In [1]:
%matplotlib inline
import os, sys
import subprocess as sp
from itertools import cycle
import networkx as nx
import re
import ntpath
import shutil
import fnmatch
from eden.util import display
read a Sto file separate the extract the interesting information from the file
it takes the file path and returns the head which is the information type and it's sequence
In [2]:
def _readStoFile(file_path =None):
head_mark0 = '#'
head_mark1 = '='
head_mark2 = 'G'
head_mark3 = 'C'
head_list = []
sequence_list = []
read_file = open(file_path ,'r')
for line in read_file:
lines = list(line)
# the read line is the head of the sequence write it in head list
if lines[0] == head_mark0 and lines[1] == head_mark1 and lines[2] == head_mark2 and lines[3] == head_mark3:
line = line.strip('#=GC ')
line = line.strip('\n')
line = line.split(' ')
line = filter(None, line)
head = line[0]
head_list.append(head)
sequence = line[1].split()
sequence_list.append(sequence)
zip_head_seqs = zip(head_list, sequence_list)
return zip_head_seqs
recognize the different types of information extracted from step1 it takes the zipped info from the funtion '_readStoFile' and returns a dictionary that identify every type of information
In [3]:
def _identifyInformationType(file_name, head_seq_list):
secondery_structure_s = []
conservation_s = []
conservation_stringth_s = []
entropy_0_s = []
entropy_1_s = []
entropy_2_s = []
entropy_3_s = []
coveriation_s = []
for i, elemant in enumerate(head_seq_list):
info_item = head_seq_list[i]
if info_item[0] == 'SS_cons':
secondery_structure_s.append(str(info_item[1]))
if info_item[0] == 'cons':
conservation_s.append(str(info_item[1]))
if info_item[0] == 'conss':
conservation_stringth_s.append(info_item[1])
if info_item[0] == 'col_entropy_0':
entropy_0_s.append(info_item[1])
if info_item[0] == 'col_entropy_1':
entropy_1_s.append(info_item[1])
if info_item[0] == 'col_entropy_2':
entropy_2_s.append(info_item[1])
if info_item[0] == 'col_entropy_3':
entropy_3_s.append(info_item[1])
if info_item[0] == 'cov_SS_cons':
coveriation_s.append(info_item[1])
file_dictionary = {"ID_file name": file_name, "conservation": conservation_s, "secondery_structure": secondery_structure_s,
"conservation_stringth": conservation_stringth_s, "entropy_3": entropy_3_s, "covariation": coveriation_s}
return file_dictionary
In [4]:
def _filterInfo(info_type):
sequence = info_type['conservation']
structure = info_type['secondery_structure']
conservation_stringth = info_type['conservation_stringth']
covariation = info_type['covariation']
entropy_3 = info_type['entropy_3']
sequence = sequence[0].strip('[\']')
#print ('seq', sequence)
structure = structure[0].strip('[\']')
#print ('stru', structure)
conservation_stringth = str(conservation_stringth[0]).strip('[\']')
covariation = str(covariation).strip('[\']')
entropy_3 = str(entropy_3[0]).strip('[\']')
zip_info_type = zip(sequence,conservation_stringth,covariation,entropy_3)
return sequence, structure, conservation_stringth, covariation, entropy_3
#return zip_info_type, structure
build a Networkx graph with all type of info (the most general graph)
this graph identifies the basepair relation beside the next relation between the nodes
In [5]:
def _buildGraph(head, sequence, structure, conservation_stringth, covariation, entropy_3):
print ("Graph title", head)
#print zip_all_info
open_pran = "<" or "(" or "[" or "{"
close_pran = ">" or ")" or "]" or "}"
stack_o = []
stack_pos_o =[]
stack_c = []
graph_list = []
G = nx.Graph()
#G.graph['sequence']= sequence
#G.graph['covariation']= covariation
