diff --git a/aria/conbox/commands.py b/aria/conbox/commands.py
index ffbf237f442720a78ac58e5e86a769de6863984a..da7660f48ba9dee944ca1785c49a0673815977c8 100644
--- a/aria/conbox/commands.py
+++ b/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,
diff --git a/aria/conbox/protein.py b/aria/conbox/protein.py
index b0e0a01e88d8c5353829c0b7b0035b0d8ba124d8..077e20a09f6aba7a596370dbda5edc4073bf644d 100644
--- a/aria/conbox/protein.py
+++ b/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))
diff --git a/aria/conbox/reader.py b/aria/conbox/reader.py
index 7b5adda828de7074e582539a638ea7a8f1f1cf28..aec6035641edfa05c648d7b9db9b5c8679c7611c 100644
--- a/aria/conbox/reader.py
+++ b/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
diff --git a/aria/conbox/templates/aria_project_v2.3.7.xml b/aria/conbox/templates/aria_project_v2.3.7.xml
index 0426a20a7c1ef0b4c661319ae275279da7974444..95360d4f78b88b9144f51388201a6c673f68fd5a 100644
--- a/aria/conbox/templates/aria_project_v2.3.7.xml
+++ b/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
diff --git a/aria/core/AriaPeak.py b/aria/core/AriaPeak.py
index 5056c79b475782991eda8e8d94fc672f28124e98..b3f58c058ee87483224c3f57634528f7209dc73f 100644
--- a/aria/core/AriaPeak.py
+++ b/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):