 +226,12 @@ class MapFile(RegexFile):
Check if plm_dict is consistent with input sequence
:param aa_seq:
"""
- logger.info("Checking consistency of contacts with input sequence")
+ LOG.info("Checking consistency of contacts with input sequence")
for line in self.lines:
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]:
- logger.error("Difference between given sequence and residu "
- "names in contact file at line %d !" % line)
+ LOG.error("Difference between given sequence and residu "
+ "names in contact file at line %d !", line)
def update_map(self, resmap):
"""
@@ -247,7 +247,7 @@ class MapFile(RegexFile):
:return:
"""
- logger.info("Checking format for file %s" % self.filepath)
+ LOG.info("Checking format for file %s", self.filepath)
# Check if given type is supported
# TODO: report this check into commands section
with open(self.filepath) as infile:
@@ -257,52 +257,52 @@ class MapFile(RegexFile):
match = self.types[self.filetype].get("regex").match(line)
else:
match = None
- logger.error("Format %s not supported !" % self.filetype)
+ 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:
- logger.debug("Format type correct")
+ LOG.debug("Format type correct")
return [
self.types[self.filetype].get("regex"),
self.filetype,
self.types[self.filetype].get("score_field")
]
elif def1match:
- logger.debug("Format type correct")
+ LOG.debug("Format type correct")
return [
self.types["default_1"].get("regex"),
self.filetype,
self.types["default_1"].get("score_field")
]
elif def2match:
- logger.debug("Format type correct")
+ LOG.debug("Format type correct")
return [
self.types["default_2"].get("regex"),
self.filetype,
self.types["default_2"].get("score_field")
]
elif def3match:
- logger.debug("Format type correct")
+ LOG.debug("Format type correct")
return [
self.types["default_3"].get("regex"),
self.filetype,
self.types["default_3"].get("score_field")
]
elif def4match:
- logger.debug("Format type correct")
+ LOG.debug("Format type correct")
return [
self.types["default_4"].get("regex"),
self.filetype,
self.types["default_4"].get("score_field")
]
if index > 2:
- logger.error("Error reading %s file." % self.filetype)
+ LOG.error("Error reading %s file.", self.filetype)
# Remove contact file
break
- logger.error("Wrong format type given ...")
+ LOG.error("Wrong format type given ...")
return [None] * 3
def read(self, protein=None, contactdef=5.0, groupby_method="min",
@@ -315,13 +315,13 @@ class MapFile(RegexFile):
:param scsc:
:return:
"""
- logger.info("Reading %s file" % self.filepath)
+ LOG.info("Reading %s file", self.filepath)
if self.filetype:
# Read file with regex related to filetype
self.load()
- logger.debug(self.lines)
+ LOG.debug(self.lines)
if protein:
- logger.info("Loading contact list")
+ LOG.info("Loading contact list")
if self.filetype == "contactlist":
self.flaglist = {
tuple(sorted(
@@ -348,7 +348,7 @@ class MapFile(RegexFile):
for contact in self.lines
if self.lines[contact].get("res1_nb") and
self.lines[contact].get("res2_nb")]
- logger.debug(self.contactlist)
+ LOG.debug(self.contactlist)
sym = False if self.filetype == "metapsicovhb" else True
self.create_map(protein, contactdef,
groupby_method=groupby_method, scsc=scsc,
@@ -358,7 +358,7 @@ class MapFile(RegexFile):
# consistent with given sequence
self.check_contacts(protein.aa_sequence.sequence)
if self.filetype == "evfold":
- logger.info("Loading evfold clash list")
+ LOG.info("Loading evfold clash list")
self.clashlist = [
next((el for el in (self.lines[contact].get("ss_filter"),
self.lines[contact].get("high_cons_filter"),
@@ -367,9 +367,9 @@ class MapFile(RegexFile):
self.lines[contact].get("res1_nb") and
