Changed infra call;New infra functions (ariaecsettings);infra for contactmap section

ariaec/commands.py

@@ -186,7 +186,7 @@ class AriaEcCommand:
 
     def create_settings(self):
         logger.debug("Create AriaEcSettings")
-        settings = AriaEcSettings()
+        settings = AriaEcSettings(self.args.command)
         logger.info("Loading default config file")
         settings.load_config(self.default_confile, pkg=True)
         if self.args.conf_file:
@@ -198,6 +198,7 @@ class AriaEcCommand:
         if self.args.output_directory:
             logger.info("Updating output directory")
             settings.infra = self.args.output_directory
+        settings.make_infra()
         return settings
 
     def run(self):

ariaec/conf/aria_ec.ini

@@ -47,10 +47,8 @@ pair_list:                                  min
 ambiguous_distance_restraint:               False
 ambiguous_distance_type:                    min
 deffpow:                                    6
-; TODO: move groupby_method to contactdef section
-groupby_method:                             min
 distance_type:                              fixed
-; TODO: move parameters below to contactdef section
+groupby_method:                             min
 ; Parameters below used only when distance_type is set to "fixed"
 restraint_distance:                         2.5
 lower_bound:                                1.0
@@ -125,7 +123,6 @@ whatif_executable:                          whatif
 ; -------------------------- Contactmap parameters --------------------------- #
 ; Plot settings
 n_factor:                                   1.5
-groupby_method:                             min
 save_fig:                                   True
 size_fig:                                   10
 plot_ext:                                   pdf

ariaec/econverter.py

@@ -39,8 +39,6 @@ class AriaEcBbConverter(object):
                                                 indent=4))
         logger.debug("Args:\n" + json.dumps(self.settings.setup.args,
                                             indent=4))
-        # Check output infrastructure
-        self.settings.make_infrastructure()
         # TODO: redirect print output to logging ? (low priority)
         # ----------------------------- Input -------------------------------- #
         self.outprefix = get_filename(self.settings.bbconv.args.get("seq",
@@ -50,14 +48,13 @@ class AriaEcBbConverter(object):
         # Load secondary structure prediction file
         self.protein.set_sec_struct(self.settings.bbconv.args.get("sspred",
                                                                   None))
-        self.reader.add_file(self.settings.bbconv.args.get("contactfile"),
-                             filetypelist=[self.settings.bbconv.args.get(
-                                 "contact_type")])
-        self.reader.read(self.protein,
+        self.reader.read(self.settings.bbconv.args.get("contactfile"),
+                         filetypelist=[self.settings.bbconv.args.get("contact_type")],
+                         protein=self.protein,
                          groupby_method=self.settings.setup.config['groupby_method'],
                          scsc=self.settings.scsc_min)
         # ---------------------------- Processing ---------------------------- #
-        # Convert plmdca contacts in couplingmatrix file (CCMPred format)
+        # Convert contacts into couplingmatrix file (CCMPred format)
         self.reader.filelist[0].mapdict["scoremap"].to_csv(
             "%s/%s.mat" % (self.settings.outdir, self.outprefix),
             index=False, header=False, sep="\t", float_format="%13.10f")

ariaec/ecsettings.py

@@ -87,26 +87,41 @@ class AriaEcSettings(Settings):
     SCSC_MIN = 'data/scsc_min.p'
     TOPO = 'data/topallhdg5.3.pro'
 
-    def __init__(self):
+    def __init__(self, name):
         super(AriaEcSettings, self).__init__(("main", "setup", "contactmap",
                                               "bbconv", "contactdef"))
-        self._infra = {"xml": '', "tbl": '', "others": ''}
+        self._infra = {}
         self._scsc_min = None
         self._ss_dist = None
         self._template = None
         self.outdir = os.getcwd()
-        self.infra = self.outdir
+        self.name = name
+
+    def _up_infra(self):
+        for d in self.infra:
+            logger.debug("set %s dir: %s" % (d, os.path.join(self.outdir, d)))
+            self._infra[d] = os.path.join(self.outdir, d)
 
     @property
     def infra(self):
+        if self.name == "setup" and not self._infra:
+            self._infra = {"xml": "", "tbl": "", "others": ""}
+            self._up_infra()
+        elif self.name == "contactmap" and not self._infra:
+            self._infra = {"graphics": ""}
+            self._up_infra()
         return self._infra
 
