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str_outliers.py
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#! /usr/bin/env python3
### ASDP PIPELINE ###
## Version : 0.0.1
## Licence : AGPLv3
## Author : Anne-Sophie Denommé-Pichon
## Description : script to get automatically outliers from expansion pipeline results from getResults.py
import collections
import csv
import logging
import math
import os
import os.path
import scipy.stats
import sys
output_directory = None
zscore_threshold = None
percentile_threshold = None
with open(os.path.join(os.path.dirname(sys.argv[0]), 'config.sh')) as config:
for line in config:
if '=' in line:
variable, value = line.split('=', 1)
if variable == 'RESULTS_OUTPUTDIR':
output_directory = value.split('#')[0].strip('"\' ') # strip double quotes, simple quotes and spaces
elif variable == 'ZSCORE_THRESHOLD':
zscore_threshold = float(value.split('#')[0].strip('"\' ')) # strip double quotes, simple quotes and spaces
elif variable == 'PERCENTILE_THRESHOLD':
percentile_threshold = float(value.split('#')[0].strip('"\' ')) # strip double quotes, simple quotes and spaces
if output_directory is None:
logging.error('RESULTS_OUTPUTDIR or ZSCORE_THRESHOLD or PERCENTILE_THRESHOLD is missing in config.sh')
sys.exit(1)
zscore_label = f'Z>={zscore_threshold}'
percentile_label = f'{percentile_threshold}%'
def load_limits():
limits = {}
with open(f'{sys.argv[0].rsplit("/", 1)[0]}{os.sep}patho.csv') as limits_file:
csvreader = csv.reader(limits_file, delimiter=';')
try:
next(csvreader)
for row in csvreader:
if row[1] != 'NA':
limits[row[0]] = int(row[1])
return limits
except StopIteration:
print('Limits file is empty', file=sys.stderr)
sys.exit(1)
def display_outliers(locus, limits, samples):
# results = {
# 'dijen': {
# 'tool': {
# 'Limit': 42,
# '5 %': 42,
# 'Z score': 42,
# '< 3': 2
# }
# }
# }
results = collections.OrderedDict()
tools_values = {}
with open(f'{output_directory}{os.sep}{locus}.tsv') as result_file:
tsvreader = csv.reader(result_file, delimiter='\t')
try:
tools = next(tsvreader)[1:]
for row in tsvreader:
dijen = row[0]
results[dijen] = collections.OrderedDict()
for tool_id, tool in enumerate(tools):
tool_value = row[tool_id + 1].replace('nofile', '.').replace('-1', '.')
tools_values.setdefault(tool, [])
results[dijen][tool] = collections.OrderedDict()
results[dijen][tool]['Limit'] = '.'
results[dijen][tool][percentile_label] = tool_value
results[dijen][tool][zscore_label] = tool_value
results[dijen][tool]['< 3'] = '.'
# > upper limit of normality or < 3
if tool_value != '.':
# count: number of repeats from the input file
for count in tool_value.split(','):
if count != '.':
tools_values[tool].append(int(count))
if int(count) < 3:
results[dijen][tool]['< 3'] = tool_value
if locus in limits:
if int(count) > limits[locus]:
results[dijen][tool]['Limit'] = tool_value
else:
results[dijen][tool]['Limit'] = 'NA'
except StopIteration:
print('Input file is empty', file=sys.stderr)
sys.exit(1)
# outlier threshold (example: 5%)
for tool, tool_values in tools_values.items():
# Test if there is at least one value given by the tool
if tool_values:
tool_percentile_limit = sorted(tool_values)[-math.ceil(len(tool_values) * percentile_threshold / 100):][0]
for dijen, dijen_outliers in results.items():
tool_percentile_outliers = dijen_outliers[tool][percentile_label]
actual_outlier = False
# count: number of repeats from the input file
for count in tool_percentile_outliers.split(','):
if count != '.':
if int(count) >= tool_percentile_limit:
actual_outlier = True
break
if not actual_outlier:
dijen_outliers[tool][percentile_label] = '.'
# Z score
for tool, tool_values in tools_values.items():
if tool_values:
if len(tool_values) > 1:
zscores = iter(scipy.stats.zscore(tool_values))
else:
zscores = iter(['.'])
for dijen_outliers in results.values():
actual_outlier = False
zscore_outliers = []
# count: number of repeats from the input file
for count in dijen_outliers[tool][zscore_label].split(','):
if count != '.':
zscore = next(zscores)
if zscore == '.':
zscore_outliers.append('.')
else:
zscore_outliers.append(f'{zscore:.3f}')
if zscore >= zscore_threshold:
actual_outlier = True
if actual_outlier:
dijen_outliers[tool][zscore_label] = ','.join(zscore_outliers)
else:
dijen_outliers[tool][zscore_label] = '.'
# Output
print('sample\tEH\tEH\tEH\tEH\tTred\tTred\tTred\tTred\tGangSTR\tGangSTR\tGangSTR\tGangSTR')
print(f'\tLimit\t{percentile_label}\t{zscore_label}\t< 3' * 3)
for dijen, dijen_outliers in results.items():
all_outliers = [dijen]
dijen_has_outliers = False
for tool, tool_outliers in dijen_outliers.items():
if tool_outliers:
for tool_outlier_value in tool_outliers.values():
if tool_outlier_value != '.':
dijen_has_outliers = True
all_outliers.extend(tool_outliers.values())
else:
all_outliers.append('.')
if dijen_has_outliers and dijen in samples:
print('\t'.join(all_outliers))
if __name__ == '__main__':
if len(sys.argv) != 3:
print(f'Usage: {sys.argv[0].split(os.sep)[-1]} <LOCUS> <SAMPLES.LIST>', file=sys.stderr)
sys.exit(1)
with open(sys.argv[2]) as samples_list:
samples = set()
for line in samples_list.readlines():
sample = line.rstrip()
if sample:
samples.add(sample)
limits = load_limits()
display_outliers(sys.argv[1], limits, samples)