From 29f95816f885e1673de2c85f9a458dcdcee17cc4 Mon Sep 17 00:00:00 2001
From: fabrice <fabrice.allain@pasteur.fr>
Date: Wed, 10 Feb 2016 19:31:04 +0100
Subject: [PATCH] Moving nb_c selection criteria in mapfilter object
---
ariaec/econverter.py | 4 ++--
ariaec/econverter.pyc | Bin 26555 -> 26563 bytes
ariaec/maplot.py | 48 +++++++++++++++++++-----------------------
ariaec/maplot.pyc | Bin 5575 -> 5092 bytes
ariaec/protmap.py | 12 ++++++++++-
ariaec/protmap.pyc | Bin 44719 -> 44991 bytes
ariaec/setup.py | 7 +++---
ariaec/setup.pyc | Bin 7849 -> 7771 bytes
8 files changed, 39 insertions(+), 32 deletions(-)
diff --git a/ariaec/econverter.py b/ariaec/econverter.py
index 12cb50b..43be5f8 100644
--- a/ariaec/econverter.py
+++ b/ariaec/econverter.py
@@ -609,13 +609,13 @@ class AriaEcXMLConverter(AriaXMLConverter):
self.write_dist_xml(restraint_dict, xml_file)
return xml_file, pair_list
- def write_maplist_restraints(self, maplist, nb_c, targetmap):
+ def write_maplist_restraints(self, maplist, targetmap):
out = ([], [])
for maptype in maplist:
logger.info("Writing %s ARIA XML distance restraints" % maptype)
outfile, pairlist = self.write_map_restraint(
- maplist[maptype]['contactmap'], nb_c,
+ maplist[maptype]['contactmap'], maplist[maptype]["nb_c"],
targetmap, listname=maptype,
scoremap=maplist[maptype].get("scoremap"))
out[0].append(outfile)
diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc
index 6bbbd21a23bd32173f036d4b551e8226d50e9e95..e26b3b94245c0af6e890d9401b7cd155d7e93ef7 100644
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diff --git a/ariaec/maplot.py b/ariaec/maplot.py
index e6e84fa..faf3c25 100644
--- a/ariaec/maplot.py
+++ b/ariaec/maplot.py
@@ -88,8 +88,8 @@ class AriaEcContactMap(object):
logger.error("First contact map should be a valid file")
sys.exit(1)
- nb_c = int(len(self.protein.aa_sequence.sequence) *
- self.settings.setup.config.get("n_factor"))
+ # nb_c = int(len(self.protein.aa_sequence.sequence) *
+ # self.settings.setup.config.get("n_factor"))
plotparams = {k: self.settings.contactmap.config.get(k, None)
for k in ('size_fig', 'plot_ext', 'plot_dpi')}
outdir = self.settings.outdir
@@ -109,8 +109,11 @@ class AriaEcContactMap(object):
mergecontactmap = mergemaps.get("contactmap")
for mapt in self.allresmap.keys():
if mapt != self.reftype:
+ # TODO: DON'T WORK !!!!
