From 6767d22c3f6918b497d92d6ffc2680c1aa9205f1 Mon Sep 17 00:00:00 2001
From: Fabrice Allain <fabrice.allain@pasteur.fr>
Date: Fri, 10 Jun 2016 14:35:06 +0200
Subject: [PATCH] Updated to python 3.5 syntax
---
ariaec/__init__.pyc | Bin 235 -> 237 bytes
ariaec/base.py | 6 ++----
ariaec/base.pyc | Bin 10170 -> 10212 bytes
ariaec/commands.py | 3 +++
ariaec/commands.pyc | Bin 10246 -> 10399 bytes
ariaec/econverter.py | 15 ++++++++++-----
ariaec/econverter.pyc | Bin 27494 -> 27809 bytes
ariaec/ecsettings.py | 12 ++++++------
ariaec/ecsettings.pyc | Bin 7842 -> 8013 bytes
ariaec/maplot.pyc | Bin 5205 -> 5250 bytes
ariaec/ndconv.pyc | Bin 4441 -> 4445 bytes
ariaec/protein.py | 39 ++++++++++++++++++++-------------------
ariaec/protein.pyc | Bin 15874 -> 16126 bytes
ariaec/protmap.py | 24 +++++++++++++-----------
ariaec/protmap.pyc | Bin 47920 -> 48716 bytes
ariaec/reader.pyc | Bin 19294 -> 19234 bytes
ariaec/setup.pyc | Bin 7631 -> 7685 bytes
bin/ec2aria.pyc | Bin 1065 -> 0 bytes
setup.py | 2 +-
version.py | 2 +-
20 files changed, 56 insertions(+), 47 deletions(-)
delete mode 100644 bin/ec2aria.pyc
diff --git a/ariaec/__init__.pyc b/ariaec/__init__.pyc
index 8beec7da806c597f90cc1923e67032e7aa62f134..6dbf12f6af78ab4e98ffa0e0249c74b06128ba80 100644
GIT binary patch
delta 64
zcmaFO_?D54`7<xqUzLe$b$b2`3=H~7iIvHzIXT7p8Tq-X`e}(dIf<Eh`r-LS*~JBk
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delta 62
zcmaFM_?nT8`7<xq8?lLObvnKb3=I0YsVSL>`bCME`FWYi`i^FX&brQKju!gi`9;~q
S1&PV2`XL#q#i<iFSpxuTpA>!o
diff --git a/ariaec/base.py b/ariaec/base.py
index 69f3148..eb0d60a 100644
--- a/ariaec/base.py
+++ b/ariaec/base.py
@@ -13,7 +13,7 @@ import sys
import numpy as np
import pkg_resources as pkgr
import matplotlib.artist as art
-from cStringIO import StringIO
+from io import StringIO
logger = logging.getLogger()
@@ -289,10 +289,8 @@ class Capturing(list):
sys.stdout = self._stringio = StringIO()
return self
- def __exit__(self, *args):
+ def __exit__(self,):
"""
-
- :param args:
:return:
"""
self.extend("\n".join(self._stringio.getvalue().splitlines()))
diff --git a/ariaec/base.pyc b/ariaec/base.pyc
index d6f1402e1fc0c50fce3f807e87cb99c13241e5d5..59ffcefb29d6191ce32bcd0a920da7a8f15909a6 100644
GIT binary patch
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delta 1143
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diff --git a/ariaec/commands.py b/ariaec/commands.py
index 21d36fd..bee32d6 100644
--- a/ariaec/commands.py
+++ b/ariaec/commands.py
@@ -27,6 +27,9 @@ def check_file(prospective_file):
class ReadableFile(argp.Action):
+ def __init__(self, *args, **kwargs):
+ super(ReadableFile, self).__init__(*args, **kwargs)
+
def __call__(self, parser, namespace, values, option_string=None):
if type(values) == list:
for prospective_file in values:
diff --git a/ariaec/commands.pyc b/ariaec/commands.pyc
index 2d377707d3f28aea7f677e655f4cea34ee2eddeb..61d20baa4bf388d23f4053573274c13d551a398e 100644
GIT binary patch
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delta 462
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diff --git a/ariaec/econverter.py b/ariaec/econverter.py
index 203e7dd..4a10916 100644
--- a/ariaec/econverter.py
+++ b/ariaec/econverter.py
@@ -13,7 +13,6 @@ import os
import sys
import json
import re
-import pkg_resources as pkgr
import aria.legacy.AminoAcid as AminoAcid
from .base import get_filename, Capturing
from .protein import Protein
@@ -307,7 +306,7 @@ assign (resid {res1} and name o) (resid {res2} and name hn) 1.8 {dminus} {dplus
# Build global secondary structure distance restraints (H-H+4, E-E+1,
# ...)
with open(outfile, 'w') as outfile:
- for a in xrange(len(sec_struct) - 1):
+ for a in range(len(sec_struct) - 1):
for b in range(a + 1, len(sec_struct)):
ss1 = sec_struct[a][2]
ss2 = sec_struct[b][2]
@@ -331,7 +330,7 @@ assign (resid {res1} and name {atm1}) (resid {res2} and name {atm2}) {dist} {sd
def write_dihedral_tbl(sec_struct, outfile, k=0.5, e=2):
# Build dihedral angle restraints (phi, psi)
with open(outfile, "w") as outfile:
- for i in xrange(len(sec_struct)):
+ for i in range(len(sec_struct)):
if (i + 1) != len(sec_struct):
if sec_struct[i][2] == sec_struct[i + 1][2]:
# Si ss identique
@@ -396,6 +395,12 @@ assign (resid {res1} and name n) (resid {res1} and name ca) (resid {res1} and na
class AriaEcXMLConverter(AriaXMLConverter):
+
+ @staticmethod
+ def _write_hbmap_tbl(hbmap, outfile, dminus, dplus, n_hb=None, hb_type="main", topo=None):
+ AriaXMLConverter._write_hbmap_tbl(hbmap, outfile, dminus, dplus, n_hb=None, hb_type="main",
+ topo=None)
+
def __init__(self, *args, **kwargs):
self.restraint_list = []
super(AriaEcXMLConverter, self).__init__(*args, **kwargs)
@@ -711,7 +716,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
self._pickler.dump(self.molecule, self._mol_set[
'output'])
- except Exception, msg:
+ except Exception as msg:
logger.error("Error writing xml seq file : %s" % msg)
@@ -732,7 +737,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
templatepath = os.path.abspath(aria_template)
ariaproj_template = Template(filename=templatepath,
- module_directory="/tmp/mako_modules")
+ module_directory="/tmp/mako_modules")
try:
t = open(templatepath, 'r')
diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc
index acf5859b87db9337d5547ea2326adfb6d8fc2812..e9e078e3844b0924216ae2cefa64f62adef2ac88 100644
GIT binary patch
delta 1324
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delta 993
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diff --git a/ariaec/ecsettings.py b/ariaec/ecsettings.py
index dd131a4..bebf738 100644
--- a/ariaec/ecsettings.py
+++ b/ariaec/ecsettings.py
@@ -5,9 +5,9 @@ from __future__ import absolute_import, division, print_function
import logging
import os
-import ConfigParser
+from configparser import SafeConfigParser
import collections
-import cPickle as Pickle
+import pickle
import pkg_resources as pkgr
from .base import format_dict
@@ -42,7 +42,7 @@ class Settings(object):
elif not pkg:
logger.error("Configuration file not found (%s)" % configpath)
return None
- config = ConfigParser.SafeConfigParser(allow_no_value=True)
+ config = SafeConfigParser(allow_no_value=True)
if pkg:
with pkgr.resource_stream(__name__, configpath) as conf:
config.readfp(conf)
@@ -62,7 +62,7 @@ class Settings(object):
def write_config(self, filename):
# Ecrit les config de toutes les sections dans un autre fichier
logger.info("Writing .ini file (%s)" % filename)
- config = ConfigParser.SafeConfigParser(allow_no_value=True)
+ config = SafeConfigParser(allow_no_value=True)
iniout = open(filename, mode="w")
for section in self._sections:
config.add_section(section)
@@ -151,12 +151,12 @@ class AriaEcSettings(Settings):
try:
# Read scsc_min_file given in aria_ec.ini
with open(self.main.config["scsc_min_file"]) as scsc:
- scsc_min = Pickle.load(scsc)
+ scsc_min = pickle.load(scsc)
except (IOError, KeyError, TypeError):
# If file can't be open or given key is invalid, load default
# package file
with pkgr.resource_stream(__name__, self.SCSC_MIN) as scsc:
- scsc_min = Pickle.load(scsc)
+ scsc_min = pickle.load(scsc)
scsc_min = dict(
(aa1, dict((aa2, tuple(atm_pair.split(', ')))
for aa2, atm_pair in atm_pairs.items()))
diff --git a/ariaec/ecsettings.pyc b/ariaec/ecsettings.pyc
index 255ed5031f4cbbcd88e62c1a883bc47f6365371f..1ddd9862f6718960ea3e9177c434ba2f8f0f7a41 100644
GIT binary patch
delta 686
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diff --git a/ariaec/maplot.pyc b/ariaec/maplot.pyc
index 52c27a55568ff104dddf5f68a89fe949ec82cd0d..7a504fb5cdc373664cc54480f4312cc4963f6c6a 100644
GIT binary patch
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diff --git a/ariaec/ndconv.pyc b/ariaec/ndconv.pyc
index 2561e1ff8777409c519f6f9e8cb594ed87ed618e..e998e9b990adb6af4d8cd5b8ec496740d5f1a6d0 100644
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diff --git a/ariaec/protein.py b/ariaec/protein.py
index 8b5a48f..0b6031f 100644
--- a/ariaec/protein.py
+++ b/ariaec/protein.py
@@ -11,6 +11,7 @@ import logging
import pkg_resources as pkgr
import aria.legacy.SequenceList as SequenceList
import aria.legacy.AminoAcid as AmnAcd
+from six import iteritems
from .base import (reg_load, Capturing, ppdict)
