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#!/usr/bin/python

## Canberraq tool

## This code is written by Davide Albanese, <albanese@fbk.eu>.
## (C) 2008 Fondazione Bruno Kessler - Via Santa Croce 77, 38100 Trento, ITALY.

## This program is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.

## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
## GNU General Public License for more details.

## You should have received a copy of the GNU General Public License
## along with this program.  If not, see <http://www.gnu.org/licenses/>.


from numpy import *
from optparse import OptionParser
import csv
from mlpy import *

# Command line parsing
parser = OptionParser()
parser.add_option("-f", action = "store", type = "string",
                  dest = "flname", help = "feature-lists file - required")
parser.add_option("-a", action = "store", type = "string",
                  dest = "aname", help = "alphabet file - required")
parser.add_option("-o", action = "store", type = "string",
                  dest = "oname", help = "output file", default = "canberra.txt")
parser.add_option("-n", "--normalize", action = "store_true", default = False,
                  dest = "norm", help = "normalized distance in complete mode")

(options, args) = parser.parse_args()
if not options.flname:
    parser.error("option -f (feature-lists file) is required")
if not options.aname:
    parser.error("option -a (alphabet file) is required")


# Import feature-lists file
try:
    fl_str = [[x for x in line.split(None)] for line in open(options.flname)]
except ValueError:
    raise ValueError("'%s' is not a valid feature-lists file" % options.flname)


# Import alphabet file
atmp = open(options.aname).read()
try:
    a_str = [x for x in atmp.split(None)]
except ValueError:
    ValueError("'%s' is not a valid alphabet file" % options.aname)

# Link feature-name to a feature-id (from first list)
fid = {}
for id, n in enumerate(a_str):
    fid[n] = id


# Build numeric position-lists
pl_num = -ones((len(fl_str), len(a_str)), dtype = int)
for i, r in enumerate(fl_str):
    for j, c in enumerate(r):
        pl_num[i, fid[c]] = j
      
# Write to file
ofile = open(options.oname, "w")
ofile_writer = csv.writer(ofile, delimiter='\t', lineterminator='\n')

distance_comp, idx1_comp, idx2_comp, dd_comp = canberraq(pl_num, True, options.norm, dist=True)
distance_core, idx1_core, idx2_core, dd_core = canberraq(pl_num, False)

ofile_writer.writerow(["Complete", distance_comp])
ofile_writer.writerow(["Core", distance_core])

ofile.close()


tmpfile = open("dist_complete.txt", "w")
tmpfile_writer = csv.writer(tmpfile, delimiter='\t', lineterminator='\n')
for r in zip(idx1_comp, idx2_comp, dd_comp):
    tmpfile_writer.writerow(r)
tmpfile.close()

tmpfile = open("dist_core.txt", "w")
tmpfile_writer = csv.writer(tmpfile, delimiter='\t', lineterminator='\n')
for r in zip(idx1_core, idx2_core, dd_core):
    tmpfile_writer.writerow(r)
tmpfile.close()