+ logger.info("Merging %s with %s map" % (
+ mergetype, mapt))
up_map = self.allresmap[mapt]["contactmap"]
- up_map[:] = up_map.add(mergecontactmap)
+ up_map[:] = up_map[:] + mergecontactmap[:]
mergekey = "%s_%s" % (mapt, mergetype)
self.allresmap[mergekey] = {}
self.allresmap[mergekey]["contactmap"] = up_map
@@ -127,29 +130,22 @@ class AriaEcContactMap(object):
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:
-
- if not self.settings.contactmap.args.get("nofilter"):
- # Get top contact map/list
- cmpmap = self.allresmap[mapt]["contactmap"].topmap(
- self.allresmap[mapt]["scoremap"], nb_c)
- cmplist = self.allresmap[mapt]['scoremap'].sortedset(
- human_idx=True)[:nb_c]
- else:
- cmpmap = self.allresmap[mapt]["contactmap"]
- cmplist = self.allresmap[mapt]['scoremap'].sortedset(
- human_idx=True)
- elif self.allresmap[mapt].get("contactmap") is not None:
- # If no score given, use all contact list
-
- cmpmap = self.allresmap[mapt]["contactmap"]
- cmplist = self.allresmap[mapt]['contactmap'].contact_list(
- human_idx=True)
- else:
- logger.warning("%s map doesn't have any score related. Can't "
- "define top list related to this map" % mapt)
- continue
+ # if self.allresmap[mapt].get("contactmap") is not None and \
+ # self.allresmap[mapt].get("scoremap") is not None:
+ # Get top contact map/list
+ # cmpmap = self.allresmap[mapt]["contactmap"].topmap(
+ # self.allresmap[mapt]["scoremap"], nb_c)
+ # cmplist = self.allresmap[mapt]['scoremap'].sortedset(
+ # human_idx=True)[:nb_c]
+ # elif self.allresmap[mapt].get("contactmap") is not None:
+ # If no score given, use all contact list
+ cmpmap = self.allresmap[mapt]["contactmap"]
+ cmplist = self.allresmap[mapt]['contactmap'].contact_list(
+ human_idx=True)
+ # else:
+ # logger.warning("%s map doesn't have any score related. Can't "
+ # "define top list related to this map" % mapt)
+ # continue
# TODO: only one function for output files
# Write contact list in txt file
diff --git a/ariaec/maplot.pyc b/ariaec/maplot.pyc
index 9485feeaeea2116ee0f066de2f444a57e1df944f..87aacf7ef15a713f3eee8a8d13dd536a03ee12be 100644
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diff --git a/ariaec/protmap.py b/ariaec/protmap.py
index 2c4d6c4..e7770cd 100644
--- a/ariaec/protmap.py
+++ b/ariaec/protmap.py
@@ -1154,13 +1154,23 @@ class MapFilter:
outprefix=outprefix, clashlist=clashlist)
# Contactmap always filtered
+ # TODO: could set a treshold instead of n_factor
+ nb_c = int(len(mapdict["contactmap"].sequence) * int(
+ self.settings.get("n_factor")))
+ nb_c = nb_c if nb_c < len(mapdict["contactmap"].contactset()) else len(
+ mapdict["contactmap"].contactset())
+ mapdict["nb_c"] = nb_c
+
logger.info("Update %s contactmap" % mtype)
mapdict["contactmap"].remove(clash_list)
if mapdict["scoremap"] is not None:
logger.info("Update %s scoremap" % mtype)
mapdict["scoremap"].remove(clash_list)
-
+ # Get nb_c top maps
+ logger.info("Select top %d contacts according to scoremap" % nb_c)
+ mapdict["contactmap"] = mapdict["contactmap"].topmap(mapdict["scoremap"],
+ nb_c)
if mapdict["distmap"] is not None:
logger.info("Update %s distmap" % mtype)
mapdict["distmap"].remove(clash_list)
diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc
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diff --git a/ariaec/setup.py b/ariaec/setup.py
index 3ef69fc..1f7ebb4 100644
--- a/ariaec/setup.py
+++ b/ariaec/setup.py
@@ -152,10 +152,11 @@ class AriaEcSetup:
# --------------------------- XML restraints ------------------------- #
# Setting contact number limit for map restraints (native, ec, ...)
- nb_c = int(len(self.protein.aa_sequence.sequence) *
- self.settings.setup.config.get("n_factor"))
+ # nb_c = int(len(self.protein.aa_sequence.sequence) *
+ # self.settings.setup.config.get("n_factor"))
+
dist_files, pair_lists = self.converter.write_maplist_restraints(
- self.allresmap, nb_c, self.targetmap)
+ self.allresmap, self.targetmap)
# --------------------------- XML SEQ file --------------------------- #
seq_file = self.converter.write_xmlseq(self.protein.seqfile_path)
diff --git a/ariaec/setup.pyc b/ariaec/setup.pyc
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--
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