Bug revision: filter.out merged when there is more than one contact file...

ariaec/base.py

@@ -21,6 +21,16 @@ from io import StringIO
 LOG = logging.getLogger()
 
 
+def addtup(tup, inc=1):
+    """
+    Increment all values by 1 in a tuple
+    :param tup:
+    :param inc:
+    :return:
+    """
+    return tuple((val + inc for val in tup))
+
+
 def titleprint(outfile, progname='', desc=''):
     """
     Init log file

ariaec/commands.py

@@ -96,6 +96,8 @@ class AriaEcCommand(object):
                             default=None, help="configuration file")
         parser.add_argument("--nolog", action="store_true",
                             default=False, help="Don't generate log files")
+        parser.add_argument("--debug", default=False, action='store_true',
+                            help="Toggle on debug mode")
         # Create subcommands
         self._create_subparsers(parser.add_subparsers(dest="command"))
         return parser
@@ -228,6 +230,9 @@ class AriaEcCommand(object):
         if self.args.output_directory:
             LOG.info("Updating output directory")
             settings.infra = self.args.output_directory
+        if self.args.debug:
+            LOG.info("Toggle on debug mode")
+            logging.getLogger().setLevel(logging.DEBUG)
         return settings
 
     def run(self):

ariaec/econverter.py

@@ -14,6 +14,7 @@ import os
 import sys
 import json
 import re
+import textwrap
 import aria.legacy.AminoAcid as AminoAcid
 from .base import get_filename
 from .protein import Protein
@@ -602,7 +603,11 @@ 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]
-        LOG.info("Selecting %d contacts:\n%s", nb_c, pair_list)
+        hum_list = [(con1 + 1, con2 +1) for con1, con2 in pair_list]
+        LOG.info("Selecting %d contacts\n%s", nb_c,
+                 '\n'.join(textwrap.wrap(' '.join(["(%2d, %2d)" % pair for
+                                                   pair in hum_list]),
+                                         width=80)))
 
         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(
@@ -648,7 +653,8 @@ class AriaEcXMLConverter(AriaXMLConverter):
         contrib_id = 0
 
         for contactidx, contact in enumerate(pair_list):
-            LOG.debug("Contact %s" % str(contact))
+            LOG.debug("Writing restraint related to contact %s" %
+                      str((contact[0] + 1, contact[1] + 1)))
 
             # Add neighbors if neigh_flag
             resx_idx = range(min_ind(contact[0] - 1),

ariaec/protmap.py

@@ -25,7 +25,7 @@ from matplotlib import pyplot as plt
 import aria.ConversionTable as ConversionTable
 import aria.legacy.AminoAcid as AminoAcid
 from matplotlib.lines import Line2D
-from .base import (tickmin, tickrot, titleprint)
+from .base import (tickmin, tickrot, titleprint, addtup)
 import sklearn.metrics as skm
 
 LOG = logging.getLogger(__name__)
@@ -1192,44 +1192,68 @@ class MapFilter(object):
 
         if mapdict.get("scoremap") is not None:
             scoremap = mapdict.get("scoremap")
+            # List of all cysteine
             cys_list = [idx for idx, val in enumerate(scoremap.index.values)
                         if val.endswith('CYS')]
             dis_bridge_list = {ss: scoremap.iat[ss] for ss
                                in list(itertools.combinations(cys_list, 2))}
             if dis_bridge_list:
+                # Get list of all disulfure bridges sorted
                 sorted_ss = zip(*sorted(dis_bridge_list.items(),
                                         key=operator.itemgetter(1),
                                         reverse=True))[0]
             else:
                 return {'clash': None, 'desc': None}
             for dis_bridge in sorted_ss:
+                # foreach disulfure bridge
+                LOG.debug('Checking %s %s', addtup(dis_bridge),
+                          scoremap.iat[dis_bridge])
                 if dis_bridge in clash_list:
                     # given contact already removed with previous filters
                     continue
                 else:
                     # Check for each cys in dis_bridge if they aready exists
                     # in unidisbridge_list
-                    exdis = next((unidis for cys in dis_bridge for unidis in
-                                  unidisbridge_list if cys in unidis))
-                    if exdis:
-                        if scoremap.iat[dis_bridge] > scoremap.iat[exdis]:
-                            # Better cys--cys contact
-                            # List cys-cys contacts that will be removed in
-                            #  unidisbridge_list
-                            remcys = (unidis for cys in dis_bridge for unidis
-                                      in unidisbridge_list if cys in unidis)
-                            for dis in remcys:
-                                # PB si un des dis supprime est
-                                clashdisbridge_list.append(dis)
-                                clashdisbridge_list.append(dis[::-1])
-                                unidisbridge_list.remove(dis)
-                            unidisbridge_list.append(dis_bridge)
-                        else:
-                            clashdisbridge_list.append(dis_bridge)
-                            clashdisbridge_list.append(dis_bridge[::-1])
-                    else:
-                        # New cys-cys contact
-                        unidisbridge_list.append(dis_bridge)
+                    exdis = None
+                    if unidisbridge_list:
+                        for cys in dis_bridge:
+                            for unidis in unidisbridge_list:
+                                if cys in unidis:
+                                    exdis = unidis
+                                    break
+                        if exdis:
+                            LOG.debug("Ss bridge %s have at least one cys in "
+                                      "common with previous ss filtered (%s). ",
+                                      addtup(dis_bridge),
+                                      map(addtup, unidisbridge_list))
+                            if scoremap.iat[dis_bridge] > scoremap.iat[exdis]:
+                                # Better cys--cys contact
+                                # List cys-cys contacts that will be removed in
+                                #  unidisbridge_list
+                                LOG.debug("%s has better score than %s",
+                                          addtup(dis_bridge),
+                                          addtup(exdis))
+                                remcys = (unidis for cys in dis_bridge for unidis
+                                          in unidisbridge_list if cys in unidis)
+                                for dis in remcys:
+                                    # PB si un des dis supprime est
+                                    clashdisbridge_list.append(dis)
+                                    clashdisbridge_list.append(dis[::-1])
+                                    unidisbridge_list.remove(dis)
+                                    LOG.debug("Added %s to clashlist %s",
+                                              addtup(dis),
+                                              map(addtup, clashdisbridge_list))
+                                unidisbridge_list.append(dis_bridge)
+                                continue
+                            else:
+                                clashdisbridge_list.append(dis_bridge)
+                                clashdisbridge_list.append(dis_bridge[::-1])
+                                LOG.debug("Added %s to ss clashlist %s",
+                                          addtup(dis_bridge),
+                                          map(addtup, clashdisbridge_list))
+                                continue
+                    LOG.debug('Adding bridge %s to ss filtered list', dis_bridge)
+                    unidisbridge_list.append(dis_bridge)
             return {'clash': clashdisbridge_list, 'desc': desc}
         else:
             # If no score given, return empty list
@@ -1481,14 +1505,17 @@ class MapFilter(object):
                 hum_list = [(x + 1, y + 1) for x, y in flt_res.get("clash")]
                 LOG.info(
                     "Removed %d contacts:\n%s", len(flt_res.get("clash")) / 2,
-                    hum_list)
+                    '\n'.join(
+                        textwrap.wrap(' '.join(["(%2d, %2d)" % pair for
+                                                pair in hum_list]),
+                                      width=80)))
             clash_dict[flt] = flt_res.get("clash")
             if flt_res.get("desc"):
                 desc_dict.update(flt_res.get("desc"))
 
         # write filter.out
         self.write_filtout(clash_dict, desc_dict, contactlist, outdir=outdir,
-                           outprefix=outprefix, clashlist=clashlist)
+                           outprefix=outprefix + '.' + mtype, clashlist=clashlist)
 
         # Contactmap always filtered
         # TODO: could set a treshold instead of n_factor

ariaec/reader.py

@@ -65,43 +65,7 @@ class MapFile(RegexFile):
             "regex": re.compile(r"^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+"
                                 r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
                                 r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>--?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>--?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>-?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>-?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>--?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>--?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>-?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>-?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>--?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>--?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>-?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>-?\d+\.\d+)\s*$"
-                                r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
-                                r"(?P<mi_score>\d)\s+"
-                                r"(?P<plm_score>-?\d+\.\d+)\s*$"),
+                                r"(?P<plm_score>--?\d+\.\d+)\s*$"),
             "score_field": "plm_score"
         },
         "evfold": {