Config File
Configuration Template¶
#############################
# NPLinker configuration file
#############################
root_dir = "<NPLinker root directory>"
# [REQUIRED] The value is required and must be a full path.
# The root directory of the NPLinker project. You need to create it first.
mode = "podp"
# [REQUIRED] Available values are "podp" and "local".
# The mode for preparing dataset.
# "podp" mode is for using the PODP platform (https://pairedomicsdata.bioinformatics.nl/) to prepare the dataset.
# "local" mode is for preparing the dataset locally. So users do not need to upload their data to the PODP platform.
podp_id = ""
# [REQUIRED-UNDER-CONDITIONS] The value is required if the mode is "podp".
# The PODP project identifier.
# Example: The identifier is "4b29ddc3-26d0-40d7-80c5-44fb6631dbf9.4" for the project
# https://pairedomicsdata.bioinformatics.nl/projects/4b29ddc3-26d0-40d7-80c5-44fb6631dbf9.4
[log]
# Settings for logging.
level = "INFO"
# [REQUIRED] Available values are "DEBUG", "INFO", "WARNING", "ERROR", and "CRITICAL".
# Log level.
use_console = true
# [REQUIRED] Available values are "true" and "false".
# Whether to write log messages to console.
file = "path/to/logfile"
# [OPTIONAL]
# The log file to append log messages.
# If not set or use empty string, log messages will not be written to a file.
# The file will be created if it does not exist. Log messages will be appended to the file if it exists.
[mibig]
# Settings for MIBiG.
to_use = true
# [REQUIRED] Available values are `true` and `false`.
# Whether to use MIBiG annotations/metadata data for the analysis.
version = "3.1"
# [REQUIRED-UNDER-CONDITIONS] The version must be same as the version of MIBiG used in BiG-SCAPE.
# The version of MIBiG data to use.
# Check all available versions at https://mibig.secondarymetabolites.org/download.
[bigscape]
# Settings for BiG-SCAPE.
version = 1
# [REQUIRED] Available values are 1 and 2. 1 for version 1.x series and 2 for version 2.x series.
# The version of BiG-SCAPE to use.
cutoff = "0.30"
# [REQUIRED] The value must be a string.
# Which cutoff to use for the analysis.
# There might be multiple cutoffs in the BiG-SCAPE output and this value must be one of them.
parameters = "version1_parameters_or_version2_parameters"
# [REQUIRED-UNDER-CONDITIONS] It's required when you want to run BiG-SCAPE in NPLinker.
# Parameters for running BiG-SCAPE.
# --------------
# For version 1:
# -------------
# The parameters MUST contain `--mix`, `--include_singletons` and `--cutoffs`. NPLinker needs them to run the analysis properly.
# The parameters must NOT contain `--inputdir`, `--outputdir`, `--pfam_dir`. NPLinker will automatically configure them.
# An example value could be: "--mibig --clans-off --mix --include_singletons --cutoffs 0.30".
# --------------
# For version 2:
# --------------
# BiG-SCAPE v2 has subcommands. NPLinker requires the `cluster` subcommand and its parameters.
# Required parameters of `cluster` subcommand are: `--mibig_version`, `--include_singletons` and `--gcf_cutoffs`.
# DO NOT set these parameters: `--pfam_path`, `--inputdir`, `--outputdir`. NPLinker will automatically configure them.
# BiG-SCPAPE v2 also runs a `--mix` analysis by default, so you don't need to set this parameter here.
# An example value could be: "--mibig_version 3.1 --include_singletons --gcf_cutoffs 0.30"
[scoring]
# Settings for scoring.
methods = ["metcalf"]
# [REQUIRED] Available values are "metcalf" and "rosetta".
# Scoring methods to use for the analysis.
Example Configuration¶
For a full example of a configuration file, see here.
Config loader¶
You can load the configuration file using the load_config function.
When you use NPLinker as an application, you can get access to the configuration object directly: