diff --git a/CHANGELOG.md b/CHANGELOG.md
index 92e29dbdddfc32faeaa779dd968316c3d8193f95..99a64c3e5f6b0660539d7010f936d9277a4fbba7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,4 @@
-## [0.0.21](https://gitlab.pasteur.fr/bis-aria/Ariaec/compare/0.1.0...0.0.21) (2019-07-05)
+## [0.0.21](https://gitlab.pasteur.fr/bis-aria/Ariaec/compare/0.1.0...0.0.21) (2019-07-08)
### Bug Fixes
diff --git a/PKG-INFO b/PKG-INFO
index 0671076341ff5be72839de1ad7cdf3deeb05af8e..7241f738e36aa612401a649ab6dc8383116d16b7 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1 +1 @@
-Version: 0.0.21
\ No newline at end of file
+Version: 0.1.01
\ No newline at end of file
diff --git a/docs/examples/bpt1/bpt1.rst b/docs/examples/bpt1/bpt1.rst
index 211fd6c56e3babecc8aa54904b86daa50c2ce14b..4b327ffad95b70defe68ec3144f33d73549c0ddc 100644
--- a/docs/examples/bpt1/bpt1.rst
+++ b/docs/examples/bpt1/bpt1.rst
@@ -15,48 +15,50 @@ can be found in the ``docs`` folder or :download:`here <../../examples.tar.gz>`.
Contact map analysis
--------------------
+**Input**
+
.. code-block:: console
- > ariaec maplot examples/bpt1/data/BPT1_BOVIN.fa examples/bpt1/data/BPT1_BOVIN.indextableplus examples/bpt1/data/BPT1_BOVIN.native.aligned.pdb examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out -o examples/bpt1/out -t pdb gremlin
+ (venv) [user@host examples] > ariaec maplot bpt1/data/BPT1_BOVIN.fa bpt1/data/BPT1_BOVIN.indextableplus bpt1/data/BPT1_BOVIN.native.aligned.pdb bpt1/data/BPT1_BOVIN_contacts.gremlin.out -o bpt1/out -t pdb gremlin
**Output**
.. code-block:: console
- ================================================================================
-
- ARIA Evolutive Contact toolbox
-
- ================================================================================
+ ================================================================================
+
+ ARIA Evolutive Contact toolbox
+
+ ================================================================================
+
+ INFO Initialize settings
+ INFO Making output directories
+ INFO Reading fasta file /c7/home/fallain/tmp/bpt1/data/bpt1_bovin.fa
+ INFO Amino acid sequence: FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
+ INFO Checking if file /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
+ INFO Format type correct (indextableplus)
+ INFO Reading secondary structure file /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus]
+ INFO Loading ss dist file
+ INFO Reading distance file /c7/home/fallain/.conda/envs/aria/lib/python2.7/site-packages/aria/conbox/data/ss_dist.txt
+ INFO Align secondary structure sequence with protein sequence
+ INFO Reading /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN.native.aligned.pdb file
+ INFO Updating distance map with pdb file
+ INFO Generate contact map using contact definition defaultdict(None, {'default_cutoff': 8.0})
+ INFO Using default cutoff
+ INFO Reading /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file
+ INFO Pdb map set as reference
+ INFO Generate contact map plot (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN.maplot.pdf)
+ INFO Generate map report file (/c7/home/fallain/tmp/bpt1/out/mapreport)
+ INFO Generate roc file (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.csv)
+ INFO Generate roc plot (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.pdf)
+ INFO Generate precall file (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.csv)
+ INFO Generate precall plot (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.precall.pdf)
+ INFO Generate contact file (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN_contacts_gremlin.contact.txt)
+ INFO Generate stat file (/c7/home/fallain/tmp/bpt1/out/maplot.contactcmp.csv)
