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bis-aria
ariaec
Commits
215ab225
Commit
215ab225
authored
Jul 25, 2019
by
Fabrice ALLAIN
Browse files
feat: support ss format
parent
79f33d7c
Changes
2
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docs/tutorial.rst
View file @
215ab225
...
...
@@ -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
...
...
src/aria/conbox/protein.py
View file @
215ab225
...
...
@@ -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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