# import skbio.Protein as skprot
# TODO: interface skbio ??
@@ -211,7 +212,7 @@ class SsList:
try:
with open(filename) as f:
self._read_ssdist(f, filename=filename)
- except Exception, message:
+ except Exception as message:
logger.error("%s" % message)
logger.error("Can't load given ss dist file...")
logger.error("Loading default ss dist file")
@@ -242,7 +243,7 @@ class SsList:
# TODO: read_dssp
-class AminoAcidSequence(SequenceList.SequenceList):
+class AminoAcidSequence(SequenceList.SequenceList, object):
startres_reg = re.compile(r"^\s*residue\s+(?P<name>[A-Za-z]{1,4})", flags=re.I)
end_reg = re.compile(r"^\s*end", flags=re.I)
@@ -277,7 +278,7 @@ class AminoAcidSequence(SequenceList.SequenceList):
:param kwargs:
:return:
"""
- SequenceList.SequenceList.__init__(self, *args, **kwargs)
+ super(AminoAcidSequence, self).__init__(*args, **kwargs)
self._topfile = topologyfile
self._topology = None
self._topok = False
@@ -303,7 +304,7 @@ class AminoAcidSequence(SequenceList.SequenceList):
self._topology = [(aa, topo[aa]) for aa in self.aalist]
self._topok = True
else:
- self._topology = list(topo.iteritems())
+ self._topology = list(iteritems(topo))
return self._topology
def __getitem__(self, key):
@@ -324,7 +325,7 @@ class AminoAcidSequence(SequenceList.SequenceList):
def readtopo(self):
"""
-
+ Parse topology file for amino acids
:return:
"""
topo = {}
@@ -346,24 +347,24 @@ class AminoAcidSequence(SequenceList.SequenceList):
resname = ""
continue
# Walk along reg dict
- for regid, reg in self.restatement_reg.iteritems():
+ for regid, reg in iteritems(self.restatement_reg):
+ if regid not in topo[resname]:
+ topo[resname][regid] = []
if regid == "bond":
match = re.findall(reg, line)
+ if match:
+ topo[resname][regid] += match
+ break
else:
match = reg.search(line)
- if match:
- if regid not in topo[resname]:
- topo[resname][regid] = []
- if regid == "bond":
- # Add 2-tuple
- topo[resname][regid] += match
- elif regid in ("improper", "dihedral"):
- # Add tuple into list since we need atm order
- topo[resname][regid].append(match.groups())
- else:
- # Add dict
- topo[resname][regid].append(match.groupdict())
- break
+ if match:
+ if regid in ("improper", "dihedral"):
+ # Add tuple into list since we need atm order
+ topo[resname][regid].append(match.groups())
+ else:
+ # Add dict
+ topo[resname][regid].append(match.groupdict())
+ break
logger.debug("Topology used:\n%s" % ppdict(topo))
return topo
diff --git a/ariaec/protein.pyc b/ariaec/protein.pyc
index 3df5777c7f7fa6aa966518bc7a9d3fbd82c53a12..94fef3012ea0cdec3a3cde4312dc5fdbcdb62a43 100644
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diff --git a/ariaec/protmap.py b/ariaec/protmap.py
index 451240e..266156b 100644
--- a/ariaec/protmap.py
+++ b/ariaec/protmap.py
@@ -41,8 +41,11 @@ class Map(pd.DataFrame):
mtype_choices = {'contact': bool, 'distance': float, "score": float}
- def _constructor_expanddim(self):
- super(Map, self)._constructor_expanddim()
+ def update(self, *args, **kwargs):
+ super(Map, self).update(*args, **kwargs)
+
+ # def _constructor_expanddim(self):
+ # super(Map, self)._constructor_expanddim()
def __init__(self, index=None, columns=None, mtype='distance',
duplicate_levels=False, data=None, dtype=None, sym=True,
@@ -660,7 +663,7 @@ class ResAtmMap(ProteinMap):
"the default cutoff)" % str(pair))
logger.info(
"Filtering values in matrix related to %s (%s)" %
- (str(pair), str(treshold)))
+ (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
@@ -757,8 +760,8 @@ class AaMap(Map):
Amino Acid Distance Matrix
"""
- def _constructor_expanddim(self):
- super(AaMap, self)._constructor_expanddim()
+ # def _constructor_expanddim(self):
+ # super(AaMap, self)._constructor_expanddim()
def __init__(self, *args, **kwargs):
if ("humanidx", "columns") not in kwargs:
@@ -781,8 +784,8 @@ class AtmMap(Map):
Atom Distance Matrix
"""
- def _constructor_expanddim(self):
- super(AtmMap, self)._constructor_expanddim()
+ # def _constructor_expanddim(self):
+ # super(AtmMap, self)._constructor_expanddim()
def __init__(self, *args, **kwargs):
super(AtmMap, self).__init__(*args, **kwargs)
@@ -1037,7 +1040,7 @@ class MapFilter:
ss_start_end = collections.defaultdict(lambda: [None, None])
# TODO: deplacer construction du dic ss_start_end dans SsList
- for res_ind in xrange(len(ss_matrix)):
+ for res_ind in range(len(ss_matrix)):
# Construction du dict ss_start_end
if res_ind == 0:
# If first residue
@@ -1082,7 +1085,7 @@ class MapFilter:
for n in (1, 2, 3, 4):
# Search type of the bond (H-1 H, E-2 E, ...)
- for i in xrange(2):
+ for i in range(2):
# Test both sides
resi = contact[i]
@@ -1331,8 +1334,7 @@ class MapFilter:
else:
op = "added"
ctype = clash
- meta_clash[clash_t]["warn"] += "\n/!\ Clash: {clash_desc} {" \
- "clash} flag for contact " \
+ meta_clash[clash_t]["warn"] += "\n/!\ Clash: {clash_desc} {clash} flag for contact " \
"{res_pos} ({res1}, {res2})".format(
clash_desc=op, clash=ctype, res_pos=icontact + 1,
res1=contact[0], res2=contact[1])
diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc
index 97bdf80fc6bac046dfcd28c7d8a8f59c05779b2f..d40663f51f5c554e656cb18edc04d897a71ce272 100644
GIT binary patch
delta 3187
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diff --git a/ariaec/reader.pyc b/ariaec/reader.pyc
index be72a36a7ff53222b0b28eba550b659a5245a599..29df7419eb4233ff489dc99cb4ba9c7f506cdf80 100644
GIT binary patch
delta 1070
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delta 1150
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diff --git a/ariaec/setup.pyc b/ariaec/setup.pyc
index 61472e585722d579ed2c331f857e43d791d42641..db150a42b10c9adc4fef86392cc074440d3d1ad8 100644
GIT binary patch
delta 224
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delta 174
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diff --git a/bin/ec2aria.pyc b/bin/ec2aria.pyc
deleted file mode 100644
index 5b9ac9c197722157d01eac0069236a7db1e68bd6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
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diff --git a/setup.py b/setup.py
index 182a0d2..2ffec38 100644
--- a/setup.py
+++ b/setup.py
@@ -97,7 +97,7 @@ setup(
'seaborn',
'scipy',
'sklearn',
- 'colorlog',
+ 'colorlog', 'mako',
# 'scikit-bio==0.4.0',
# 'aria==2.3'
],
diff --git a/version.py b/version.py
index e0ce953..76bddd8 100644
--- a/version.py
+++ b/version.py
@@ -1,2 +1,2 @@
# Do not edit this file, pipeline versioning is governed by git tags
-__version__=v0.1.11-dev2-8-g4239f50
\ No newline at end of file
+__version__=v0.1.11-dev2-16-gb1e477c
\ No newline at end of file
--
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