* Requirements

** Input File
   The input file should be a resulting PSM (peptide-spectrum match) output file
   from a database search such as Mascot or Andromeda in tab delimited format.
   The minimum required columns are :
   - Sequence :: The amino acid sequence of a PSM
   - Modifications :: A column that describes the modifications of the sequence.
   (Note for MaxQuant this information is already provided in =Modified Sequence=)
   - PrecursorArea :: (or Intensity) the AUC (or SPCs) for each PSM
   - IonScore :: Mascot (or search engine equivalent) score for each PSM
   - q_value :: Percolator (or search engine equivalent) score for each PSM
       Note that PEP can be used in place of q_value with the rough observational
       approximation that PEP / 10 = q_value
   - Charge

*** Renaming Columns
   A base configuration file for renaming column headers is provided with =gpgrouper=
   To generate it, simply run =gpgrouper getconfig= and a config file will be generated.
   The configuration file can be specified by the =--configfile= flag in =gpgrouper run=, but if not specified
   and the default =gpgrouper_config.ini= file exists, it will be used.

   This file can be edited with addition of new column aliases as needed, though it should be set up to work
   with ProteomeDiscoverer+Mascot and MaxQuant already.

*** Additional info for MaxQuant
   For MaxQuant output, the =evidence.txt= PSMs file should be used as input. gpgrouper is designed
   to be run separately for each experiment. As of writing, it is not configured to work with multiple 
   label-free experiments searched together under say MaxQuant. Therefore, separate experiments
   need to be separated. In other words, if MaxQuant is used to search multiple experiments at 
   once (potentially with match between runs) the evidence.txt file needs to be separated into separate "experiment" files.
   A simple [[https://gist.github.com/asalt/82548c387e68dc228bb8b2124268a913][script]] is available for doing just this.

** FASTA Database File
   The database file should be a pre-constructed tab delimited file for matching
   PSMs to their respective GeneIDs.
   The required columns are =TaxonID=, =HomologeneID=, =GeneID=,
   =ProteinGI=, =FASTA=.
   Note that PyGrouper uses =GeneID= to group PSMs, so if a GeneID is lacking for
   a desired grouping another identifier can be substituted in such as =ProteinGI=.
   =HomologeneID= can be an empty column if this information is not available
   or desired.