Commit 62e288e4 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

docs: move tutorial section

parent d04bbc49
...@@ -21,10 +21,11 @@ list of PDB files. ...@@ -21,10 +21,11 @@ list of PDB files.
Be sure to check if the following packages are correctly installed with Be sure to check if the following packages are correctly installed with
your python installation or virtual environment. your python installation or virtual environment.
- **pip** (>= 9.0) - **pip** (>= 18.0)
- **setuptools** (>= 18.0) - **git** (>= 2.0)
- **cns-solve** (1.21) - **cns-solve** (1.21)
- **pbxplore** (>= 1.3.8) - **ccpnmr analysis** (optional)
- **ccpn data model** (optional)
Then the easiest solution is to call the **pip** command below : Then the easiest solution is to call the **pip** command below :
...@@ -33,7 +34,8 @@ Then the easiest solution is to call the **pip** command below : ...@@ -33,7 +34,8 @@ Then the easiest solution is to call the **pip** command below :
For more information about installation and usage, please refer to the For more information about installation and usage, please refer to the
[ARIAEC documentation](http://bis-aria.pages.pasteur.fr/ariaec) [ARIAEC documentation](http://bis-aria.pages.pasteur.fr/ariaec)
**ARIA contains patches for CNS-solve which needs to be compiled after the installation. Please follow [post installation instructions](http://bis-aria.pages.pasteur.fr/ariaec/installation.html#post-installation-instructions).** **ARIA contains patches for CNS-solve which needs to be compiled after the
installation. Please follow [post installation instructions](http://bis-aria.pages.pasteur.fr/ariaec/installation.html#post-installation-instructions).**
## Contributing ## Contributing
......
...@@ -8,20 +8,11 @@ ...@@ -8,20 +8,11 @@
usage usage
contributing contributing
.. toctree::
:maxdepth: 4
:caption: API
Core package <api/aria.core>
Conbox package <api/aria.conbox>
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:caption: Tutorial :caption: Tutorial
tutorial/setup tutorial
tutorial/run
tutorial/analysis
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
...@@ -29,3 +20,11 @@ ...@@ -29,3 +20,11 @@
examples/bpt1/bpt1 examples/bpt1/bpt1
examples/malecoli/malecoli examples/malecoli/malecoli
.. toctree::
:maxdepth: 4
:caption: API
Core package <api/aria.core>
Conbox package <api/aria.conbox>
...@@ -203,8 +203,8 @@ version 1.2 : ...@@ -203,8 +203,8 @@ version 1.2 :
2. Edit the file ``cns_solve_env`` in the directory ``cns_solve_1.1`` to define 2. Edit the file ``cns_solve_env`` in the directory ``cns_solve_1.1`` to define
the location of the CNSsolve directory. the location of the CNSsolve directory.
3. Go to directory ``cns_solve_1.1`` and type ``make install``. This should start 3. Go to the directory ``cns_solve_1.1`` and type ``make install``. This should
the compilation process. start the compilation process.
.. Footnotes .. Footnotes
......
========
Tutorial
========
Project preparation
===================
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
Project template
----------------
Setup
-----
Running ARIA
============
...@@ -17,7 +17,7 @@ ARIAEC ...@@ -17,7 +17,7 @@ ARIAEC
.. code-block:: shell .. code-block:: shell
ariaec [-h] COMMAND ariaec COMMAND [OPTIONS] ARGS
**Commands** **Commands**
...@@ -56,14 +56,14 @@ ARIAEC ...@@ -56,14 +56,14 @@ ARIAEC
.. rst-class:: table-hover .. rst-class:: table-hover
.. list-table::
:header-rows: 1
:widths: 25 60
+--------------------------------------------------------+-----------------------------------------------------+ * - Name
| Name | Description | - Short Description
+========================================================+=====================================================+ * - ``-h``, ``--help``
| ``-h``, ``--help`` | show help message and exit | - show help message and exit
+--------------------------------------------------------+-----------------------------------------------------+
Setup Setup
+++++ +++++
...@@ -71,21 +71,23 @@ Translate contact maps as distance restraints and initialize a new ARIA XML proj ...@@ -71,21 +71,23 @@ Translate contact maps as distance restraints and initialize a new ARIA XML proj
.. code-block:: shell .. code-block:: shell
ariaec setup SEQFILE INFILE [INFILE ...] -o OUTPUT_DIRECTORY [-c CONF_FILE] -t INTYPE [INTYPE ...] ariaec setup [OPTIONS] SEQFILE INFILE [INFILE ...] -o OUTPUT_DIRECTORY -t INTYPE [INTYPE ...]
