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repeat-extractor.py
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repeat-extractor.py
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#!/usr/bin/env python
from __future__ import unicode_literals
from extractor import *
#ref = 'AGCTGTGGGAGGGAGCCAGTGGATTTGGAAACAGAAATGGCTTGGCCTTGCCTGCCTGCCTGCCTGCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCCTCCTGCAATCCTTTAACTTACTGAATAACTCATGATTATGGGCCACCTGCAGGTACCATGCTAG'
#alt = 'AGCTGTGGGAGGGAGCCAGTGGATTTGGAAACAGAAATGGCTTCGCCTTGCCTGCCTGCCTGCCTGCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCGTCCTTCCTTCCCTCCTGCAATCCTATAACTTACTGAATAACTCATGATTATGGGCCACCTGCAGGTACCATGCTAG'
#units = ['TCCT', 'GCCT']
#print 'version:', extractor.VERSION
#describe_repeats(ref, alt, units)
THRESHOLD = 10000
class Repeat(object):
"""
Simple repeat structure.
"""
__slots__ = ['start', 'end', 'count']
def __init__(self, start, end, count=0):
"""
Initialize the repeat structure.
:arg integer start: Start position of the repeat.
:arg integer end: End position of the repeat.
:arg integer count: Number of repeats.
"""
self.start = start
self.end = end
self.count = count
def short_sequence_repeat_extractor(string, min_length=1):
"""
Extract the short tandem repeat structure from a string.
:arg string string: The string.
:arg integer min_length: Minimum length of the repeat structure.
"""
length = len(string)
k_max = length // 2 + 1
if k_max > THRESHOLD:
k_max = THRESHOLD // 2
repeats = []
i = 0
last_repeat = i
while i < length:
max_count = 0
max_k = 1
for k in range(min_length, k_max):
count = 0
for j in range(i + k, length - k + 1, k):
if string[i:i + k] != string[j:j + k]:
break
count += 1
if count > 0 and count >= max_count:
max_count = count
max_k = k
if max_count > 0:
if last_repeat < i:
repeats.append(Repeat(last_repeat, i))
repeats.append(Repeat(i, i + max_k, max_count))
last_repeat = i + max_k * (max_count + 1)
i += max_k * (max_count + 1)
if last_repeat < i:
repeats.append(Repeat(last_repeat, i))
return repeats
min_count = 3
min_length = 3
with open('strlist.txt', 'r') as infile:
lines = infile.readlines()
sequences = {}
for line in lines:
label, string = line.split('\t')
if label in sequences:
sequences[label].append(string.strip())
else:
sequences[label] = [string.strip()]
standard = {
'Amel': [],
'CSF1P0': ['AGAT'],
'D10S1248': ['GGAA'],
'D12S391': ['AGAT', 'AGAC'],
'D13S317': ['TATC'],
'D16S539': ['GATA'],
'D18S51': ['GAAA'],
'D19S433': ['AAGG'],
'D1S1656': ['TAGA', 'TG'],
'D21S11': ['TCTA', 'TCTG'],
'D22S1045': ['ATT'],
'D2S1338': ['TGCC', 'TTCC'],
'D2S441': ['TCTA'],
'D3S1358': ['AGAT', 'TCTA'],
'D5S818': ['AGAT'],
'D7S820': ['GATA'],
'D8S1179': ['TATC'],
'FGA': ['TTTC', 'CTTT', 'TTCC'],
'PentaD': ['AAAGA'],
'PentaE': ['AAAGA'],
'TH01': ['TCAT'],
'TPOX': ['AATG'],
'vWA': ['TCTA', 'TCTG', 'TCCA'],
'DYS391': ['TCTA']
}
#select = 'D13S317'
#unit_list = standard[select]
#reference = sequences[select][0]
#sample = sequences[select][14]
#description, rep_start, rep_end = describe_repeats(reference, sample, unit_list)
#print '{}({}_{}):l.{}'.format(select, rep_start, rep_end, description)
for sequence in sequences:
# best = 0
# for string in sequences[sequence]:
# repeats = short_sequence_repeat_extractor(string, min_length)
# score = 0
# for repeat in repeats:
# if repeat.count + 1 >= min_count:
# score += (repeat.end - repeat.start) * (repeat.end - repeat.start) * (repeat.count + 1)
# if score > best:
# reference = string
# best = score
# repeats = short_sequence_repeat_extractor(reference, min_length)
# units = {}
# for repeat in repeats:
# if repeat.count + 1 >= min_count:
# units[reference[repeat.start:repeat.end]] = repeat.count + 1
# unit_list = []
# for unit in units:
# unit_list.append(unit)
unit_list = standard[sequence]
reference = sequences[sequence][0]
print sequence + ':',
print reference
if len(unit_list) > 0:
print 'repeat units:', unit_list
else:
print 'repeat units: []'
for string in sequences[sequence]:
rep_start = 1
rep_end = len(reference)
if len(unit_list) > 0:
description, rep_start, rep_end = describe_repeats(reference, string, unit_list)
else:
description = describe_dna(reference, string)
print '{}({}_{}):l.{}'.format(sequence, rep_start, rep_end, description)
print