diff --git a/ariaec/commands.py b/ariaec/commands.py index 866b10c1c7745e52b7ce14702f7ee2da04d2af91..1a6e3ad8515e15f4139288a3ba2eb1c0c02b2d02 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 0dfe9f2a0b886fc7e0d99cad86cde37fed2d6d04..5910e55769165f5de6e86926a14dd4dffab713f0 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 fcb55694aaa7f4ecf2e802e91cfccddb3785d3c7..047e1ec839602d501f969bad224fcebe43966195 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 0852314d099c329d1702dc8929831706d9a912cc..ae7e0c278395ac68a8c43e0ab9ec54cedc61afb8 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 8c50e7bfb6ca77d5de01a763e1291c68768b5d33..e34f43723092801e25fc2605755ea4960b08b1fa 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