.. MacSyFinder - Detection of macromolecular systems in protein datasets
    using systems modelling and similarity search.            
    Authors: Sophie Abby, Bertrand Néron                                 
    Copyright © 2014  Institut Pasteur, Paris.                           
    See the COPYRIGHT file for details                                    
    MacsyFinder is distributed under the terms of the GNU General Public License (GPLv3). 
    See the COPYING file for details.  
    
.. _database:

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Database API
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The "database" object handles the indexes of the sequence dataset in fasta format, and other useful information on the input dataset. 

      
MacSyFinder needs several indexes to run, and speed up the analyses.
 
  * index for hmmsearch (Hmmer program)
  * index for MacSyFinder

hmmsearch needs to index the sequences to speed up the analyses. The indexes are built by the external tools 
*formatdb* (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ncbi.tar.gz) or *makeblastdb*. MacSyFinder tries to find formatdb indexes in the same directory as the sequence file. If the indexes are present 
MacSyFinder uses these index, otherwise it builds these indexes using formatdb or makeblastdb.

MacSyFinder needs also to have the length of each sequence and its position in the database to compute some statistics on Hmmer hits. Thus it also builds an index (with .idx suffix) that is stored in the same directory as the sequence dataset. If this file is found in the same folder than the input dataset, MacSyFinder will use it. Otherwise, it will build it.

The user can force MacSyFinder to rebuild these indexes with the "--idx" option on the command-line. 
   
Additionally, for ordered datasets ( db_type = 'gembase' or 'ordered_replicon' ), MacSyFinder builds an internal "database" from these indexes to store information about replicons, their begin and end positions, and their topology.
The begin and end positions of each replicon are computed from the sequence file, and the topology from the parsing of the topology file (--topology-file, see :ref:`topology-files`).
  
  
database API reference
======================
.. automodule:: macsypy.database
   :members:
   :private-members:
   :special-members: