# --------------------------------------------------------------------------------------------------------------- # File : metastasis.piana_conf # Author : Ramon Aragues # Creation : 28.10.2005 # Contents : piana configuration file that produces results for genes identified in Nature. 2005 Jul 28;436(7050):518-24. # --------------------------------------------------------------------------------------------------------------- # 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 described in piana/README.piana_examples for producing results for genes that # mediate breast metastatis to lung, discovered by the team of Joan Massague and published in # Nature. 2005 Jul 28;436(7050):518-24. # # - apart from this configuration file, the user must use piana.py command line options: # # --> 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=../../projects/metastasis/data/metastasis_gene_names.txt input-id-type=geneName # we set species to all because experiments were done on mice and humans input-proteins-species=all # we leave to blank these parameters so the user can set them through the command line piana-dbname=blank piana-dbhost=blank piana-dbuser=blank piana-dbpass=blank use-secondary-db=blank depth=1 hub-threshold=0 use-self-ints=yes list-source-dbs=all inverse-dbs=no list-source-methods=all inverse-methods=no output-id-type=geneName output-proteins-species=human results-prefix=metastasis_results results-dir=./ alternative-id-types=uniacc:unientry:gi:geneName:md5:proteinPiana list-keywords=cancer:carcinoma:tumor:metastasis:apoptosis:death 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 # =============================================================================================================== # print the interaction table in html format print-table;output-target=blank;id-type=blank;print-mode=all;format-mode=html # print the interaction network in dot format, highlighting proteins in the network that contain keywords related to cancer print-network;output-target=blank;id-type=blank;print-mode=all;format-mode=dot # print the interaction network in dot format, highlighting proteins in the network that contain keywords related to cancer # print only those interactions between root proteins or between root proteins and linker proteins # -> this will print the network that connects the root proteins between them print-network;output-target=blank;id-type=blank;print-mode=connecting;format-mode=dot # print all the information associated to the proteins in the network print-all-prots-info;output-target=blank;id-type=blank;output-mode=compact;format-mode=html # identify linkers, proteins that connect at least two root nodes print-connect-prots-info;output-target=blank;id-type=blank;output-mode=compact;format-mode=txt print-connect-prots-info;output-target=blank;id-type=blank;output-mode=compact;format-mode=html exit;