**Arguments** **Arguments**
.. rst-class:: table-hover .. rst-class:: table-hover
.. list-table::
:header-rows: 1
:widths: 25 60
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - Name
| Name | Short description | - Short Description
+=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+ * - ``seq``
| ``seq`` | Sequence file [``FASTA``] | - Sequence file [``FASTA``]
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``infile [infile ...]``
| ``infile [infile ...]`` | Contact or pdb file(s) used to build aria distance restraints | - Contact or pdb file(s) used to build aria distance restraints
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
.. _ConKit: http://www.conkit.org/en/latest/ .. _ConKit: http://www.conkit.org/en/latest/
...@@ -95,40 +97,42 @@ Translate contact maps as distance restraints and initialize a new ARIA XML proj ...@@ -95,40 +97,42 @@ Translate contact maps as distance restraints and initialize a new ARIA XML proj
.. rst-class:: table-hover .. rst-class:: table-hover
.. list-table::
:header-rows: 1
:widths: 25 60
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - Name
| Name | Description | - Short Description
+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+ * - ``-h``, ``--help``
| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None) | - show help message and exit
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``-d``, ``--debug``
| ``-c CONF_FILE``, ``--conf CONF_FILE`` | configuration file (default: None) | - Increase output verbosity (default: False)
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``--nolog``
| ``--nolog`` | Don't generate log files (default: False) | - Don't generate log files (default: False)
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY``
| ``-d``, ``--debug`` | Increase output verbosity (default: False) | - Output directory (default: None)
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``-c CONF_FILE``, ``--conf CONF_FILE``
| ``-t intype [intype ...]`` | Contact Map file format:sup:`*` | - configuration file (default: None)
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``-t intype [intype ...]``
| ``-d DISTFILE``, ``--distfile DISTFILE`` | Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints | - Contact Map file format:sup:`*`
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``-d DISTFILE``, ``--distfile DISTFILE``
| ``-s SSPRED``, ``--ssfile SSPRED`` | Secondary structure prediction file. Supported formats are psipred, psipred2, psipred3, ss2 and indextableplus | - Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``-s SSPRED``, ``--ssfile SSPRED``
| ``-p ARIAPROJECT``, ``--ariaproject ARIAPROJECT`` | ARIA project file. This project will be updated with data generated during the ``ariaec setup`` call | - Secondary structure prediction file. Supported formats are psipred, psipred2, psipred3, ss2 and indextableplus
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``-p ARIAPROJECT``, ``--ariaproject ARIAPROJECT``
| ``-r SEQRANGE``, ``--range SEQRANGE`` | Index range if we don't want tu use the whole sequence and map | - ARIA project file. This project will be updated with data generated during the ``ariaec setup`` call
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``-r SEQRANGE``, ``--range SEQRANGE``
| ``-n REF``, ``--native REF`` | Native pdb. Allow TP/FP detection | - Index range if we don't want tu use the whole sequence and map
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``-n REF``, ``--native REF``
| ``--hb HB`` | H-bonds contact file (eg: metapsicov.hb) | - Native pdb. Allow TP/FP detection
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``--hb HB``
| ``--ssidx`` | Use secondary structure index | - H-bonds contact file (eg: metapsicov.hb)
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``--no-filter``
| ``--no-filter`` | Do not filter contact map | - Do not filter contact map
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``--extract-all``
| ``--extract-all`` | Extract data or all data and parameters if an ARIA project is defined with ``-p`` option | - Extract data or all data and parameters if an ARIA project is defined with ``-p`` option
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ * - ``--ssidx``
| :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`` | - :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``
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
Bbconv Bbconv
...@@ -138,7 +142,7 @@ Translate BBcontacts as distance restraints which can be used during ...@@ -138,7 +142,7 @@ Translate BBcontacts as distance restraints which can be used during
.. code-block:: shell .. code-block:: shell
ariaec bbconv [-h] contactfile sspred seq [msa] -t contactype ariaec bbconv [OPTIONS] CONTACTFILE SSPRED SEQ [MSA] -t CONTACTYPE
**Arguments** **Arguments**
......
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