From 92f7149b372cb50f91dce1b8fba74edc485be4fe Mon Sep 17 00:00:00 2001
From: Fabrice Allain <fabrice.allain@pasteur.fr>
Date: Wed, 18 May 2016 12:39:19 +0200
Subject: [PATCH] syntax modifications (report file name)
---
ariaec/commands.py | 2 +-
ariaec/maplot.py | 2 +-
ariaec/protmap.py | 4 ++--
ariaec/test/__init__.py | 6 ++++++
bin/ec2aria.py | 3 ---
5 files changed, 10 insertions(+), 7 deletions(-)
diff --git a/ariaec/commands.py b/ariaec/commands.py
index 866b10c..1a6e3ad 100644
--- a/ariaec/commands.py
+++ b/ariaec/commands.py
@@ -79,7 +79,7 @@ class AriaEcCommand:
u"restraints toolbox",
formatter_class=argp.ArgumentDefaultsHelpFormatter)
parser.add_argument("-o", "--output", dest="output_directory",
- type=str, help="Output directory")
+ type=str, help="Output directory", required=True)
parser.add_argument("-c", "--conf", action=ReadableFile, dest="conf_file",
default=None, help="configuration file")
parser.add_argument("--nolog", action="store_true",
diff --git a/ariaec/maplot.py b/ariaec/maplot.py
index 0dfe9f2..5910e55 100644
--- a/ariaec/maplot.py
+++ b/ariaec/maplot.py
@@ -127,7 +127,7 @@ class AriaEcContactMap(object):
for mapname, mapt, mapath in self.allresmap.keys():
- prefix = "_".join((mapname, self.refname))
+ prefix = "_".join((mapname, self.refname)).replace(".", "_")
if mapname == self.refname:
if not self.settings.contactmap.args.get("onlyreport", False):
diff --git a/ariaec/protmap.py b/ariaec/protmap.py
index fcb5569..047e1ec 100644
--- a/ariaec/protmap.py
+++ b/ariaec/protmap.py
@@ -312,8 +312,8 @@ class ProteinMap(Map):
def report(self, cmpmap, scoremap=None, outprefix="", outdir="", plotdir="",
plot_ext="pdf", plotag=True):
- reportpath = "%s/%s.report" % (outdir, outprefix)
- logger.info("Generate report file (%s)" % reportpath)
+ reportpath = "%s/%s.mapreport" % (outdir, outprefix)
+ logger.info("Generate map report file (%s)" % reportpath)
with open(reportpath, 'w') as reportf:
y_true = list(self.values.astype(int).flat)
y_pred = list(cmpmap.values.astype(int).flat)
diff --git a/ariaec/test/__init__.py b/ariaec/test/__init__.py
index 0852314..ae7e0c2 100644
--- a/ariaec/test/__init__.py
+++ b/ariaec/test/__init__.py
@@ -1,3 +1,9 @@
"""
ARIA EC test module
"""
+
+# TODO
+# Essayer de faire au moins un test par fonction/methode
+#
+# setup.py
+# - run
diff --git a/bin/ec2aria.py b/bin/ec2aria.py
index 8c50e7b..e34f437 100644
--- a/bin/ec2aria.py
+++ b/bin/ec2aria.py
@@ -6,10 +6,7 @@
"""
from __future__ import absolute_import, division, print_function
-# TODO: PLMContact object
-# TODO: PLMContactsList object
# TODO: replace all aria_ec ref into script name
-# TODO: nc factor function
# TODO: Utiliser scikit-bio pour traiter les sequences biologiques
import logging
--
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