fix: solve issue with missing alignment for evcoupling contacts

aria/conbox/commands.py

@@ -157,7 +157,8 @@ class CLI(object):
         parser = argp.ArgumentParser(
             formatter_class=argp.ArgumentDefaultsHelpFormatter)
         parser.add_argument("-o", "--output", dest="output_directory", type=str,
-                            help="Output directory", required=True, action=ReadableDir)
+                            help="Output directory", required=True,
+                            action=ReadableDir)
         parser.add_argument("--nolog", action="store_true",
                             default=False, help="Don't generate log files")
         parser.add_argument("-d", "--debug", dest="verbose", default=False,

aria/conbox/protein.py

@@ -15,9 +15,8 @@ import re
 import sys
 from six import iteritems, text_type
 from copy import copy
-
 from ..core.legacy import AminoAcid as AmnAcd
-from .common import (reg_load, ppdict)
+from .common import (reg_load, ppdict, Capturing)
 
 # import skbio.Protein as skprot
 # TODO: interface skbio ??
@@ -583,10 +582,12 @@ class AminoAcidSequence(SequenceList.SequenceList, object):
         # TODO: smarter reader checking type of file (fasta, etc ...)
         # TODO: capturing has some troubles with unicode ...
         # with Capturing() as output:
-        if os.path.splitext(filename)[1] == '.seq':
-            self.ReadSeq(text_type(filename))
-        else:
-            self.ReadFasta(text_type(filename))
+        with Capturing() as output:
+            if os.path.splitext(filename)[1] == '.seq':
+                    self.ReadSeq(text_type(filename))
+            else:
+                self.ReadFasta(text_type(filename))
+        LOG.info("".join(output).capitalize())
         self.sequence = "".join(
             (AmnAcd.AminoAcid(str(_))[0]
              for _ in self.aalist))

aria/conbox/reader.py

@@ -19,7 +19,6 @@ from conkit.core.sequencefile import SequenceFile
 from .common import sort_2dict
 from .protmap import (ResMap, ResAtmMap)
 
-
 LOG = logging.getLogger(__name__)
 # TODO: check if Atom is still used ...
 Atom = collections.namedtuple("Atom", ["name", "coords"])
@@ -330,7 +329,8 @@ class MapFile(RegexFile):
             if "check_type" in kwargs else True
         super(MapFile, self).__init__(*args, **kwargs)
         if not self.conioflag and self.checkflag:
-            LOG.info("Conkit doesn't support {ftype}".format(
+            LOG.info("The file format {ftype} is not supported by the conkit "
+                     "plugin. Switching to homemade parsers.".format(
                 ftype=self.filetype))
             LOG.debug("Using {module}".format(module=__name__))
             self.regex, self.filetype, self.sort = self.check_maptype()
@@ -388,8 +388,10 @@ class MapFile(RegexFile):
         -------
 
         """
-        LOG.info("Checking if file %s correspond to %s format", self.filepath,
-                 self.filetype)
+        LOG.info(
+            "Checking if file %s correspond to our definition of %s format",
+            self.filepath,
+            self.filetype)
         # Check if given type is supported
         # TODO: report this check into commands section
         if os.stat(self.filepath).st_size == 0:
@@ -405,10 +407,11 @@ class MapFile(RegexFile):
                 if self.filetype in self.types:
                     match = self.types[self.filetype].get("regex").match(line)
                 else:
-                    LOG.error("Format %s not supported !", self.filetype)
+                    LOG.error("Format %s not supported. Please refer"
+                              " to the documentation for supported files",
+                              self.filetype)
                     match = None
                 if match:
-                    LOG.info("Format type correct")
                     return [
                         self.types[self.filetype].get("regex"),
                         self.filetype,
@@ -431,7 +434,8 @@ class MapFile(RegexFile):
                     # Stop checking after second line
                     LOG.error("Can't read %s file.", self.filetype)
                     break
-        LOG.error("Wrong format type given ...")
+        LOG.error("Wrong format type given. Please refer to the "
+                  "documentation to check if the given format is correct.")
         return [None] * 3
 
     def load(self, *args):
@@ -584,7 +588,8 @@ class ContactMapFile(MapFile):
                           path=kwargs.get("path"),
                           desc=self.filetype) if self.sort else None
         distmap = ResMap(protein.aa_sequence.sequence, mtype='distance',
-                         seqidx=protein.index, idxnames=idxnames, path=kwargs.get("path"),
+                         seqidx=protein.index, idxnames=idxnames,
+                         path=kwargs.get("path"),
                          colnames=colnames, sym=kwargs['sym'],
                          desc=self.filetype) if self.filetype == "metapsicovhb" else None
 
@@ -645,7 +650,7 @@ class ContactMapFile(MapFile):
                 if self.filetype == "metapsicovhb":
                     self.distlist.append(self.lines[contact].get("res_dist"))
 
