Config

Instead of setting multiple CLI options, you can create a config file.

You can create a config using the xlranker init command. This will run an interactive prompt that will create a custom config. If you just want the default configs, run xlranker init --default.

Config Options

network (Required)

path to the network containing peptide sequences. Described in input_data/peptide_pairs.

data_folder (Required)

path to a directory containing multi-omic data used by the machine learning model. Described in input_data/omic_data.

seed (Defaults to None)

integer to seed random number generators. If not set, random seed selected.

custom_mapping_table (Defaults to None, strongly recommended)

path to a custom mapping table (recommended). Can either be a FASTA file or a TSV file. Described in input_data/fasta and input_data/custom_mapping_table. If not set, uses UNIPROT human one sequence per gene acquired on May 29, 2025.

is_fasta (Defaults to True)

true if the custom_mapping_table is a FASTA file.

fasta_type

Valid options GENCODE or UNIPROT. Type of FASTA file used. Must be set if custom_mapping_table is set.

only_human (Defaults to true)

true if the data in the pipeline only contains human data. If true, allows for better negative pair generation and PPI information.

output (Defaults to xlranker_output)

Output directory for the pipeline. Contains the final network, info file, and plots.