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testing the rules.py
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testing the rules.py
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# -*- coding: utf-8 -*-
"""
Created on Tue Feb 09 12:32:42 2016
@author: Krishna
"""
# -*- coding: utf-8 -*-
"""
Created on Thu Jan 28 19:44:22 2016
@author: Krishna
"""
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 05 18:43:15 2016
@author: Krishna
"""
import os
import re
import time
start_time = time.time()
#q=open('C:\Users\Krishna\Desktop\up down analysis for orgs\checking rules.txt','w')
a = open('F:\M.Tech\patterns for gmk_down.txt','r').readlines()
a1 = open('F:\M.Tech\patterns for gmk_up.txt','r').readlines()
a=a+a1
rg1 = open(r'L:\My Online Documents\MTech\ruless occurence\keyword start7.txt', 'w')
rg2 = open(r'L:\My Online Documents\MTech\ruless occurence\line start7.txt', 'w')
rg3 = open(r'L:\My Online Documents\MTech\ruless occurence\fullstop.txt', 'w')
rg4 = open(r'L:\My Online Documents\MTech\ruless occurence\gs control.txt', 'w')
rg5 = open(r'L:\My Online Documents\MTech\ruless occurence\golden line7.txt', 'w')
rg6 = open(r'L:\My Online Documents\MTech\ruless occurence\r four.txt', 'w')
rs1 = open(r'L:\My Online Documents\MTech\ruless occurence\minus one.txt', 'w')
rs2 = open(r'L:\My Online Documents\MTech\ruless occurence\minus two.txt', 'w')
rs3 = open(r'L:\My Online Documents\MTech\ruless occurence\plus one.txt', 'w')
ra1 = open(r'L:\My Online Documents\MTech\ruless occurence\activation one.txt', 'w')
ra2 = open(r'L:\My Online Documents\MTech\ruless occurence\activation two.txt', 'w')
ra3 = open(r'L:\My Online Documents\MTech\ruless occurence\activation three.txt', 'w')
ra4 = open(r'L:\My Online Documents\MTech\ruless occurence\activation four.txt', 'w')
rd1 = open(r'L:\My Online Documents\MTech\ruless occurence\deficient one.txt', 'w')
rd2 = open(r'L:\My Online Documents\MTech\ruless occurence\deficient two.txt', 'w')
rde1 = open(r'L:\My Online Documents\MTech\ruless occurence\deletion one7.txt', 'w')
ri1 = open(r'L:\My Online Documents\MTech\ruless occurence\induced one.txt', 'w')
ri2 = open(r'L:\My Online Documents\MTech\ruless occurence\induced two.txt', 'w')
ri3 = open(r'L:\My Online Documents\MTech\ruless occurence\induced three.txt', 'w')
ri4 = open(r'L:\My Online Documents\MTech\ruless occurence\induced four.txt', 'w')
rin1 = open(r'L:\My Online Documents\MTech\ruless occurence\inhibition one.txt', 'w')
rk1 = open(r'L:\My Online Documents\MTech\ruless occurence\knockout one.txt', 'w')
rk2 = open(r'L:\My Online Documents\MTech\ruless occurence\knkockout two7.txt', 'w')
rko1 = open(r'L:\My Online Documents\MTech\ruless occurence\ko7.txt', 'w')
rm1 = open(r'L:\My Online Documents\MTech\ruless occurence\mutant one.txt', 'w')
rm2 = open(r'L:\My Online Documents\MTech\ruless occurence\mutant two.txt', 'w')
rn1 = open(r'L:\My Online Documents\MTech\ruless occurence\null7.txt', 'w')
rr1 = open(r'L:\My Online Documents\MTech\ruless occurence\gmks start7.txt', 'w')
rst1 = open(r'L:\My Online Documents\MTech\ruless occurence\stimulated one.txt', 'w')
rst2 = open(r'L:\My Online Documents\MTech\ruless occurence\stimulated two.txt', 'w')
rt1 = open(r'L:\My Online Documents\MTech\ruless occurence\\treated one.txt', 'w')
