Commit ca6b27d1 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN

Merge branch 'master' of gitlab.pasteur.fr:bis-aria/ariaec

parents dd414fac fa0951f3
......@@ -44,10 +44,7 @@ coverage:
- htmlcov/
only:
refs:
- production
- master
changes:
- src/**/*
pages:
image: $CI_REGISTRY_IMAGE:latest
......
ARIA -- Ambiguous Restraints for Iterative Assignment
A software for automated NOE assignment
Version 2.3
Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin,
Wolfgang Rieping, and Michael Nilges
All rights reserved.
NO WARRANTY. This software package is provided 'as is' without warranty of
any kind, expressed or implied, including, but not limited to the implied
warranties of merchantability and fitness for a particular purpose or
a warranty of non-infringement.
Distribution of substantively modified versions of this module is
prohibited without the explicit permission of the copyright holders.
\ No newline at end of file
......@@ -4,7 +4,6 @@
[![chat](https://img.shields.io/badge/chat-mattermost-informational.svg)](https://chatlab.pasteur.fr/bis-aria/channels/aria)
[![documentation](https://img.shields.io/badge/docs-latest-blue.svg)](http://bis-aria.pages.pasteur.fr/ariaec)
[![aria paper](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtl589-blue.svg)](https://doi.org/10.1093/bioinformatics/btl589)
[![pipeline status](https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/pipeline.svg)](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
[![coverage report](https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/coverage.svg)](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
......
......@@ -285,10 +285,11 @@ analysis pipeline.
Contact map analysis
--------------------
To quickly see several plots and stats related to the reference structure
or/with the EC contact maps. We can use the ``maplot`` subcommand. The first
argument in this command will always be set as the reference map/pdb for the
contact map, ROC or precision-recall plots.
Aside ConKit_ :abbr:`Command Line Interface CLI)` tools, the
:ref:`maplot <./usage>` command line has been implemented to show statistics
between contact maps and the reference which can be a structure in PDB_ format.
The first argument in this command will always be set as the reference map/pdb
for the contact map, ROC or precision-recall plots.
.. code-block:: console
......
......@@ -51,6 +51,7 @@ class SsList(object):
r'\s+(?P<h_conf>\d?\.?\d*)'
r'\s+(?P<e_conf>\d?\.?\d*)'
r'\s+(?P<c_conf>\d?\.?\d*)'),
'ss': re.compile(r'^(?P<ss_pred>[HECBTG]+)'),
}
# psipred_reg = re.compile(r'^(?P<up_index>\d+)'
# r'\s+(?P<up_residue>[AC-IK-NP-TVWYZ])'
......@@ -184,8 +185,18 @@ class SsList(object):
filename, sstype)
self.ssdict = reg_load(ssregex, filename)
# Change the format of the ssdict if we have ss type format
if sstype == "ss":
tmpdict = {}
for sstridx in sorted(self.ssdict.keys()):
for ssidx, ss in enumerate(self.ssdict[sstridx]["ss_pred"]):
tmpdict[ssidx + 1] = {"ss_pred": ss}
self.ssdict = tmpdict
ss_index_dict = {'H': 1, 'C': 1, 'E': 1}
for line_id in sorted(self.ssdict.keys()):
# Modif champ ss_pred
# Si line_id
if line_id != min(self.ssdict.keys()) and \
......
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