+ INFO Contact list: [(1, 39), (1, 42), (1, 51), (3, 22), (3, 25), (3, 45), (3, 47), (3, 51), (4, 23), (4, 38), (4, 39), (4, 42), (4, 49), (5, 23), (6, 19), (7, 37), (8, 12), (8, 31), (8, 33), (9, 19), (9, 34), (9, 37), (9, 41), (10, 33), (10, 36), (11, 33), (11, 35), (12, 8), (12, 20), (12, 31), (12, 33), (13, 33), (13, 34), (14, 31), (14, 33), (14, 36), (15, 31), (16, 29), (16, 31), (17, 41), (17, 43), (18, 28), (18, 29), (18, 45), (19, 6), (19, 9), (19, 28), (19, 29), (20, 12), (20, 25), (20, 27), (21, 28), (22, 3), (22, 25), (22, 28), (23, 4), (23, 5), (23, 26), (23, 29), (23, 43), (24, 28), (25, 3), (25, 20), (25, 22), (25, 28), (25, 46), (25, 53), (26, 23), (27, 20), (27, 48), (27, 52), (28, 18), (28, 19), (28, 21), (28, 22), (28, 24), (28, 25), (29, 16), (29, 18), (29, 19), (29, 23), (30, 33), (30, 37), (30, 38), (31, 8), (31, 12), (31, 14), (31, 15), (31, 16), (32, 37), (32, 38), (32, 40), (32, 41), (33, 8), (33, 10), (33, 11), (33, 12), (33, 13), (33, 14), (33, 30), (34, 9), (34, 13), (34, 37), (35, 11), (36, 10), (36, 14), (36, 39), (36, 50), (37, 7), (37, 9), (37, 30), (37, 32), (37, 34), (37, 41), (38, 4), (38, 30), (38, 32), (38, 41), (39, 1), (39, 4), (39, 36), (40, 32), (41, 9), (41, 17), (41, 32), (41, 37), (41, 38), (42, 1), (42, 4), (43, 17), (43, 23), (43, 47), (44, 47), (45, 3), (45, 18), (45, 49), (46, 25), (46, 49), (46, 50), (47, 3), (47, 43), (47, 44), (47, 51), (48, 27), (48, 52), (49, 4), (49, 45), (49, 46), (49, 53), (50, 36), (50, 46), (50, 53), (51, 1), (51, 3), (51, 47), (52, 27), (52, 48), (53, 25), (53, 49), (53, 50)]
+ INFO Generate contact map plot (/c7/home/fallain/tmp/bpt1/out/.maplot.pdf)
+ INFO Generate contact file (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN_native_aligned.contact.txt)
- INFO Initialize settings
- INFO Making output directories
- reading FASTA file examples/bpt1/data/BPT1_BOVIN.fa
- INFO Amino acid sequence: FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
- INFO Checking if file examples/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
- INFO Format type correct (indextableplus)
- INFO Reading secondary structure file examples/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus]
- INFO Loading ss dist file
- INFO Reading distance file ss_dist.txt
- INFO Align secondary structure sequence with protein sequence
- INFO Reader focused on file(s) ['examples/bpt1/data/BPT1_BOVIN.native.aligned.pdb', 'examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out'] ['pdb', 'gremlin']
- INFO Reading examples/bpt1/data/BPT1_BOVIN.native.aligned.pdb file
- INFO Updating distance map with pdb file
- INFO Generate contact map using contact definition defaultdict(None, {'bool': None, 'default_cutoff': 8.0})
- INFO Using default cutoff
- INFO Reading examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file
- INFO Pdb map set as reference
- INFO Generate contact map plot (examples/bpt1/out/BPT1_BOVIN.maplot.pdf)
- INFO Generate contact file (examples/bpt1/out/BPT1_BOVIN_native_aligned.contact.txt)
- INFO Generate map report file (examples/bpt1/out/mapreport)
- INFO Generate roc file (examples/bpt1/out/graphics/maplot.roc.csv)
- INFO Generate roc plot (examples/bpt1/out/graphics/maplot.roc.pdf)
- INFO Generate precall file (examples/bpt1/out/graphics/maplot.roc.csv)
- INFO Generate precall plot (examples/bpt1/out/graphics/maplot.precall.pdf)
- INFO Generate contact file (examples/bpt1/out/BPT1_BOVIN_contacts_gremlin.contact.txt)
- INFO Generate stat file (examples/bpt1/out/maplot.contactcmp.csv)
- INFO Contact list: [(1, 39), (1, 42), (1, 51), (3, 22), (3, 25), (3, 45), (3, 47), (3, 51), (4, 23), (4, 38), (4, 39), (4, 42), (4, 49), (5, 23), (6, 19), (7, 37), (8, 12), (8, 31), (8, 33), (9, 19), (9, 34), (9, 37), (9, 41), (10, 33), (10, 36), (11, 33), (11, 35), (12, 8), (12, 20), (12, 31), (12, 33), (13, 33), (13, 34), (14, 31), (14, 33), (14, 36), (15, 31), (16, 29), (16, 31), (17, 41), (17, 43), (18, 28), (18, 29), (18, 45), (19, 6), (19, 9), (19, 28), (19, 29), (20, 12), (20, 25), (20, 27), (21, 28), (22, 3), (22, 25), (22, 28), (23, 4), (23, 5), (23, 26), (23, 29), (23, 43), (24, 28), (25, 3), (25, 20), (25, 