# --------------------------------------------------------------------------------------------------------------- # File : get_double_cog_expansions.piana_conf # Author : Ramon Aragues # Creation : 17.10.2004 # Contents : configuration file that gets simple expansions for proteins in an input file # --------------------------------------------------------------------------------------------------------------- # This file is used to configure parameters for piana.py for some specific use described below # # if you want piana.py to be configured by this file, set command line option --configuration-file=this_file_name # # ---------------------------- description of this particular configuration file -------------------------------- # # This is the configuration file for getting double cog expansions for proteins in an input file. Expansions # will be printed to the default name. A double expansion means that first we expand all the proteins # in the network with interactions of other proteins that share the COG, and then, starting from the # expanded network, we will expand root proteins again (we have to do it twice, to be sure we propagate # previous expansions) # # output-id-type recommended is md5 (in case the output file is going to be inserted into pianaDB afterwards) # # # - apart from this configuration file, the user must use piana.py command line options: # # --> input-file # --> input-id-type # --> output-id-type # --> results-prefix # --> piana-dbname # --> piana-dbhost # --> piana-dbuser (depends on the system) # --> piana-dbpass (depends on the system) # # These parameters are required in the command line! In this file, they are set to blank, obliging the user # to set them on the command line (although, they could have values assigned and still be ignored, since # the command line has preference over the parameter values in this file) # --------------------------------------------------------------------------------------------------------------- # # # # Attention! - All non-configuration lines in this file must start with '#' (unless empty line) # - A configuration line that is preceded by '#' is not taken into account # - Configuration file parameters equal to blank are ignored # # --------------------------------------------------------------------------------------------------------------- # =============================================================================================================== # configuration of execution parameters # --------------------------------------------------------------------------------------------------------------- # set here the input parameters for this specific configuration that are not required in the command-line # =============================================================================================================== exec-mode=batch memory-usage=high input-file=blank input-id-type=blank input-proteins-species=all piana-dbname=blank piana-dbhost=blank piana-dbuser=blank piana-dbpass=blank use-secondary-db=blank depth=1 hub-threshold=blank use-self-ints=yes list-source-dbs=all inverse-dbs=no list-source-methods=all inverse-methods=no output-id-type=blank output-proteins-species=all results-prefix=blank results-dir=./ alternative-id-types=unientry:uniacc:gi:md5 list-keywords=blank file-over-expressed=blank file-infra-expressed=blank expression-id-type=blank >>>>>>> Do not remove this line: used to mark transition from the parameters section to the execution commands section <<<< # =============================================================================================================== # configuration of execution commands # =============================================================================================================== # Set here the commands that piana.py will execute # # these commands can be ordered as desired by the user: it is up to the user to make sure the command sequence makes # sense (eg. not asking to write a table without building a network first) # # commands that can be used are those listed in piana.py --help # # some commands require extra information that can be set in this file as well (eg. command "species-network" # requires a species_name, which will be provided as well in this configuration file) # # even if you don't want to give any value to the command arguments, you must leave the argument and set it to blank # # =============================================================================================================== # # the following commands perform the actions described in the description of this particular configuration file # # - The commands will be executed in the same order as they appear in this file # - All commands must be followed by ";", even if they do not have arguments # - Configuration lines should not finish with ";" # - if you don't want the configuration line to set a given argument, write "blank" after the "=" sign # - default names for output files (used in case you set it to blank) are: results_prefix.command_name_creating_output # in some cases, extra information will be added to the results file name (eg. "_compact" or "_extended" output mode) # - in all commands that set protein_type, if nothing is found for protein_type (or input-id-type) alternative-id-types # are used instead (and will print protein codes as "alternative_type_name:protein_code" ) # # =============================================================================================================== expand-interactions;expansion-type=cog;expansion-nodes=all;expansion-threshold=0;exp-output-mode=add;output-target=blank;id-type=blank expand-interactions;expansion-type=cog;expansion-nodes=root;expansion-threshold=0;exp-output-mode=print;output-target=blank;id-type=blank exit;