#!/usr/bin/env python3
"""
Renumber the segments of a GFA assembly graph.
The largest segment is renamed 01, down to the smallest segment 99.
The amount of zero-padding required is determined automatically.
"""

from gfapy import Gfa
import argparse
import math

argparser = argparse.ArgumentParser(description = __doc__)
argparser.add_argument("-o", "--out", action="store", default="/dev/stdout", help="output GFA file [/dev/stdout]")
argparser.add_argument("--version", action="version", version="gfapy-renumber 0.1.0")
argparser.add_argument("gfa", help="input GFA file")
args = argparser.parse_args()

g = Gfa.from_file(args.gfa)
names = g.segment_names
width = math.ceil(math.log10(len(names)))
names.sort(key = lambda u: g.segment(u).length, reverse = True)
for i, name in enumerate(names):
	g.segment(name).name = str(1 + i).rjust(width, "0")
g.to_file(args.out)