rt2 = open(r'L:\My Online Documents\MTech\ruless occurence\treated two.txt', 'w')
rs4 = open(r'L:\My Online Documents\MTech\ruless occurence\minus three7.txt', 'w')
rs5 = open(r'L:\My Online Documents\MTech\ruless occurence\plus two.txt', 'w')
rs6 = open(r'L:\My Online Documents\MTech\ruless occurence\plus three.txt', 'w')
keyword1 = open('F:\M.Tech\mouse_gs_small_simple.txt','r').readlines() # this has the small GS
keyword2 = open('F:\M.Tech\mouse_gs_number_large.txt','r').readlines() # this has the large GS
keywords = keyword1+keyword2
#keywords = ['GS', 'GSS']
#gmk = 'knockout'
c=0
def find_matches(s, gmk):
#print 'deff enter'
#print("FINDMATCHES--- %s seconds ---" % (time.time() - start_time))
r=0
if gmk in s: # checking if gmk is in the line
l = re.split('\s|(?<!\d)[,.]|[,.](?!\d)|;|[()]|-', s) # split the line by comma, semicolon and space to check for gmks and gs. Also http://goo.gl/RPQNbT
filter(None, l) # remove empty elements in the list
for gs in keywords: # gene symbols
gs = gs.rstrip() #remove lagging whitespace characters
gs=gs.lower()
if gs in s: # search for GS in line. using 'gs in s' led to a lot of partial word matches
gs1 = re.split('\s|(?<!\d)[,.]|[,.](?!\d)|;|-', gs)
gs1=filter(None, gs1)
gmk1 = re.split('\s|(?<!\d)[,.]|[,.](?!\d)|;|-', gmk)
gmk1=filter(None, gmk1)
if any(l[i:i+len(gs1)]==gs1 for i in xrange(len(l)-len(gs1)+1)) and (any(l[i:i+len(gmk1)]==gmk1 for i in xrange(len(l)-len(gmk1)+1))): # this ensures that both gs and gmk are in l, as a unit(i.e. and in order) otherwise it was detecting things like 'beta c' from beta cells
# UPTO THIS POINT WE HAVE ESTABLISHED THAT THE GMK AND GS ARE INDEED IN THE LINE
k1 = '_KEYWORD_1_'
k2 = '_KEYWORD_2_'
#print gmk
text = re.sub(re.escape(gmk), k1, s, flags=re.I) # because of this replacement, we dont have the problem of counting r from behind etc.
#text = re.sub(re.escape(gs), k2, text, flags=re.I)
text = re.sub(r'(\b%s\b)' % (re.escape(gs)), k2, text, flags=re.I)
#text = s.replace(gmk, k1)
#text = text.replace(gs, k2)
#print text
lt = text.split()
#lt = re.split('\s|(?<!\d)[,.]|[,.](?!\d)|;|[()]|-', text)
d_idx = {k1:[], k2:[]}
#print d_idx[k1]
for k,v in enumerate(lt):
if k1 in v:
d_idx[k1].append(k)
if k2 in v:
d_idx[k2].append(k)
distance = 8
data = []
for idx1 in d_idx[k1]:
for idx2 in d_idx[k2]:
d = abs(idx1 - idx2)
if d<=distance:
data.append((d,idx1,idx2))
data.sort(key=lambda x: x[0])
for i in range (0, len(data)):
#print "Least distance: ", data[0][0]
#print file
#print gs, gmk
#print "Number of occurences: ", len(data)
if data[i][0]<4: # if r less than 4
rg6.write(file)
rg6.write('\n')
rg6.write (' r is %d ' % data[i][0])
rg6.write('\n')
rg6.write(gs)
rg6.write('\n')
rg6.write(gmk)
rg6.write('\n')
rg6.write('Found %s in %s' % (gmk,s.strip()))
rg6.write('\n')
if data:
r=cl(s, gmk, gs, data)
#print r # tells how many times the rules function was called
def cl(s1, gmk1, gs1, data1): # output will be the confidence level
# print("CL--- %s seconds ---" % (time.time() - start_time))
# print 'def enter'
# print 'gmk1 is %s' %gmk1
# print 'gs1 is %s' %gs1
# print 'data1 is:'
#print data1
gs11 = gs1
br0=''
br3=''
br=''
#s1 = re.sub(gs1, '_8MILLION8_', s1, flags=re.I)
s1 = re.sub(r'(\b(%s)\b)' % (gs1), r'_8MILLION8_', s1, flags=re.I)
