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#!/usr/bin/python3
# -*- coding: utf-8 -*-
# std import
import sys
import argparse
import os.path
from collections import defaultdict
import csv
import re
import math
class Variant(object):
def __init__(self, type, comment):
self.type = type
self.comment = comment
def __eq__(self, other):
if self.type != other.type:
return False
if self.comment != other.comment:
return False
return True
def __str__(self):
return "%s_%s" % (str(self.type), str(self.comment))
def __repr__(self):
return "<%s - %s>" % (self.type, self.comment)
def __hash__(self):
return hash(self.type + self.comment)
def main():
""" The main function of vde no argument """
enable_input = [name.split("2")[0] for name in list(globals().keys())
if name.endswith("2eva")]
parser = argparse.ArgumentParser(
prog="vde",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("-e", "--experiment",
type=str,
help="File of experimente result.",
required=True)
parser.add_argument("-t", "--truth",
type=str,
help="File of truth result.",
required=True)
parser.add_argument("-d", "--delta",
type=int,
help="Acceptable diff betwen truth and experimente.",
default=5)
parser.add_argument("-ef", "--experiment-format",
type=str,
help="Format of experiment file",
choices=enable_input,
default="eva")
parser.add_argument("-tf", "--truth-format",
type=str,
help="Format of truth file",
choices=enable_input,
default="eva")
# parsing cli argument
argument = vars(parser.parse_args())
expfunc = globals()[argument["experiment_format"]+"2eva"]
truthfunc = globals()[argument["truth_format"]+"2eva"]
experiment, count = expfunc(argument["experiment"])
truth, count = truthfunc(argument["truth"])
result = compare(experiment, truth, argument["delta"])
result_printing(result, count)
def result_printing(result, count):
""" Printing the result in csv format """
head = ",".join(("type", "TP", "FP", "recall", "precision"))
print(head)
for gap in list(result.keys()):
total = result[gap]["TP"] + result[gap]["FP"]
prec = 1 if total == 0 else result[gap]["TP"]/float(total)
recall = 1 if count[gap] == 0 else result[gap]["TP"]/float(count[gap])
print((",".join((str(gap),
str(result[gap]["TP"]),
str(result[gap]["FP"]),
str(recall),
str(prec)))))
def compare(exp, truth, delta):
""" Compare experimente and truth return TP FP precision and recall
for each type """
result = defaultdict(lambda: defaultdict(int))
exp_pos = set(exp.keys())
tru_pos = set(truth.keys())
for exact_pos in set(exp_pos & tru_pos):
for variant in exp[exact_pos]:
if variant in truth[exact_pos]:
result[variant.type]["TP"] += 1
else:
result[variant.type]["FP"] += 1
not_found = set(exp_pos - (exp_pos & tru_pos))
for fuzzy_pos in set(exp_pos - (exp_pos & tru_pos)):
end = False
for pos in range(fuzzy_pos - delta, fuzzy_pos + delta + 1):
for variant in exp[fuzzy_pos]:
if variant.type in ("snp", "multi_snp"):
result[variant.type]["FP"] += 1
try:
not_found.remove(fuzzy_pos)
except KeyError:
pass
end = True
break
if variant in truth[pos]:
result[variant.type]["TP"] += 1
try:
not_found.remove(fuzzy_pos)
except KeyError:
pass
end = True
break
if end :
break
for pos in not_found:
for variant in set(exp[pos]):
result[variant.type]["FP"] += 1
return result
def eva2eva(filename):
""" Read eva file and return value in dict
position is key and type is value """
__check_file_exist(filename)
data = defaultdict(list)
count = defaultdict(int)
with open(filename) as csvfile:
linereader = csv.reader(csvfile)
for val in linereader:
data[int(val[0])].append(Variant(val[1], val[2]))
count[val[1]] += 1
return data, count
def breakpoints2eva(filename):
""" Read breakpoint file and return value in dict
position is key and type is value """
__check_file_exist(filename)
data = defaultdict(list)
count = defaultdict(int)
mtg2eva = {"HOM": "homo",
"HET": "hete",
"SNP": "snp",
"MSNP": "multi_snp",
"DEL": "deletion",
"BACKUP": "backup"}
findpos = re.compile(r'pos_([-\d]+)')
findtype = re.compile(r'_([a-zA-Z]+)$')
findcomment = re.compile(r'contig_\d+_(.+)_pos')
with open(filename) as filehand:
for line in filehand:
line = line.strip()
if line.startswith(">left_contig_"):
data[int(findpos.search(line).group(1))].append(Variant(
mtg2eva[findtype.search(line).group(1)],
findcomment.search(line).group(1)))
count[mtg2eva[findtype.search(line).group(1)]] += 1
return data, count
def __add_in_data_count(pos, type_gap, data, counter):
""" Add value pos: type_gap in data and increment counter[data] """
data[pos].add(type_gap)
counter[type_gap] += 1
def __check_file_exist(filename):
""" If file doesn't exist trow assert """
assert os.path.isfile(filename), "Error when I try open " + filename
if(__name__ == '__main__'):
main()
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