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Commit 62e288e4 authored by Fabrice ALLAIN's avatar Fabrice ALLAIN
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docs: move tutorial section

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README.md
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......@@ -21,10 +21,11 @@ list of PDB files.
Be sure to check if the following packages are correctly installed with
your python installation or virtual environment.
- **pip** (>= 9.0)
- **setuptools** (>= 18.0)
- **pip** (>= 18.0)
- **git** (>= 2.0)
- **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 :
......@@ -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
[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
......
docs/contents.rst
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......@@ -8,20 +8,11 @@
usage
contributing
.. toctree::
:maxdepth: 4
:caption: API
Core package <api/aria.core>
Conbox package <api/aria.conbox>
.. toctree::
:maxdepth: 2
:caption: Tutorial
tutorial/setup
tutorial/run
tutorial/analysis
tutorial
.. toctree::
:maxdepth: 2
......@@ -29,3 +20,11 @@
examples/bpt1/bpt1
examples/malecoli/malecoli
.. toctree::
:maxdepth: 4
:caption: API
Core package <api/aria.core>
Conbox package <api/aria.conbox>
docs/installation.rst
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......@@ -203,8 +203,8 @@ version 1.2 :
2. Edit the file ``cns_solve_env`` in the directory ``cns_solve_1.1`` to define
the location of the CNSsolve directory.
3. Go to directory ``cns_solve_1.1`` and type ``make install``. This should start
the compilation process.
3. Go to the directory ``cns_solve_1.1`` and type ``make install``. This should
start the compilation process.
.. Footnotes
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docs/tutorial.rst 0 → 100644
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========
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
============
docs/usage.rst
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......@@ -17,7 +17,7 @@ ARIAEC
.. code-block:: shell
ariaec [-h] COMMAND
ariaec COMMAND [OPTIONS] ARGS
**Commands**
......@@ -56,14 +56,14 @@ ARIAEC
.. rst-class:: table-hover
.. list-table::
:header-rows: 1
:widths: 25 60
+--------------------------------------------------------+-----------------------------------------------------+
| Name | Description |
+========================================================+=====================================================+
| ``-h``, ``--help`` | show help message and exit |
+--------------------------------------------------------+-----------------------------------------------------+
* - Name
- Short Description
* - ``-h``, ``--help``
- show help message and exit
Setup
+++++
......@@ -71,21 +71,23 @@ Translate contact maps as distance restraints and initialize a new ARIA XML proj
.. 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**
.. rst-class:: table-hover
.. list-table::
:header-rows: 1
:widths: 25 60
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Name | Short description |
+=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``seq`` | Sequence file [``FASTA``] |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``infile [infile ...]`` | Contact or pdb file(s) used to build aria distance restraints |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
* - Name
- Short Description
* - ``seq``
- Sequence file [``FASTA``]
* - ``infile [infile ...]``
- Contact or pdb file(s) used to build aria distance restraints
.. _ConKit: http://www.conkit.org/en/latest/
......@@ -95,40 +97,42 @@ Translate contact maps as distance restraints and initialize a new ARIA XML proj
.. rst-class:: table-hover
.. list-table::
:header-rows: 1
:widths: 25 60
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Name | Description |
+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None) |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-c CONF_FILE``, ``--conf CONF_FILE`` | configuration file (default: None) |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--nolog`` | Don't generate log files (default: False) |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-d``, ``--debug`` | Increase output verbosity (default: False) |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-t intype [intype ...]`` | Contact Map file format:sup:`*` |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-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 |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-s SSPRED``, ``--ssfile SSPRED`` | Secondary structure prediction file. Supported formats are psipred, psipred2, psipred3, ss2 and indextableplus |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-p ARIAPROJECT``, ``--ariaproject ARIAPROJECT`` | ARIA project file. This project will be updated with data generated during the ``ariaec setup`` call |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-r SEQRANGE``, ``--range SEQRANGE`` | Index range if we don't want tu use the whole sequence and map |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-n REF``, ``--native REF`` | Native pdb. Allow TP/FP detection |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--hb HB`` | H-bonds contact file (eg: metapsicov.hb) |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--ssidx`` | Use secondary structure index |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--no-filter`` | Do not filter contact map |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--extract-all`` | Extract data or all data and parameters if an ARIA project is defined with ``-p`` option |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| :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`` |
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
* - Name
- Short Description
* - ``-h``, ``--help``
- show help message and exit
* - ``-d``, ``--debug``
- Increase output verbosity (default: False)
* - ``--nolog``
- Don't generate log files (default: False)
* - ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY``
- Output directory (default: None)
* - ``-c CONF_FILE``, ``--conf CONF_FILE``
- configuration file (default: None)
* - ``-t intype [intype ...]``
- Contact Map file format:sup:`*`
* - ``-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
* - ``-s SSPRED``, ``--ssfile SSPRED``
- Secondary structure prediction file. Supported formats are psipred, psipred2, psipred3, ss2 and indextableplus
* - ``-p ARIAPROJECT``, ``--ariaproject ARIAPROJECT``
- ARIA project file. This project will be updated with data generated during the ``ariaec setup`` call
* - ``-r SEQRANGE``, ``--range SEQRANGE``
- Index range if we don't want tu use the whole sequence and map
* - ``-n REF``, ``--native REF``
- Native pdb. Allow TP/FP detection
* - ``--hb HB``
- H-bonds contact file (eg: metapsicov.hb)
* - ``--no-filter``
- Do not filter contact map
* - ``--extract-all``
- 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``
Bbconv
......@@ -138,7 +142,7 @@ Translate BBcontacts as distance restraints which can be used during
.. code-block:: shell
ariaec bbconv [-h] contactfile sspred seq [msa] -t contactype
ariaec bbconv [OPTIONS] CONTACTFILE SSPRED SEQ [MSA] -t CONTACTYPE
**Arguments**
......
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