#s1=s1.replace(gs1, '_8MILLION8_')
gs1='_8MILLION8_'
#l = re.split('\s|(?<!\d)[,.]|[,.](?!\d)|;|"|\'|[()]|-', s)
l = s1.split()
beg_gmk = ['over-activation', 'overexpression', 'loss of', 'knockout', 'haplo-insuffiency', 'haploinsufficiency', 'inactivation', 'knock-out', 'deletion', 'inhibition', 'knockdown', 'silencing']
beg_other = ['Global gene expression', 'Gene expression profiling', 'Expression data', 'Gene expression analysis']
for i in range(0,len(beg_gmk)):
if re.search(r'(^!Series_.*?\s"%s)' %beg_gmk[i], s1, re.I|re.S): # this rule looks optimum
rr1.write(file)
rr1.write('\n')
rr1.write(gs11)
rr1.write('\n')
rr1.write('Found %s in %s' % (gmk1,s1.strip()))
rr1.write('\n')
for i in range(0,len(beg_other)):
if re.search(r'(^!Series_.*?\s"%s)' %beg_other[i], s1, re.I|re.S): # this rule looks optimum
rg2.write(file)
rg2.write('\n')
rg2.write(gs11)
rg2.write('\n')
rg2.write('Found %s in %s' % (gmk1,s1.strip()))
rg2.write('\n')
if re.search(r'(^!Series_\w.*?\s"Keywords:)', s1):
ll=s1.split(',')
v=0
for i in range(0,len(ll)):
if gmk1 and gs1 in ll[i]:
v=4
rg1.write(file)
rg1.write('\n')
rg1.write(gs11)
rg1.write('\n')
rg1.write('Found %s in %s' % (gmk1,s1.strip()))
rg1.write('\n')
if v!=4:
rg1.write('COMMA SEPARATED')
rg1.write('\n')
rg1.write(file)
rg1.write('\n')
rg1.write(gs11)
rg1.write('\n')
rg1.write('Found %s in %s' % (gmk1,s1.strip()))
rg1.write('\n')
if re.search(r'(%s\(control\))' %gs1, s1, re.I|re.S): #gs1(control)
rg4.write(file)
rg4.write('\n')
rg4.write(gs11)
rg4.write('\n')
rg4.write('Found %s in %s' % (gmk1,s1.strip()))
rg4.write('\n')
if re.search(r'(The object of this study was to identify genes transcriptionally upregulated.*?downregulated)', s1):
rg5.write(file)
rg5.write('\n')
rg5.write(gs11)
rg5.write('\n')
rg5.write('Found %s in %s' % (gmk1,s1.strip()))
rg5.write('\n')
for ii in range(0,len(data1)):
#print 'loop'
a = data1[ii]
lo = min(a[1], a[2])
hi = max(a[1], a[2])
brr = l[max(0, lo-8):hi+8]
br= " ".join(brr)
br00 = l[max(0, lo):hi+1] # we dont need the 8 words here and there as the fullstop is between gmk1 and gs1
br0= ' '.join(br00)
br33 = l[max(0, lo-3):hi+3]
br3= ' '.join(br33)
if (re.search(r'(%s.*?\..*?%s)' % (re.escape(gs1), re.escape(gmk1)), br0, re.I|re.S)) or (re.search(r'(%s.*?\..*?%s)' % (re.escape(gmk1), re.escape(gs1)), br0, re.I|re.S)): #gs1 fullstop gmk1 and viceversa
rg3.write(file)
rg3.write('\n')
rg3.write(gs11)
rg3.write('\n')
rg3.write('Found %s in %s' % (gmk1, br.strip())) # change to s1
rg3.write('\n')
if gmk1 == 'activation':
if re.search(r'(activation by %s)' %gs1, br0, re.I|re.S):
ra1.write(file)
ra1.write('\n')
ra1.write(gs11)
ra1.write('\n')
ra1.write('Found %s in %s' % (gmk1,s1.strip()))
ra1.write('\n')
if re.search(r'(probably.*?%s activation)' %gs1, br, re.I|re.S):
ra2.write(file)
ra2.write('\n')
ra2.write(gs11)
ra2.write('\n')
ra2.write('Found %s in %s' % (gmk1,s1.strip()))
ra2.write('\n')
if re.search(r'(critical for.*?%s activation)' %gs1, br, re.I|re.S):
ra3.write(file)
ra3.write('\n')
ra3.write(gs11)
ra3.write('\n')
ra3.write('Found %s in %s' % (gmk1,s1.strip()))
ra3.write('\n')
if re.search(r'(%s.*?activation of)' %gs1, br3, re.I|re.S):
ra4.write(file)
ra4.write('\n')
ra4.write(gs11)
ra4.write('\n')
ra4.write(br0)
ra4.write('\n')