22), (25, 28), (25, 46), (25, 53), (26, 23), (27, 20), (27, 48), (27, 52), (28, 18), (28, 19), (28, 21), (28, 22), (28, 24), (28, 25), (29, 16), (29, 18), (29, 19), (29, 23), (30, 33), (30, 37), (30, 38), (31, 8), (31, 12), (31, 14), (31, 15), (31, 16), (32, 37), (32, 38), (32, 40), (32, 41), (33, 8), (33, 10), (33, 11), (33, 12), (33, 13), (33, 14), (33, 30), (34, 9), (34, 13), (34, 37), (35, 11), (36, 10), (36, 14), (36, 39), (36, 50), (37, 7), (37, 9), (37, 30), (37, 32), (37, 34), (37, 41), (38, 4), (38, 30), (38, 32), (38, 41), (39, 1), (39, 4), (39, 36), (40, 32), (41, 9), (41, 17), (41, 32), (41, 37), (41, 38), (42, 1), (42, 4), (43, 17), (43, 23), (43, 47), (44, 47), (45, 3), (45, 18), (45, 49), (46, 25), (46, 49), (46, 50), (47, 3), (47, 43), (47, 44), (47, 51), (48, 27), (48, 52), (49, 4), (49, 45), (49, 46), (49, 53), (50, 36), (50, 46), (50, 53), (51, 1), (51, 3), (51, 47), (52, 27), (52, 48), (53, 25), (53, 49), (53, 50)]
- INFO Generate contact map plot (examples/bpt1/out/.maplot.pdf)
Setup
diff --git a/docs/tutorial.rst b/docs/tutorial.rst
index f4b5d31d6eac2a5f0d4cdd421ac8dec5897c7e4e..35343ceec604a13f581592ac2e50e2346947bc05 100644
--- a/docs/tutorial.rst
+++ b/docs/tutorial.rst
@@ -1,27 +1,37 @@
-========
-Tutorial
-========
+=========
+Workflows
+=========
-Project preparation
-===================
+Structure calculation with EC restraints
+========================================
The ``ariaec`` Command Line Interface (CLI) is the main tool for
converting and analyze contact map information. The main command of this
interface is ``ariaec setup`` which create an ARIA project XML file. Then we can
follow the usual steps for an ARIA project.
+
Configuration file
------------------
-All the parameters for ``ariaec`` commands are encapsulated on a configuration file in INI format
+All the parameters for ``ariaec`` commands are encapsulated on a configuration
+file in INI format. Each time you need to overwrite the default parameters,
+another configuration file can be used with the updated parameters. There is
+no need to give all the parameters in order to have a correct configuration
+file.
+
+
+
+A more detailed description of the parameters is in :doc:`configuration`
+section.
-Project template
-----------------
+Restraints & project conversion
+-------------------------------
-Setup
------
+Build infrastructure
+--------------------
Running ARIA
diff --git a/docs/usage.rst b/docs/usage.rst
index 6f1c402ee803bff2f9a886a43dd848220d98d9da..9151d3e92933b1248c3314bccf764ac228a4022d 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -17,7 +17,7 @@ ARIAEC
.. code-block:: shell
- ariaec COMMAND [OPTIONS] ARGS
+ ariaec COMMAND ARGS [OPTIONS]
**Commands**
@@ -71,7 +71,7 @@ Translate contact maps as distance restraints and initialize a new ARIA XML proj
.. code-block:: shell
- ariaec setup [OPTIONS] SEQFILE INFILE [INFILE ...] -o OUTPUT_DIRECTORY -t INTYPE [INTYPE ...]
+ ariaec setup SEQFILE INFILE [INFILE ...] -o OUTPUT_DIRECTORY [OPTIONS] -t INTYPE [INTYPE ...]
**Arguments**
@@ -135,6 +135,12 @@ Translate contact maps as distance restraints and initialize a new ARIA XML proj
- :sup:`*` Accepted contact map formats combining formats supported by ConKit_ with few supplementary formats: ``gremlin``, ``pconsc1``, ``pconsc3``, ``pconsc2``, ``bbcontacts``, ``metapsicov_stg1``, ``membrain``, ``metapsicovhb``, ``comsat``, ``casprr``, ``ccmpred``, ``plm``, ``bclcontact``, ``epcmap``, ``evfold``, ``native``, ``pconsc``, ``psicov``, ``freecontact``, ``genericstructure``, ``ncont``, ``plmc``, ``plmdca``, ``metapsicov_stg2``, ``native_full``, ``metapsicov``, ``evcoupling``, ``contactlist``, ``plmev``, ``mmcif``, ``casp``, ``pdb``, ``flib``
+.. warning::
+
+ The contact map format option needs to have the same number of format that
+ the number of contact of pdb files. Since this is a greedy option, it needs
+ to be at the end of the command in order to work correctly.
