Commit 215ab225 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

feat: support ss format

parent 79f33d7c
...@@ -285,10 +285,11 @@ analysis pipeline. ...@@ -285,10 +285,11 @@ analysis pipeline.
Contact map analysis Contact map analysis
-------------------- --------------------
To quickly see several plots and stats related to the reference structure Aside ConKit_ :abbr:`Command Line Interface CLI)` tools, the
or/with the EC contact maps. We can use the ``maplot`` subcommand. The first :ref:`maplot <./usage>` command line has been implemented to show statistics
argument in this command will always be set as the reference map/pdb for the between contact maps and the reference which can be a structure in PDB_ format.
contact map, ROC or precision-recall plots. 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 .. code-block:: console
......
...@@ -51,6 +51,7 @@ class SsList(object): ...@@ -51,6 +51,7 @@ class SsList(object):
r'\s+(?P<h_conf>\d?\.?\d*)' r'\s+(?P<h_conf>\d?\.?\d*)'
r'\s+(?P<e_conf>\d?\.?\d*)' r'\s+(?P<e_conf>\d?\.?\d*)'
r'\s+(?P<c_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+)' # psipred_reg = re.compile(r'^(?P<up_index>\d+)'
# r'\s+(?P<up_residue>[AC-IK-NP-TVWYZ])' # r'\s+(?P<up_residue>[AC-IK-NP-TVWYZ])'
...@@ -184,8 +185,18 @@ class SsList(object): ...@@ -184,8 +185,18 @@ class SsList(object):
filename, sstype) filename, sstype)
self.ssdict = reg_load(ssregex, filename) 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} ss_index_dict = {'H': 1, 'C': 1, 'E': 1}
for line_id in sorted(self.ssdict.keys()): for line_id in sorted(self.ssdict.keys()):
# Modif champ ss_pred # Modif champ ss_pred
# Si line_id # Si line_id
if line_id != min(self.ssdict.keys()) and \ if line_id != min(self.ssdict.keys()) and \
......
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