ra4.write('Found %s in %s' % (gmk1,s1.strip()))
ra4.write('\n')
if gmk1 == 'deficient':
if re.search(r'(%s deficient)' %gs1, br0, re.I|re.S):
rd1.write(file)
rd1.write('\n')
rd1.write(gs11)
rd1.write('\n')
rd1.write('Found %s in %s' % (gmk1, br))
rd1.write('\n')
if re.search(r'(deficient\s.*?\sexhibited\s.*?\s%s)' %gs1, br0, re.I|re.S):
rd2.write(file)
rd2.write('\n')
rd2.write(gs11)
rd2.write('\n')
rd2.write('Found %s in %s' % (gmk1,br))
rd2.write('\n')
# if gmk1 == 'deletion':
# for all_gs in keywords:
#all_gs=all_gs.rstrip()
# if re.search(r'(\s%s-deletion\s.*?\s%s)' % (re.escape(all_gs), re.escape(gs1)), s1, re.I|re.S):
# rde1.write(file)
# rde1.write('\n')
# rde1.write(gs11)
# rde1.write('\n')
# rde1.write('Found %s in %s' % (gmk1,s1.strip()))
# rde1.write('\n')
if gmk1 == '-/-':
#print br0
# if r<3: # THIS RULE IS PROBABLY NOT NEEDED
# rs4.write(file)
# rs4.write('\n')
# rs4.write(gs11)
# rs4.write('\n')
# rs4.write('Found %s in %s' % (gmk1,s1.strip()))
# rs4.write('\n')
if re.search(r'(-/-%s)' %gs1, br0, re.I|re.S):
rs1.write(file)
rs1.write('\n')
rs1.write(gs11)
rs1.write('\n')
rs1.write('Found %s in %s' % (gmk1,s1.strip()))
rs1.write('\n')
if re.search(r'(%s-/-)' %gs1, br0, re.I|re.S):
rs2.write(file)
rs2.write('\n')
rs2.write(gs11)
rs2.write('\n')
rs2.write('Found %s in %s' % (gmk1,s1.strip()))
rs2.write('\n')
if gmk1 == '+':
if re.search(r'(%s+)' %gs1, br0, re.I|re.S):
rs3.write(file)
rs3.write('\n')
rs3.write(gs11)
rs3.write('\n')
rs3.write('Found %s in %s' % (gmk1,s1.strip()))
rs3.write('\n')
if re.search(r'(%s\(\+\))' %gs1, br3, re.I|re.S):
rs5.write(file)
rs5.write('\n')
rs5.write(gs11)
rs5.write('\n')
rs5.write('Found %s in %s' % (gmk1,s1.strip()))
rs5.write('\n')
else:
rs6.write(file)
rs6.write('\n')
rs6.write(gs11)
rs6.write('\n')
rs6.write('Found %s in %s' % (gmk1,s1.strip()))
rs6.write('\n')
if gmk1 == 'induced':
if re.search(r'(%s.*?was shown\s.*?\sinduced)' %gs1, br0, re.I|re.S):
ri1.write(file)
ri1.write('\n')
ri1.write(gs11)
ri1.write('\n')
ri1.write('Found %s in %s' % (gmk1,s1.strip()))
ri1.write('\n')
if re.search(r'(%s.*?-induced)' %gs1, br0, re.I|re.S):
ri2.write(file)
ri2.write('\n')
ri2.write(gs11)
ri2.write('\n')
ri2.write('Found %s in %s' % (gmk1,s1.strip()))
ri2.write('\n')
if re.search(r'(induced.*?to %s)' %gs1, br0, re.I|re.S):
ri3.write(file)
ri3.write('\n')
ri3.write(gs11)
ri3.write('\n')
ri3.write('Found %s in %s' % (gmk1,s1.strip()))
ri3.write('\n')
if re.search(r'(induced.*?while %s)' %gs1, br0, re.I|re.S):
ri4.write(file)
ri4.write('\n')
ri4.write(gs11)
ri4.write('\n')
ri4.write('Found %s in %s' % (gmk1,s1.strip()))
ri4.write('\n')
if gmk1 == 'inhibition':
if re.search(r'(hypothesized\s.*?\sinhibition\s.*?\s%s )' %gs1, br, re.I|re.S):
rin1.write(file)
rin1.write('\n')
rin1.write(gs11)
rin1.write('\n')
rin1.write('Found %s in %s' % (gmk1,s1.strip()))
rin1.write('\n')
if gmk1 == 'knockout':
if re.search(r'(effect of %s knockout)' %gs1, br3, re.I|re.S):
rk1.write(file)
rk1.write('\n')
rk1.write(gs11)
rk1.write('\n')
rk1.write('Found %s in %s' % (gmk1,s1.strip()))
rk1.write('\n')
if re.search(r'(double knockout)', br3, re.I|re.S): # for the time being
rk2.write(file)
rk2.write('\n')
rk2.write(gs11)
rk2.write('\n')
rk2.write('Found %s in %s' % (gmk1,s1.strip()))
rk2.write('\n')
if gmk1 == 'KO':