for i, k in enumerate(structure):
#node labeled with all info
seqCovConssEnt = sequence[i] + covariation[i] + conservation_stringth[i] + entropy_3[i]
G.add_node(i, label = seqCovConssEnt)
# connect with the next node
if i > 0:
G.add_edge(i-1, i, label= 'x')
"""find basepair and connect them"""
if structure[i] == open_pran:
j = i
stack_o.append(structure[j])
stack_pos_o.append(j)
open_len = len(stack_o)
if structure[i] == close_pran:
stack_c.append(structure[i])
stack_o.pop()
j = stack_pos_o.pop()
G.add_edge(i, j, label = 'b')
graph_list += [G.copy()]
#print graph_list
return graph_list
transform the general graph to the wanted graph based on parameters passed by the '_graphParametersList' function
In [6]:
'''Recognize basepairs and include them to the generated graph'''
def _buildParameterizedGraph(head, graph_params, structure):
print ("Graph title", head)
#print zip_all_info
open_pran = "<" or "(" or "[" or "{"
close_pran = ">" or ")" or "]" or "}"
stack_o = []
stack_pos_o =[]
stack_c = []
G = nx.Graph()
params = list(graph_params)
for i, k in enumerate(structure):
G.add_node(i, label = params[0])
if i > 0:
G.add_edge(i-1, i, label= 'x')
if structure[i] == open_pran:
j = i
stack_o.append(structure[j])
stack_pos_o.append(j)
open_len = len(stack_o)
if structure[i] == close_pran:
stack_c.append(structure[i])
stack_o.pop()
j = stack_pos_o.pop()
G.add_edge(i, j, label = 'b')
return G
In [7]:
def _transformGraph(G, head, graphParmeter, structure):
graph_list = []
for i, param in enumerate(graphParmeter):
graphs = _buildParameterizedGraph(head, param, structure)
graph_list += [graphs.copy()]
return graph_list
In [8]:
def _graphParametersList(sequence, structure, conservation_stringth, covariation, entropy_3):
seqCov = zip(sequence, covariation)
seqCovConss = zip(sequence, covariation, conservation_stringth)
seqCovConssEnt = zip(sequence, covariation, entropy_3)
covSeq = zip(covariation, sequence)
param_list = [seqCov, seqCovConss, seqCovConssEnt, covSeq]
return param_list
read one STO file, extract the desired info, and then build the graph
it takes the STO file path and returns it's graph
In [9]:
def _FileToGraphConvertor(file_path=None):
head = ntpath.splitext(ntpath.basename(file_path))[0]
zip_head_seqs = _readStoFile(file_path)
#print zip_head_seqs
info_type = _identifyInformationType(head, zip_head_seqs)
sequence, structure, conservation_stringth, covariation, entropy_3 = _filterInfo(info_type)
graph_list = _buildGraph(head, sequence, structure, conservation_stringth, covariation, entropy_3)
for G in graph_list:
display.draw_graph(G, size=40, node_size=400, font_size=20, node_border=True, prog='neato', title_key= 'head')
params_list = _graphParametersList(sequence, structure, conservation_stringth, covariation, entropy_3)
transform_graph_list = _transformGraph(G, head, params_list, structure)
for G in transform_graph_list:
display.draw_graph(G, size=40, node_size=400, font_size=20, node_border=True, prog='neato', title_key= 'head')
In [10]:
file_path = "/home/alsheikm/GitDir/EeDN_work/StoExamples/StoExmapleSmall/positives-sto/550-53949-1-0.sto"
File_to_Graph = _FileToGraphConvertor(file_path)
read a folder of STO files and then call '_FileToGraphWrapper' function
it taked the directory path and returns list of their's graphs
In [12]:
def _FolderToGraphConvertor(directory = None):
for file_name in os.listdir(directory):
file_complete_path = os.path.join(directory, file_name)
read_file = _FileToGraphConvertor(file_complete_path)
In [13]:
pos_dir = "/home/alsheikm/GitDir/EeDN_work/StoExamples/StoExmapleSmall/positives-sto"
