Commit 92f7149b authored by Fabrice Allain's avatar Fabrice Allain
Browse files

syntax modifications (report file name)

parent a2908521
......@@ -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",
......
......@@ -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):
......
......@@ -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)
......
"""
ARIA EC test module
"""
# TODO
# Essayer de faire au moins un test par fonction/methode
#
# setup.py
# - run
......@@ -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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