     @infra.setter
-    def infra(self, outdir):
-        self.outdir = os.path.abspath(outdir)
-        for d in self._infra:
-            logger.debug("set %s dir: %s" % (d, os.path.join(self.outdir, d)))
-            self._infra[d] = os.path.join(self.outdir, d)
+    def infra(self, root):
+        """
+        Change infra root
+        :param root:
+        :return:
+        """
+        self.outdir = os.path.abspath(root)
+        if self.infra:
+            self._up_infra()
 
     @property
     def scsc_min(self):
@@ -132,7 +147,7 @@ class AriaEcSettings(Settings):
         else:
             return self._scsc_min
 
-    def make_infrastructure(self):
+    def make_infra(self):
         logger.info("Making infrastructure in %s" % self.outdir)
         for direct in self.infra:
             logger.debug("Making %s directory" % self.infra[direct])

ariaec/maplot.py

@@ -56,7 +56,7 @@ class AriaEcContactMap(object):
         self.file_reader.read(self.settings.contactmap.args.get("infiles"),
                               filetypelist=self.settings.contactmap.args.get("contact_types"),
                               protein=self.protein,
-                              groupby_method=self.settings.contactmap.config[
+                              groupby_method=self.settings.setup.config[
                                   'groupby_method'],
                               scsc=self.settings.scsc_min)
 
@@ -95,6 +95,7 @@ class AriaEcContactMap(object):
                                     **plotparams)
                 continue
 
+            scoremap = self.allresmap[mapt].get('scoremap', None)
             if self.allresmap[mapt].get("contactmap") is not None and \
                     self.allresmap[mapt].get("scoremap") is not None:
 
@@ -121,8 +122,8 @@ class AriaEcContactMap(object):
             # Write contact list in txt file
             cmpmap.write_contacts("_".join((self.outprefix, mapt)),
                                   outdir=outdir)
-            # Write comparison stats in csv file
-            cmpmap.compare_contactmap(refmap, cmplist, prefix,
+            # Write comparison stats
+            cmpmap.compare_contactmap(refmap, scoremap, cmplist, prefix,
                                       distmap=self.refmap["distmap"],
                                       human_idx=True,
                                       outdir=outdir)

ariaec/protmap.py

@@ -2,15 +2,13 @@
                     ARIA Evolutionary Constraints Tools
 """
 from __future__ import absolute_import, division, print_function
-# import sys
-import os
-
-# ariapath = os.path.abspath(os.path.join(os.environ['ARIA2'], 'src/py'))
-# sys.path.insert(0, ariapath)
 
-import re
 import matplotlib
+
 matplotlib.use("Agg", warn=False)
+
+import os
+import re
 import logging
 import collections
 import itertools
@@ -290,10 +288,11 @@ class ProteinMap(Map):
             if save_fig:
                 self.saveplot(**kwargs)
 
-    def compare_contactmap(self, cmpmap, contactlist, outprefix, outdir="",
-                           distmap=None,
-                           human_idx=True):
+    def compare_contactmap(self, cmpmap, scoremap, contactlist, outprefix,
+                           outdir="", distmap=None, human_idx=True):
         # CSV file giving TP/FP contacts
+        print(*self.astype(int).values.flat)
+        print(cmpmap.values)
         outfile = open("%s/%s.contact.csv" % (outdir, outprefix), 'w')
         logger.info("Writing stat file %s" % outfile)
         offset = 1 if human_idx else 0

ariaec/setup.py

@@ -39,8 +39,6 @@ class AriaEcSetup:
                                                 indent=4))
         logger.debug("Args:\n" + json.dumps(self.settings.setup.args,
                                             indent=4))
-        # Check output infrastructure
-        self.settings.make_infrastructure()
         # -------------------------------------------------------------------- #
         # ----------------------------- Input -------------------------------- #
         # -------------------------------------------------------------------- #
@@ -270,4 +268,4 @@ if __name__ == "__main__":
 
     logging.basicConfig(level=logging.DEBUG)
     logger = logging.getLogger("Setup")
-    AriaEcSettings().load_config('aria_ec.ini')
+    AriaEcSettings('setup').load_config('aria_ec.ini')

setup.py

@@ -96,6 +96,7 @@ setup(
         'pandas',
         'seaborn',
         'scipy',
+        'sklearn',
         'colorlog',
         # 'scikit-bio==0.4.0',
         # 'aria==2.3'