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pfms_trans.py
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pfms_trans.py
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import os
import numpy as np
path_pfms='/wrk/shni/eel/matrices/other_pfms/'
path_output='/wrk/shni/eel/matrices/'
class Pfm_trans():
def __init__(self, filename):
self.name=filename
def content(self):
matrix=open(path_pfms+self.name).read()
result=[]
for line in matrix.strip().split('\n'):
result.append(int(number) for number in line.strip().split('\t'))
return result
def trans(self):
result=self.content()
return zip(*result)
def normalize(self):
result=self.trans()
for j in range(len(result)):
tmplist=list(result[j])
for i in range(len(tmplist)):
tmplist[i]=float(result[j][i])/sum(result[j]) if tmplist[i] != 0 else 0
result[j]=tmplist
return result
with open (path_output+'/transed_pfms.txt', 'w') as file_write:
for files in os.listdir(path_pfms):
pfm=Pfm_trans(files)
file_write.write('>'+pfm.name+'\n')
for lines in pfm.normalize():
file_write.write('\t'.join(str(char) for char in lines)+'\n')
file_write.write('\n')
del(pfm)
file_write.close()