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BayesPhyloInPython2/readSeq.py
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def patterns(sequence_file): | |
# | |
import re, os, glob, itertools, fnmatch, sys, shutil | |
from itertools import combinations | |
from collections import Counter | |
script_dir = os.path.dirname(os.path.realpath(sys.argv[0])) | |
# path = os.path.join(script_dir, 'nexus') | |
genes = [] | |
data = {} | |
# print 'Reading nexus files...' | |
for filename in glob.glob(os.path.join(script_dir, sequence_file)): | |
m = re.match('(.+).nex', os.path.basename(filename)) | |
gene_name = m.group(1) | |
# print 'gene_name=', gene_name | |
genes.append(gene_name) | |
f = open(filename, 'r').read() | |
m = re.search('ntax\s*=\s*(\d+)', f, re.M | re.S) | |
ntax = int(m.group(1)) | |
# print 'ntax=', ntax | |
m = re.search('nchar\s*=\s*(\d+)', f, re.M | re.S) | |
nchar = int(m.group(1)) | |
# print 'nchar=', nchar | |
m = re.search('Matrix\s+(.+?);', f, re.M | re.S) | |
matrix = m.group(1).strip() | |
matrix_lines = matrix.split('\n') | |
taxon_names = [] | |
sequences = {} | |
sequences_list = [] | |
for line in matrix_lines: | |
parts = line.strip().split() | |
assert len(parts) == 2 | |
taxon_name = parts[0] | |
sequence = parts[1] | |
taxon_names.append(taxon_name) | |
sequences_list.append(sequence) | |
sequences[taxon_name] = sequence | |
pattern_list = [] | |
k=0 | |
while k < nchar: | |
site_pattern = '' | |
for i,m in enumerate(sequences_list): | |
site_pattern += m[k] | |
pattern_list.append(site_pattern) | |
k+=1 | |
pattern_dict = dict() | |
for i in pattern_list: | |
pattern_dict[i] = pattern_dict.get(i, 0) + 1 | |
tmp = [] | |
for key in pattern_dict.keys(): ###convert dict to key of tupules | |
# print 'key=', key | |
tmp.append((pattern_dict[key],key)) | |
sorted_values = sorted(tmp) ###sorted according to key smaller to larger | |
sorted_values.sort(cmp = lambda x,y:cmp(x[1],y[1])) ###sorted according to values in alphabetical order | |
return ntax, pattern_dict | |