self.lines[contact].get("res2_nb")]
if len(self.contactlist) != len(self.clashlist):
- logger.error("When reading input file, clash list is not "
+ LOG.error("When reading input file, clash list is not "
"the same length than contactlist")
- logger.debug(self.clashlist)
+ LOG.debug(self.clashlist)
class ContactMapFile(MapFile):
@@ -431,11 +431,11 @@ class ContactMapFile(MapFile):
if (int(residx1.split("-")[0]) != resid1) or \
(resid2 != int(residx2.split("-")[0])):
- logger.error("Wrong resid humanidx (%d, %d) in contact (%d) is "
- "not the same in resmap (%d, %d)" % (
- resid1, resid2, contact_id,
- int(residx1.split("-")[0]),
- int(residx2.split("-")[0])))
+ LOG.error("Wrong resid humanidx (%d, %d) in contact (%d) is "
+ "not the same in resmap (%d, %d)",
+ resid1, resid2, contact_id,
+ int(residx1.split("-")[0]),
+ int(residx2.split("-")[0]))
contactmap.set_value(residx1, residx2, True)
if self.sort:
@@ -445,9 +445,9 @@ class ContactMapFile(MapFile):
if distmap is not None:
distmap.set_value(residx1, residx2, dist)
- logger.debug("%s contact map:\n%s" % (self.filetype, contactmap))
+ LOG.debug("%s contact map:\n%s", self.filetype, contactmap)
self.mapdict["contactmap"] = contactmap
- logger.debug("%s score map:\n%s" % (self.filetype, scoremap))
+ LOG.debug("%s score map:\n%s", self.filetype, scoremap)
self.mapdict["scoremap"] = scoremap
if distmap is not None:
self.mapdict["distmap"] = distmap
@@ -479,7 +479,7 @@ class PDBFile(MapFile):
flaglist=flaglist, path=path,
seqidx=protein.index, desc=self.filetype)
resmap[:] = self.update_map(resmap, sym=sym)
- logger.debug("pdb distance map:\n%s" % resmap)
+ LOG.debug("pdb distance map:\n%s", resmap)
self.mapdict["alldistmap"] = resmap
self.mapdict["distmap"] = resmap.reduce(groupby=groupby_method)
self.mapdict["allcontactmap"] = resmap.contact_map(
@@ -489,7 +489,7 @@ class PDBFile(MapFile):
def update_map(self, resmap, sym=True):
# Map only on heavy atoms
# TODO: check if same sequence in pdb file
- logger.info("Updating distance map with pdb file")
+ LOG.info("Updating distance map with pdb file")
newmap = resmap.copy()
heavylist = []
error_list = set()
@@ -517,7 +517,7 @@ class PDBFile(MapFile):
dist = distance.euclidean(coordx, coordy)
if indx[0] in list(resmap.index.get_level_values("residuex"))\
and indy[0] in list(resmap.index.get_level_values("residuex")):
- logger.debug("Update distance value (%s, %s)" % (indx, indy))
+ LOG.debug("Update distance value (%s, %s)", indx, indy)
newmap.at[indx, indy] = dist
if sym:
# If symmetric matrix
@@ -536,8 +536,8 @@ class PDBFile(MapFile):
newmap.loc[idx] = None
if sym:
newmap.loc[:][idx] = None
- logger.error("Can't update pdb distance map for pos in pdb file "
- "%s with %s" % (list(error_list), missidx))
+ LOG.error("Can't update pdb distance map for pos in pdb file "
+ "%s with %s", list(error_list), missidx)
return newmap
@@ -572,12 +572,12 @@ class ProtFileListReader:
filetypelist) != list else filetypelist
if not filetypelist or len(filepathlist) != len(filetypelist):
filetypelist = [os.path.splitext(_)[1][1:] for _ in filepathlist]
- logger.info("Reader focused on file(s) %s %s" % (filepathlist,
- filetypelist))
+ LOG.info("Reader focused on file(s) %s %s", filepathlist,
+ filetypelist)
for i, filepath in enumerate(filepathlist):
if os.path.exists(filepath):
# TODO: check_type functionstr
- logger.debug("Adding %s file to watchlist" % filetypelist[i])
+ LOG.debug("Adding %s file to watchlist", filetypelist[i])
if filetypelist[i].lower() == "pdb" and \
os.path.splitext(filepath)[1][1:] == "pdb":
self.filelist.append(PDBFile(filepath))
@@ -589,7 +589,7 @@ class ProtFileListReader:
