Documentation
--------------


Description:
^^^^^^^^^^^^
This tool is an interactive command line framework kinda tool,
which is use to get biological sample with scraping. it does not requires any 
programming skill to run. evry module is explained and available in help menu.
Note that this tool is completely based on web-scraping from trusted websites.
any changes occurance on that website will make this tool completely useless.
so, basically this tool is not stable for forever. but still i will keep maintaining this tool.

-----------

Options
-------
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   <div id="features">

+-------------+--------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| Features    | Details                                                                                          | Examples                                                                    |
+=============+==================================================================================================+=============================================================================+
| Set         | use for setting id, item type, doc type etc `Options.set <#set_options>`_.                       | ``set id=1798174254 type=nuccore doc=html report=genbank``                  |
+-------------+--------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| Get         | use for getting the data after setting creds with ``set``. `Options.get <#get_options>`_.        | ``get gene`` , ``get sequence`` , ``get comment`` , ``get all``             |
+-------------+--------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| Search      | use for searching for any term available `Options.search <#search>`_.                            | ``searchd /roma52`` or ``searchl /roma52``                                  |
+-------------+--------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| Clear       | use for clearing the console as usual                                                            | ``cls``                                                                     |
+-------------+--------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| FTP*        | use for getting any data files from http://ncbi.nlm.nih.gov                                      | ``ftp``                                                                     |
+-------------+--------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| Options     | use to get options for selected module                                                           | ``options``                                                                 |
+-------------+--------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| Help        | use to get all available help options                                                            | ``help``                                                                    |
+-------------+--------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| Visualize+  | use to open the scrapping page on browser if something is not working                            | ``visualize``                                                               |
+-------------+--------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------+
| Exit        | use to exit the console                                                                          | ``exit``                                                                    |
+-------------+--------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------+


*(+) options are under development*


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   </div>

--------------

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   <div id="set_options">

Set Options
^^^^^^^^^^^

+-----------------+----------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------+
| Options         | Details                                                                                                                                      | Examples                                               |
+=================+==============================================================================================================================================+========================================================+
| ID              | NCBI use separate IDs for all data, so we can use the IDs to get required data, You can get the IDs of any species by ``searchl`` command.   | ``set id=<ID here>``                                   |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------+
| Item Type       | NCBI use specific name for every category of species data you want to get. `Item.type <#type>`_.                                             | ``set <Item Value>``                                   |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------+
| Report Type     | NCBI use specific report type for different purposes `Item.report <#type>`_.                                                                 | ``set <Report Name>``                                  |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------+
| Document Type   | NCBI use html and text format. **NOTE**: *there is no CUSTOM* ``get`` *option available for text format. it will give whole page at once.*   | ``set <doc type>`` html(custom options) or text(all)   |
+-----------------+----------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------+

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   </div>

--------------

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   <div id="type">

Item-type Informations
^^^^^^^^^^^^^^^^^^^^^^

+------------+--------------------------------------------------+---------------+
| Item       | Details                                          | Values        |
+============+==================================================+===============+
| Nucleoid   | use to get nucleotide samples and other infos.   | ``nuccore``   |
+------------+--------------------------------------------------+---------------+
| Genes      | use to get Genes samples and other infos.        | ``gene``      |
+------------+--------------------------------------------------+---------------+
| Protein    | use to get Protein samples and other infos.      | ``protein``   |
+------------+--------------------------------------------------+---------------+
| Probe      | use to get Probes infos.                         | ``probe``     |
+------------+--------------------------------------------------+---------------+
| Popset     | use to get Popset infos.                         | ``popset``    |
+------------+--------------------------------------------------+---------------+

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--------------

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   <div id="report">

Report-type Informations
^^^^^^^^^^^^^^^^^^^^^^^^

+-----------+--------------------------------------------------+---------------+
| Reports   | Details                                          | Values        |
+===========+==================================================+===============+
| Genbank   | use to get nucleotide samples and other infos.   | ``genbank``   |
+-----------+--------------------------------------------------+---------------+
| FASTA     | use to get Genes samples and other infos.        | ``fasta``     |
+-----------+--------------------------------------------------+---------------+

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   <div id="get_options">

Get Options
^^^^^^^^^^^

+----------------+------------------------------------------------------+---------------------+
| Options        | Details                                              | Examples            |
+================+======================================================+=====================+
| Name           | Use to get db based name of species.                 | ``get name``        |
+----------------+------------------------------------------------------+---------------------+
| Introduction   | Use to get introduction of species.                  | ``get intro``       |
+----------------+------------------------------------------------------+---------------------+
| Comments       | Use to get comment on the report.                    | ``get comment``     |
+----------------+------------------------------------------------------+---------------------+
| Gene           | Use to get gene of the selected species.             | ``get gene``        |
+----------------+------------------------------------------------------+---------------------+
| Stem Loop      | Use to get Stem Loop of the report.                  | ``get stem-loop``   |
+----------------+------------------------------------------------------+---------------------+
| Peptide        | Use to get Peptide of the report.                    | ``get peptide``     |
+----------------+------------------------------------------------------+---------------------+
| CDS            | Use to get CDS of the report.                        | ``get cds``         |
+----------------+------------------------------------------------------+---------------------+
| Source         | Use to get Source of the report.                     | ``get source``      |
+----------------+------------------------------------------------------+---------------------+
| All            | Use to get complete page in text format of report.   | ``get all``         |
+----------------+------------------------------------------------------+---------------------+

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--------------

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   <div id="search">

Search options
^^^^^^^^^^^^^^

To search All detailed summary of search term:

.. code:: sh

    searchl <ITEM VALUE> <TERM>

To search All IDs of search TERM:

.. code:: sh

    searchd <ITEM VALUE> <TERM>

+------------+----------------------------------------------------+---------------+
| Item       | Details                                            | Values        |
+============+====================================================+===============+
| Nucleoid   | Use to search nucleotide samples and their list.   | ``nuccore``   |
+------------+----------------------------------------------------+---------------+
| Genes      | Use to search samples and other infos.             | ``gene``      |
+------------+----------------------------------------------------+---------------+
| Protein    | Uses to search Protein samples and other infos.    | ``protein``   |
+------------+----------------------------------------------------+---------------+
| Probe      | Uses to search Probes lists.                       | ``probe``     |
+------------+----------------------------------------------------+---------------+
| Popset     | Uses to search Popset lists.                       | ``popset``    |
+------------+----------------------------------------------------+---------------+

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   </div>