Usage

You can either compute the scaffolding from a Command Line Interface (CLI), or directly call the function in Python3 from the imported package.

Usage details

• Quick usage of khloraa scaffolding python package
• Input data and files
• Output data and files

Command line interface

Usage:

python3.9 -m khloraascaf [-h] [--mult-upbound MULTIPLICITY_UPPERBOUND] [--presscore-upbound PRESENCE_SCORE_UPPERBOUND] [--solver {GUROBI,CBC}] [--out-directory OUTPUT_DIRECTORY] [--instance-name INSTANCE_NAME] [--debug]
                                contig_attributes contig_links starter_id

Positional arguments:

Argument name	Description
contig_attributes	The multiplicities and the presence score of the contigs
contig_links	The links between the oriented contigs
starter_id	The identifier of the starter contig

Optional arguments:

Flag(s) and name	Description
-h, --help	Show the help message
--mult-upbound MULTIPLICITY_UPPERBOUND	The upper bound for unknown multiplicities
--presscore-upbound PRESENCE_SCORE_UPPERBOUND	The upper bound for unknown presence score
--solver {gurobi,cbc}	The MILP solver to use
--out-directory OUTPUT_DIRECTORY	The output directory path
--instance-name INSTANCE_NAME	Custom prefix for outputs
--debug	Outputs debugs

Python function

from khloraascaf import scaffolding
from pathlib import Path

scaffolding(
    Path('tests/data/ir_sc/contig_attrs.tsv'),
    Path('tests/data/ir_sc/contig_links.tsv'),
    'C0',
)

See khloraascaf.scaffolding() function API reference.