-                if self.filetype in ("evfold", "plmdca", "plm", "plmev"):
+                if self.filetype in ("evcoupling", "plmdca", "plm", "plmev"):
                     self.clashlist.append(next(
                         (el for el in (
                             self.lines[contact].get("ss_filter"),
@@ -673,8 +678,12 @@ class ContactMapFile(MapFile):
             alignment = pairwise2.align.localxs(
                 seq, protein.aa_sequence.sequence, -1, -1,
                 one_alignment_only=True)[0]
-            LOG.info('Alignment of amino acid sequence with contact file\n'
-                     '%s' % pairwise2.format_alignment(*alignment))
+            LOG.info(
+                'Alignment of sequence in contact file ({0})'
+                ' with reference ({1})\n{2}'.format(
+                    self.filetype,
+                    os.path.basename(protein.aa_sequence.fileName),
+                    pairwise2.format_alignment(*alignment)))
             shift = re.match(r'^-*', alignment[1])
             shift = len(shift.group(0)) if shift else 0
             if shift:
@@ -813,16 +822,19 @@ class PDBFile(MapFile):
                           float(self.lines[atomy]['z']))
 
                 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")):
+                if indx[0] in list(resmap.index.get_level_values("residuex")) \
+                        and indy[0] in list(
+                    resmap.index.get_level_values("residuex")):
                     LOG.debug("Update distance value (%s, %s)", indx, indy)
                     newmap.at[indx, indy] = dist
                     if sym:
                         # If symmetric matrix
                         newmap.at[indy, indx] = dist
-                elif indx[0] not in list(resmap.index.get_level_values("residuex")):
+                elif indx[0] not in list(
+                        resmap.index.get_level_values("residuex")):
                     error_list.add(indx[0])
-                elif indy[0] not in list(resmap.index.get_level_values("residuex")):
+                elif indy[0] not in list(
+                        resmap.index.get_level_values("residuex")):
                     error_list.add(indy[0])
         if error_list:
             # Listing related humanidx in the initial df
@@ -841,6 +853,7 @@ class PDBFile(MapFile):
 
 class DistanceMapFile(MapFile):
     """Distance matrix file"""
+
     def __init__(self, filepath, filetype):
         super(MapFile).__init__(filepath, filetype)
         raise NotImplementedError
@@ -926,8 +939,8 @@ class MapFileListReader(object):
         maptypes = [maptypes] if type(maptypes) != list else maptypes
         if not maptypes or len(maps) != len(maptypes):
             maptypes = [os.path.splitext(_)[1][1:] for _ in maps]
-        LOG.info("Reader focused on file(s) %s %s", maps,
-                 maptypes)
+        # LOG.info("Analyzing input file(s) %s %s", maps,
+        #          maptypes)
         for i, filepath in enumerate(maps):
             if os.path.exists(filepath):
                 # TODO: check_type functionstr

aria/conbox/templates/aria_project_v2.3.7.xml

@@ -51,7 +51,7 @@
         <hbdb_potential enabled="${hbdb_potential_enabled}"/>
         <scoring method="${scoring_method}"/>
       </annealing_parameters>
-      <md_parameters dynamics="${}" random_seed="${md_parameters_random_seed}" tad_temp_high="${}" tad_timestep_factor="${}" cartesian_temp_high="${}" cartesian_first_iteration="${}" timestep="${}" temp_cool1_final="${}" temp_cool2_final="${}" steps_high="${md_parameters_steps_high}" steps_refine="${}" steps_cool1="${md_parameters_steps_cool1}" steps_cool2="${md_parameters_steps_cool2}"/>
+      <md_parameters dynamics="${md_parameters_dynamics}" random_seed="${md_parameters_random_seed}" tad_temp_high="${md_parameters_tad_temp_high}" tad_timestep_factor="${md_parameters_tad_timestep_factor}" cartesian_temp_high="${md_parameters_cartesian_temp_high}" cartesian_first_iteration="${md_parameters_cartesian_first_iteration}" timestep="${md_parameters_timestep}" temp_cool1_final="${md_parameters_temp_cool1_final}" temp_cool2_final="${md_parameters_temp_cool2_final}" steps_high="${md_parameters_steps_high}" steps_refine="${md_parameters_steps_refine}" steps_cool1="${md_parameters_steps_cool1}" steps_cool2="${md_parameters_steps_cool2}"/>
     </cns>
     <job_manager default_command="csh -f">
       <host enabled="yes" command="${host_command}" executable="${host_executable}" n_cpu="${n_cpus}" use_absolute_path="yes"/>
@@ -84,4 +84,4 @@
     <noe_restraint_list pickle_output="${pickle_output}" text_output="yes" xml_output="no"/>
     <spectra write_assigned="no" write_assigned_force="no" iteration="last" write_unambiguous_only="yes"/>
   </report>
-</project>
+</project>
\ No newline at end of file

aria/core/AriaPeak.py

@@ -1371,7 +1371,8 @@ class DistanceRestraint(AbstractPeak):
 
     # TODO: call Id -> Number? or is it another thing?
 
-    counter = 0
+    # counter = 0
+    counter = 100000
 
     def __init__(self, id=None):