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| # -*- coding: utf-8 -*-
import os, sys
import re
import numpy as np
from Bio import pairwise2
import networkx as nx
import matplotlib.pyplot as plt
def network_project():
File "<ipython-input-8-4b069aa68b05>", line 1
def network_project():
^
SyntaxError: unexpected EOF while parsing
gene=[]
header=[]
lecture=''
i=0
j=0
file='exemple_sequence.txt'
lecture=open(file,"r")
seq=''
for line in lecture:
File "<ipython-input-17-ee7616045115>", line 1
for line in lecture:
^
SyntaxError: unexpected EOF while parsing
sequence=len(re.findall(r"[>]",line))
Traceback (most recent call last):
File "<ipython-input-18-5b6993129435>", line 1, in <module>
sequence=len(re.findall(r"[>]",line))
NameError: name 'line' is not defined
if(sequence>0):
File "<ipython-input-19-097ba0cab013>", line 1
if(sequence>0):
^
SyntaxError: unexpected EOF while parsing
gene.append(seq)
seq=''
sequence=0
header.append(line[1:-1])
Traceback (most recent call last):
File "<ipython-input-23-2c9773132d5f>", line 1, in <module>
header.append(line[1:-1])
NameError: name 'line' is not defined
i=i+1
else:
File "<ipython-input-25-64c43b55f0b0>", line 1
else:
^
SyntaxError: invalid syntax
seq=seq+line[:-1]
Traceback (most recent call last):
File "<ipython-input-26-5ca41cc41d17>", line 1, in <module>
seq=seq+line[:-1]
NameError: name 'line' is not defined
gene.append(seq)
lecture.close()
score=[]
for i in range(len(gene)):
File "<ipython-input-30-6371b26cf076>", line 1
for i in range(len(gene)):
^
SyntaxError: unexpected EOF while parsing
for j in range((i+1),len(gene)):
File "<ipython-input-31-1264f3241f7e>", line 1
for j in range((i+1),len(gene)):
^
SyntaxError: unexpected EOF while parsing
score.append(pairwise2.align.globalms(gene[i],gene[j], 3, -2, -1, -.5,score_only=True))
liste=[]
seuil=(np.mean(score)+0.05*np.std(score))
C:\Users\Amandine\Anaconda3\lib\site-packages\numpy\core\fromnumeric.py:2957: RuntimeWarning: Mean of empty slice.
out=out, **kwargs)
C:\Users\Amandine\Anaconda3\lib\site-packages\numpy\core\_methods.py:135: RuntimeWarning: Degrees of freedom <= 0 for slice
keepdims=keepdims)
s=0
edge_labels={}
for i in range(len(gene)):
File "<ipython-input-37-6371b26cf076>", line 1
for i in range(len(gene)):
^
SyntaxError: unexpected EOF while parsing
for j in range((i+1),len(gene)):
File "<ipython-input-38-1264f3241f7e>", line 1
for j in range((i+1),len(gene)):
^
SyntaxError: unexpected EOF while parsing
if(score[s]>seuil):
File "<ipython-input-39-029433cbe1f7>", line 1
if(score[s]>seuil):
^
SyntaxError: unexpected EOF while parsing
liste.append((header[i],header[j]))
Traceback (most recent call last):
File "<ipython-input-40-d41a38bfa2d3>", line 1, in <module>
liste.append((header[i],header[j]))
IndexError: list index out of range
edge_labels[(header[i],header[j])]=score[s]
Traceback (most recent call last):
File "<ipython-input-41-aabbbf916451>", line 1, in <module>
edge_labels[(header[i],header[j])]=score[s]
IndexError: list index out of range
s=s+1
G=nx.Graph()
G.add_nodes_from(header)
G.add_edges_from(liste)
pos=nx.spring_layout(G)
node_s=[]
t=0
for t in range(len(gene)):
File "<ipython-input-49-a4f1e5ab6d2b>", line 1
for t in range(len(gene)):
^
SyntaxError: unexpected EOF while parsing
node_s.append(20*np.log(len(seq[t])))
Traceback (most recent call last):
File "<ipython-input-50-b1d4c0a30894>", line 1, in <module>
node_s.append(20*np.log(len(seq[t])))
IndexError: string index out of range
nx.draw_networkx_nodes(G,pos,node_color='green',label=True,alpha=1,node_size=node_s)

Width=dict(edge_labels)
for key,value in Width.items() :
File "<ipython-input-53-2b9e3955cfe0>", line 1
for key,value in Width.items() :
^
SyntaxError: unexpected EOF while parsing
Width[key] = np.log10(value)/2
Traceback (most recent call last):
File "<ipython-input-54-cbae24bb3a3e>", line 1, in <module>
Width[key] = np.log10(value)/2
NameError: name 'value' is not defined
nx.draw_networkx_edges(G,pos,width=Width.values(),style='solid',edge_color='red',alpha=1)

nx.draw_networkx_edge_labels(G,pos,edge_labels=edge_labels,font_size=2,alpha=0.5,font_color='black')
Out[56]: {}

nx.draw_networkx_labels(G,pos,font_size=3,font_color='blue')
Out[57]: {}

namefordoc=input('Nom du PDF sans .pdf ?\n')
Nom du PDF sans .pdf ?
file
plt.savefig(namefordoc+'.pdf')
<Figure size 432x288 with 0 Axes> |