neg_dir = "/home/alsheikm/GitDir/EeDN_work/StoExamples/StoExmapleSmall/negatives-sto"
output_dir = "/home/alsheikm/GitDir/EeDN_work/StoExamples/output"
pos_Graphs = _FolderToGraphConvertor(pos_dir)
neg_Graphs = _FolderToGraphConvertor(neg_dir)
Graph_to_targetFile = _createTargetFiles(pos_dir, neg_dir, output_dir)
generate target files
it takes the divided STO files directory and returnes a target files with 1s for files belong to class 0, and -1 for files belong to class 1
In [94]:
def _createTargetFiles(pos_dir = None, neg_dir = None, output_dir = None):
file_extention = '.target'
output_file_name = 'data'
#target_list = []
#htmlcode = HTML.list(target_list)
target_file_name = output_dir + "/" + output_file_name + file_extention
target_file = open(target_file_name, 'w')
for pos_file in os.listdir(pos_dir):
target_file.write('1\n')
#target_list.append('1')
for pos_file in os.listdir(pos_dir):
target_file.write('-1\n')
#target_list.append('-1')
target_file.close()
#print target_list
In [ ]:
'''seperate classes into diffeerent folders'''
def _classesToFolders(files_dir, partition_dir):
pos_partition_file = "positive-partitions-test.tab"
neg_partition_file = "negative-partitions-test.tab"
pos_class_0_path = "/home/alsheikm/GitDir/EeDN_work/StoExamples/pos_class_0"
pos_class_1_path = "/home/alsheikm/GitDir/EeDN_work/StoExamples/pos_class_1"
neg_class_0_path = "/home/alsheikm/GitDir/EeDN_work/StoExamples/neg_class_0"
neg_class_1_path = "/home/alsheikm/GitDir/EeDN_work/StoExamples/neg_class_1"
tab_list = os.listdir(partition_dir)
for tab_file in os.listdir(partition_dir):
files_list = os.listdir(files_dir)
for folder_name in os.listdir(files_dir):
folder_path = os.path.join(files_dir, folder_name)
if tab_file == pos_partition_file and folder_name == 'positives-sto':
read_pos_tab = open(os.path.join(partition_dir, tab_file), 'r')
for line in read_pos_tab:
line_parts= line.split()
file_name = line_parts[0]
file_class_num = line_parts[1]
'''copy file to the pos_class_0 folder'''
if file_class_num == '0':
for file in os.listdir(folder_path):
file_path = os.path.join(folder_path, file)
file = ntpath.splitext( ntpath.basename(file_path))[0]
if fnmatch.fnmatch(file, file_name):
shutil.copy(file_path, pos_class_0_path)
'''copy file to the pos_class_1 folder'''
if file_class_num == '1':
for file in os.listdir(folder_path):
file_path = os.path.join(folder_path, file)
file = ntpath.splitext( ntpath.basename(file_path))[0]
if fnmatch.fnmatch(file, file_name):
shutil.copy(file_path, pos_class_1_path)
if tab_file == neg_partition_file and folder_name == 'negatives-sto':
read_neg_tab = open(os.path.join(partition_dir, tab_file), 'r')
for line in read_neg_tab:
line_parts= line.split()
file_name = line_parts[0]
file_class_num = line_parts[1]
'''copy file to the pos_class_0 folder'''
if file_class_num == '0':
for file in os.listdir(folder_path):
file_path = os.path.join(folder_path, file)
file = ntpath.splitext( ntpath.basename(file_path))[0]
if fnmatch.fnmatch(file, file_name):
shutil.copy(file_path, neg_class_0_path)
'''copy file to the pos_class_1 folder'''
if file_class_num == '1':
for file in os.listdir(folder_path):
file_path = os.path.join(folder_path, file)
file = ntpath.splitext( ntpath.basename(file_path))[0]
if fnmatch.fnmatch(file, file_name):
shutil.copy(file_path, neg_class_1_path)
In [ ]:
files_dir = "/home/alsheikm/GitDir/EeDN_work/StoExamples/StoExmapleSmall"
partition_dir = "/home/alsheikm/GitDir/EeDN_work/StoExamples/partitionsFiles"
Class_to_folder = _classesToFolders(files_dir, partition_dir)