# filetypelist[i]))
# TODO: DistanceMapFile condition
if not self.filelist[-1].regex:
- logger.warning("Can't read %s" % filepath)
+ LOG.warning("Can't read %s", filepath)
self.filelist.pop()
def read(self, filepathlist, filetypelist=None, protein=None, scsc=None,
diff --git a/ariaec/setup.py b/ariaec/setup.py
index 335a376c45c399144b5dc9e1d2d1fa5d58150f0e..273bacbe337ea9552bd930c6b4246404992990a4 100644
--- a/ariaec/setup.py
+++ b/ariaec/setup.py
@@ -16,7 +16,7 @@ from .econverter import AriaEcXMLConverter
# TODO: S'inspirer de pandas/__init__.py pour les dependances
# from basictools import *
-logger = logging.getLogger(__name__)
+LOG = logging.getLogger(__name__)
class AriaEcSetup:
@@ -44,10 +44,10 @@ class AriaEcSetup:
:return:
"""
# Check input
- logger.debug("Settings:\n" + json.dumps(self.settings.setup.config,
- indent=4))
- logger.debug("Args:\n" + json.dumps(self.settings.setup.args,
- indent=4))
+ LOG.debug("Settings:\n" + json.dumps(self.settings.setup.config,
+ indent=4))
+ LOG.debug("Args:\n" + json.dumps(self.settings.setup.args,
+ indent=4))
self.settings.make_infra()
# -------------------------------------------------------------------- #
# ----------------------------- Input -------------------------------- #
@@ -89,7 +89,7 @@ class AriaEcSetup:
# ---------------------------- target map ---------------------------- #
if self.settings.setup.args.get("distfile") and \
self.settings.setup.config.get("distance_type") == "distfile":
- logger.info("Loading target distance file")
+ LOG.info("Loading target distance file")
# Read distance file
self.reader.read(
self.settings.setup.args.get("distfile"),
@@ -146,7 +146,7 @@ class AriaEcSetup:
# Setting contact number limit for hbmap
n_hb = int(len(self.protein.aa_sequence.sequence) *
self.settings.setup.config.get("nf_longrange_hb"))
- logger.info("Writing tbl files ...")
+ LOG.info("Writing tbl files ...")
tbl_files = self.converter.write_tbl_restraints(
self.protein, hbmap=self.hbmaps, n_hb=n_hb)
@@ -229,7 +229,7 @@ class AriaEcSetup:
raise TypeError('Contact list must be 2-tuple !')
contacts = contacts_list if not nc else contacts_list[:nc]
d_type = False
- logger.debug("Contact list %s" % contacts)
+ LOG.debug("Contact list %s", contacts)
for contact in contacts:
if d_type:
@@ -240,7 +240,7 @@ class AriaEcSetup:
resid1 = int(contact[0])
resid2 = int(contact[1])
- logger.debug("Contact %s" % (str(contact)))
+ LOG.debug("Contact %s", str(contact))
if distmap is not None:
dist = distmap.ix[(resid1, resid2)]
else:
@@ -279,5 +279,5 @@ if __name__ == "__main__":
from .ecsettings import AriaEcSettings
logging.basicConfig(level=logging.DEBUG)
- logger = logging.getLogger("Setup")
+ LOG = logging.getLogger("Setup")
AriaEcSettings('setup').load_config('aria_ec.ini')
diff --git a/bin/ec2aria.py b/bin/ec2aria.py
index e34f43723092801e25fc2605755ea4960b08b1fa..72b3342be8a820983b52ec02b46927bf038678f6 100644
--- a/bin/ec2aria.py
+++ b/bin/ec2aria.py
@@ -6,26 +6,15 @@
"""
from __future__ import absolute_import, division, print_function
-# TODO: replace all aria_ec ref into script name
# TODO: Utiliser scikit-bio pour traiter les sequences biologiques
import logging
-# Adding aria path
-# if 'ARIA2' not in os.environ:
-# sys.exit("This program needs ARIA2 !")
-# else:
-# ariapath = os.path.abspath(os.path.join(os.environ['ARIA2'], 'src/py'))
-# sys.path.insert(0, ariapath)
-
-# Adding ariaec path
-# TODO: remove this part if setup.py works !!!
-# sys.path.insert(0, os.path.abspath(os.path.dirname(os.path.dirname(__file__))))
from ariaec.base import CustomLogging
import ariaec.commands as ecio
-logger = logging.getLogger(__name__)
+LOG = logging.getLogger(__name__)
def main():