mcl2rawcafe Namespace Reference

Functions
def	mcl2rawcafe

Variables
string	__author__ = "Fabio H. K. Mendes"
tuple	parser = argparse.ArgumentParser(description=__doc__, prog="mcl2rawcafe.py")
tuple	args = parser.parse_args()

Detailed Description

This script defines and runs the mcl2rawcafe function, which tabulates genes/peptides per species for each cluster from a mcl dump file.
The output is a raw (unfiltered) table that can be used as CAFE's input.

Function Documentation

def mcl2rawcafe.mcl2rawcafe	(		mcl_dump,
			path_output_file,
			species_ids
	)

[str] mcl_dump: path to mcl's dump file
[str] path_output_file: path to output .txt file
[str] species_ids: unique species identifiers (separated by white spaces, enclosed within double quotes)
                   (e.g., "ENSBTA ENSCJA ENSCAF ENSECA ENSP00 ENSMMU ENSMUS ENSNLE ENSPTR ENSPAN ENSPPY ENSRNO")

Variable Documentation

string mcl2rawcafe.__author__ = "Fabio H. K. Mendes"

tuple mcl2rawcafe.args = parser.parse_args()

tuple mcl2rawcafe.parser = argparse.ArgumentParser(description=__doc__, prog="mcl2rawcafe.py")