+
Bbconv
++++++
Translate BBcontacts as distance restraints which can be used during
@@ -142,7 +148,7 @@ Translate BBcontacts as distance restraints which can be used during
.. code-block:: shell
- ariaec bbconv [OPTIONS] CONTACTFILE SSPRED SEQ [MSA] -t CONTACTYPE
+ ariaec bbconv CONTACTFILE SSPRED SEQ [MSA] [OPTIONS] -t CONTACTYPE
**Arguments**
@@ -191,7 +197,7 @@ Contactmap analysis and visualisation tool.
.. code-block:: shell
- ariaec maplot [-h] [--filter] [--onlyreport] [--no-filter] [--ssidx] [--prefix] [--prefixname PREFIXNAME] seq sspred infile [infile ...] -t intype [intype ...] --merge mergetype [mergetype ...]
+ ariaec maplot SEQ SSPRED INFILE [INFILE ...] [OPTIONS] -t INTYPE [INTYPE ...] --merge MERGETYPE [MERGETYPE ...]
**Arguments**
diff --git a/src/aria/conbox/maplot.py b/src/aria/conbox/maplot.py
index 4d624485912f479584f2b471681f307b63df5303..3b3d3fda35514bd3cb010901ef9545bffa8669ba 100644
--- a/src/aria/conbox/maplot.py
+++ b/src/aria/conbox/maplot.py
@@ -128,7 +128,7 @@ class AriaEcContactMap(object):
mergecontactmap = mergemaps.get("maplot")
for mapname, mapt in self.allresmap.keys():
if mapt != self.reftype:
- # TODO: DON'T WORK !!!!
+ # TODO: DOESN'T WORK !!!!
LOG.info("Merging %s with %s map",
mergetype, mapt)
up_map = self.allresmap[mapt]["maplot"]
@@ -191,11 +191,14 @@ class AriaEcContactMap(object):
cmpmap.write_contacts(mapname,
scoremap=scoremap,
outdir=outdir)
- cmpmap.compare_contactmap(refmap, cmplist, prefix,
+ cmpmap.compare_contactmap(refmap, cmplist,
+ prefix if prefix else "cmp",
distmap=self.refmap["distmap"],
human_idx=True,
outdir=outdir)
- refmap.compareplot(cmpmap, outprefix=prefix,
+ LOG.info(prefix)
+ refmap.compareplot(cmpmap,
+ outprefix=prefix if prefix else "ref",
outdir=outdir,
save_fig=self.settings.maplot.config.get(
"save_fig"),
diff --git a/src/aria/conbox/protmap.py b/src/aria/conbox/protmap.py
index 33c73404c921452d153d5c9434e0547ad4f6a2ee..5bae9d02197b657a8cc1c965f5384fa520e55bb3 100644
--- a/src/aria/conbox/protmap.py
+++ b/src/aria/conbox/protmap.py
@@ -490,7 +490,7 @@ class ProteinMap(Map):
Parameters
----------
outdir :
- param outprefix: (Default value = '')
+ param outprefix: (Default value = 'protein')
size_fig :
param plot_ext: (Default value = 10)
plot_dpi :
@@ -2470,16 +2470,6 @@ class MapFilter(object):
"""
# TODO: utiliser self.clash_dict au lieu de meta_clash
- """
-
- :param clash_dict:
- :param desc_dict:
- :param contactlist:
- :param outdir:
- :param outprefix:
- :param clashlist:
- :param human_idx:
- """
meta_clash = {
"cons": {
"flag": 888, "msg": "", "warn": "",
diff --git a/src/aria/core/xmlutils.py b/src/aria/core/xmlutils.py
index f858498f5735d2aa858f873dfc77b9325aa75da8..3e0572cb463b54cb3eb081c092708064816dd432 100644
--- a/src/aria/core/xmlutils.py
+++ b/src/aria/core/xmlutils.py
@@ -101,6 +101,9 @@ class XMLElement:
def get_cdata(self):
return self.__cdata
+ def get_name(self):
+ return self.__name if self.__name else self.__class__.__name__
+
# def get_name(self):
# raise
# attr = '_%s__name' % self.__class__.__name__
@@ -133,6 +136,12 @@ class XMLElement:
return 'XMLElement(name=%s, tag_order=%s)' % \
(self.get_name(), str(self.get_tag_order()))
+ def __repr__(self):
+ print('XMLElement(name=%s, tag_order=%s)' % \
+ (str(self.get_name()), str(self.get_tag_order())))
+ return 'XMLElement(name=%s, tag_order=%s)' % \
+ (str(self.get_name()), str(self.get_tag_order()))
+
class ContentConverter:
"""