if re.search(r'(double KO\W)', br3, re.I|re.S): # for the time being
rko1.write(file)
rko1.write('\n')
rko1.write(gs11)
rko1.write('\n')
rko1.write('Found %s in %s' % (gmk1,s1.strip()))
rko1.write('\n')
if gmk1 == 'mutant':
if re.search(r'(harboring.*?%s mutant)' %gs1, br, re.I|re.S):
rm1.write(file)
rm1.write('\n')
rm1.write(gs11)
rm1.write('\n')
rm1.write('Found %s in %s' % (gmk1,s1.strip()))
rm1.write('\n')
if re.search(r'(mutant.*?causes.*?%s)' %gs1, br0, re.I|re.S):
rm2.write(file)
rm2.write('\n')
rm2.write(gs11)
rm2.write('\n')
rm2.write('Found %s in %s' % (gmk1,s1.strip()))
rm2.write('\n')
# if gmk1 == 'null':
# for all_gs in keywords:
#all_gs=all_gs.rstrip()
# if re.search(r'(matched %s\s.*?\s%s.*?null)' % (re.escape(gs1), re.escape(all_gs)), s, re.I|re.S): #doing %gs1, %all_gs gave syntax error. THIS NEW WAY IS THE RIGHT WAY TO DO IT
# rn1.write(file)
# rn1.write('\n')
# rn1.write(gs11)
# rn1.write('\n')
# rn1.write('Found %s in %s' % (gmk1,s.strip()))
# rn1.write('\n')
# if gmk1 == 'deletion':
#
# for all_gs in gs_list1:
#
# if re.search(r'(%s-deletion.*?%s)' % (re.escape(all_gs), re.escape(gs1)), br3, re.I|re.S):
#
# rde1.write(file)
# rde1.write('\n')
# rde1.write(gs11)
# rde1.write('\n')
# rde1.write('Found %s in: %s' % (gmk1,br)) #change to s1.strip() later
# rde1.write('\n')
#
#
# if gmk1 == 'null':
# for all_gs in gs_list1:
#
# if re.search(r'(%s.*?%s.*?null)' % (re.escape(gs1), re.escape(all_gs)), br3, re.I|re.S): #doing %gs, %all_gs gave syntax error. THIS NEW WAY IS THE RIGHT WAY TO DO IT
#
# rn1.write(file)
# rn1.write('\n')
# rn1.write(gs11)
# rn1.write('\n')
# rn1.write('Found %s in: %s' % (gmk1,br3)) #change to s1.strip() later
# rn1.write('\n')
if gmk1 == 'stimulated':
if re.search(r'(.*?-stimulated.*?%s)' %gs1, br, re.I|re.S):
rst2.write(file)
rst2.write('\n')
rst2.write(gs11)
rst2.write('\n')
rst2.write('Found %s in %s' % (gmk1,s1.strip()))
rst2.write('\n')
if re.search(r'(%s-stimulated)' %gs1, br0, re.I|re.S):
rst1.write(file)
rst1.write('\n')
rst1.write(gs11)
rst1.write('\n')
rst1.write('Found %s in %s' % (gmk1,s1.strip()))
rst1.write('\n')
if gmk1 == 'treated':
if re.search(r'(treated.*?control.*?%s)' %gs1, br0, re.I|re.S):
rt1.write(file)
rt1.write('\n')
rt1.write(gs11)
rt1.write('\n')
rt1.write('Found %s in %s' % (gmk1,s1.strip()))
rt1.write('\n')
if re.search(r'(control or %s-treated)' %gs1, br3, re.I|re.S):
rt2.write(file)
rt2.write('\n')
rt2.write(gs11)
rt2.write('\n')
rt2.write('Found %s in %s' % (gmk1,s1.strip()))
rt2.write('\n')
return 4
c=0
print 1
for path, dirs, files in os.walk(r'L:\My Online Documents\MTech\temp'):
for file in files:
sentences = open(os.path.join(path,file),'r').readlines();
#print sentences
c = c+1
r=0
print c # one value printed for each file
#print file
print("--- %s seconds ---" % (time.time() - start_time))
k=0
hg=0
for s in sentences:
s=s.lower()
s = s.rstrip()
if s.startswith('!series_title') or s.startswith('!series_summary') or s.startswith('!series_overall_design'):
#if s.startswith('!Series_title') or s.startswith('!Series_summary') or s.startswith('!Series_overall_design'):
print 'line enter'
for gmk in a:
gmk = gmk.rstrip() #to remove the lagging \n in many GMKs
gmk=gmk.lower()
find_matches(s, gmk)
print("--- %s seconds ---" % (time.time() - start_time))