.. 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.  
    
.. _gembase_convention:

**************
Gembase format
**************


In order to allow the users running MacSyFinder on a bunch of genomes in a single run, we propose to adopt the following convention to fulfill the requirements for the "gembase db_type". It consists in providing for each protein, both the replicon name and a protein identifier separated by a "_" in the first field of fasta headers. "_" are accepted in the replicon name, but not in the protein identifier. Hence, the last "_" is the separator between the replicon name and the protein identifier.
For instance::

  >PlasmidA_0001 YP_003225072.1_ | putative stcE protein 
  MKLKYLSCMILASLAMGAFAATAADNNSAIYFNTTQPVNDLQGGLAAEVK
  FAQSQILSAHPKEGESQQHLTSLRKSLLLVRLVKADDKTPVQVEARDAND
  KILGTLTLSPPSSLPDTVYHLDGVPADGIDFTPQNGTKKIINTVAEVNKL
  SDASGSSIKSYLANNALVEIQTANGRWIRDMYLPQGAELEGKMVRFVSYA
  GYNSTVFYGDRKVTLSVGNTLLFKYVNGQWFRSGELENNRIAYAQHTWSA
  ELPAHWIVPGLNLVIKQGNLSGSLNDINVGAPGELLLHTIDIGMLTTPRG
  RFDFAKDKEAHREYFQTIPVSRMIVNNYAPLHLKEVMLPTGTLLTDADPG
  >PlasmidA_0002 YP_003225073.1_ | type II secretion protein EtpC
  MLFFLSSRRDRNLFIKDIALKMLTPNWVLCVILLIAGYQLVSVIRHFWLT
  PATSASDLSHVSVSETAVTDEHTEENFVFTLFGTASPPLSEGKVQKTTSS
  LSDDLLSGGDLDVRGILYSSVTEHSVAIFAHNNRQFSLGIGEKVPGYDAT
  ISAIFSDHIVINYQGKNASLPLRYDNPAKRNAQDDNNLIVGPVTTQANFR
  VKNIFDIMSLSPVTVNNTLSGYRLSPGKASSLFYNAGLHDNDLAVLLNGS
  ELRDTRQAKQIMKQLTELKEIKITVERDGQLYDAFIAVGEN
  ....
  >ChromosomeA_0001 _YP_003573410.1_ | adhesin-like protein
  MKKLFLFAALLMTGFAFYSCEDVVDNPAQDPAQSWNYSVSVKFADFDFNG
  AVDENSVPYTYKAPTTLYVLNEENTLMGTITTDAAPAIGDYGTYAGTLTG
  SIGNNLIITTKIGNDLTKQDGTLKSAIENGIVQTAEVPIKIYNANSGTLT
  TASAKMDNTAAIAYTSLGYIKGGDKILFVEGNQTFEWTVNEEFDPYTSTD
  LYIALPMNTDPETEYTISSDSKDGYTRGGTFKLADYPTLAAGKVSNYIGG
  IPFIQTGVDLTKWDAYMRTDPNNTWYMNNINNGWPATFSQEVEDGKSFIV
  TQSGPTLDSLNVVVGGVTGKEVNVTLNNIRLGKDRSINIGDKHGWVEYDG
  THDIYGWGAKANVTLIGENECETLYIQCPATKKGEGTLNYKNLSIDSYGS
  >ChromosomeA_0020 _YP_003573411.1_ | hypothetical protein
  MKRIVLITLVSILTTFQAIAQVANGFYRVQNNASSRYITLRDNAVGTVDY
  SSTNVDLSNIVTWSGFDKVKSNPASIIYVEQHDSKYDLKVQGTGIYAITG
  GRTYLELRPKDSGYILAVTYNGMEGRLYDSEEDVDGEGYVKRSGNSAYQY
  WSFIPVDTENNYIGLQPTVQVGDNYYGTLYASYPFKAASSGIKFYYVDAI
  ....
  >NC_001548_0015 _YP_003225080.1_ | type II secretion protein EtpJ  (translation)
  MSQQRVKGFTLLEMLLALAVFAALSISAFQVLQSGIRAHELSQDKVRRLA
  ELQRGGSQIERDLMQMIPRHSRGSEGLLLAAPHLLKSDDWGISFTRNSWL
  NPAGMLPRPELQWVGYRLRQQKLERLSYFYVDHPSGIAPDVRVVLEGVHA
  FRLRFFVNGTWQARWDSTSILPQAVEVTLVMDDFAELTRLFLVSKETAE

This input file contains 3 replicons: PlasmidA (which 2 first protein identifiers are 0001 and 0002), ChromosomeA (which 2 first protein identifiers are 0001 and 0020) and NC_001548 (which first protein identifier is 0015).

.. _topology-files:

**************
Topology files
**************

To be able to attribute a topology per replicon/genome when using the Gembase format, we propose the user to build a "topology file" in the form of a tabular file with two columns separated by a ":". The 1st column is the replicon name, and the 2nd the corresponding topology. Comments can be written after a "#". 

For example::

  # comment line
  PlasmidA : circular
  ChromosomeA : linear
  ChromosomeB : circular
  
.. note::
    A topology file can be specified on the command-line with the "``--topology-file``" parameter.