diff --git a/README.md b/README.md index 5ea70b4f4015593e6b2b86cde380bc07e2f59cf9..9485def8fd4b1b3f00d323f22118c3fae8d86323 100644 --- a/README.md +++ b/README.md @@ -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 diff --git a/docs/contents.rst b/docs/contents.rst index 52d2f28f5d8cde74bff524accae7a1052b7c8da0..4e7e833e11b4517781612af047571e69f1908b19 100644 --- a/docs/contents.rst +++ b/docs/contents.rst @@ -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> + diff --git a/docs/installation.rst b/docs/installation.rst index fc0c882b87844531d97f361975c3b9e692d92bc7..6512966d94aea58c010ce90deec656902c63adaa 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -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 diff --git a/docs/tutorial.rst b/docs/tutorial.rst new file mode 100644 index 0000000000000000000000000000000000000000..f4b5d31d6eac2a5f0d4cdd421ac8dec5897c7e4e --- /dev/null +++ b/docs/tutorial.rst @@ -0,0 +1,29 @@ +======== +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 +============ + diff --git a/docs/usage.rst b/docs/usage.rst index 1ae0e6f2df3f244dc34ad96d44e688b661a07964..6f1c402ee803bff2f9a886a43dd848220d98d9da 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -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**