[Tutor] irregular/parse/sort

Sun Mar 22 22:44:26 CET 2009

I've been using re.sub() to try and take the below pattern1 and convert it  
to pattern2 (which are below) below that is mycode1. Does anyone have any  
suggestions as to how I can figure this out?

pattern1
NTR+A0001 0.01
GLU-A0003 8.21 
GLU-A0008 3.619
ARG+A0010 14
ARG+A0023 14
ARG+A0024 14
ASP-A0028 0.01
ARG+A0034 13.193
ASP-A0039 2.973
LYS+A0040 10.634
LYS+A0043 12.693
ASP-A0051 3.994
ASP-A0055 0.01
GLU-A0057 9.017
ARG+A0062 14
TYR-A0064 13.028
GLU-A0066 4.081
LYS+A0073 11.193
ASP-A0076 0.01
TYR-A0084 14
HIS+A0086 0.01
TYR-A0087 14
LYS+A0091 11.193
LYS+A0092 10.275
LYS+A0095 11.193
ASP-A0097 2.96
TYR-A0098 14
ASP-A0101 0.01
LYS+A0114 14
TYR-A0116 14
ASP-A0123 0.01
HIS+A0125 7.15
GLU-A0126 3.269
LYS+A0127 11.693
ASP-A0128 2.324
HIS+A0129 7.15
GLU-A0134 3.612
LYS+A0137 12.134
GLU-A0150 2.546
ASP-A0153 0.01
HIS+A0162 9.547
ARG+A0166 14
LYS+A0167 11.693
TYR-A0169 13.641
LYS+A0177 9.547
GLU-A0184 2.952
LYS+A0185 10.634
LYS+A0188 10.634
GLU-A0193 4.078
ARG+A0199 14
ASP-A0201 1.973
LYS+A0209 11.693
GLU-A0213 3.279
GLU-A0219 4.706
LYS+A0223 11.693
ARG+A0226 13.193
GLU-A0227 4.377
GLU-A0228 9.459
GLU-A0230 4.274
ARG+A0232 14
TYR-A0234 14
ASP-A0239 2.317
GLU-A0248 3.982
LYS+A0253 10.547
ASP-A0261 2.335
ARG+A0267 14
LYS+A0272 14
TYR-A0275 10.21
HIS+A0276 7.15
ASP-A0280 3.317
LYS+A0281 11.193
ARG+A0292 12.693
ASP-A0294 2.473
ASP-A0304 2.3
LYS+A0305 11.693
GLU-A0308 2.083
LYS+A0312 11.193
GLU-A0314 4.517
LYS+A0315 11.693
GLU-A0322 15.177
ASP-A0327 0.01
LYS+A0328 10.298
ASP-A0330 0.01
HIS+A0331 0.01
LYS+A0341 6.65
ASP-A0344 0.01
ASP-A0346 2.03
GLU-A0347 3.149
ARG+A0351 14
GLU-A0354 4.52
LYS+A0357 11.193
LYS+A0358 11.634
GLU-A0359 3.945
ASP-A0369 5.467
HIS+A0370 0.01
HIS+A0372 14
ASP-A0380 0.751
LYS+A0382 13.193
LYS+A0393 12.693
ASP-A0394 2.724
TYR-A0402 14
GLU-A0406 3.551
GLU-A0407 4.924
ASP-A0408 1.824
GLU-A0411 5.186
HIS+A0412 6.852
ARG+A0418 23.69
TYR-A0422 14
HIS+A0425 6.65
ASP-A0434 0.01
ASP-A0437 0.01
TYR-A0440 10.555
LYS+A0443 11.155
LYS+A0449 11.693
CTR-A0449 3.014
_MG+A0452 5.257
NTR+B0001 8.547
GLU-B0003 4.312
GLU-B0008 2.577
ARG+B0010 14
ARG+B0023 14
ARG+B0024 14
ASP-B0028 0.724
ARG+B0034 13.193
ASP-B0039 3.21
LYS+B0040 11.193
LYS+B0043 12.377
ASP-B0051 8.766
ASP-B0055 0.01
GLU-B0057 1.955
ARG+B0062 14
TYR-B0064 12.243
GLU-B0066 3.279
LYS+B0073 12.193
ASP-B0076 0.01
TYR-B0084 14
HIS+B0086 0.01
TYR-B0087 14
LYS+B0091 11.693
LYS+B0092 10.547
LYS+B0095 11.134
ASP-B0097 1.839
TYR-B0098 14
ASP-B0101 0.01
LYS+B0114 14
TYR-B0116 14
ASP-B0123 0.01
HIS+B0125 7.15
GLU-B0126 4.746
LYS+B0127 11.693
ASP-B0128 2.457
HIS+B0129 6.65
GLU-B0134 2.737
LYS+B0137 12.193
GLU-B0150 3.33
ASP-B0153 0.611
HIS+B0162 9.664
ARG+B0166 14
LYS+B0167 10.599
TYR-B0169 14
LYS+B0177 10.547
GLU-B0184 3.501
LYS+B0185 11.693
LYS+B0188 12.634
GLU-B0193 3.281
ARG+B0199 14.134
ASP-B0201 1.52
LYS+B0209 10.547
GLU-B0213 3.073
GLU-B0219 3.317
LYS+B0223 11.134
ARG+B0226 12.634
GLU-B0227 4.577
GLU-B0228 7.332
GLU-B0230 3.865
ARG+B0232 14
TYR-B0234 14
ASP-B0239 1.797
GLU-B0248 4.706
LYS+B0253 10.275
ASP-B0261 2.68
ARG+B0267 14
LYS+B0272 10.547
TYR-B0275 10.988
HIS+B0276 7.65
ASP-B0280 3.077
LYS+B0281 12.193
ARG+B0292 13.193
ASP-B0294 2.473
ASP-B0304 2.77
LYS+B0305 11.193
GLU-B0308 3.108
LYS+B0312 12.193
GLU-B0314 3.568
LYS+B0315 11.693
GLU-B0322 9.138
ASP-B0327 13.172
LYS+B0328 10.24
ASP-B0330 0.01
HIS+B0331 4.598
LYS+B0341 6.15
ASP-B0344 0.01
ASP-B0346 1.247
GLU-B0347 2.911
ARG+B0351 14
GLU-B0354 4.113
LYS+B0357 11.134
LYS+B0358 11.693
GLU-B0359 4.509
ASP-B0369 4.63
HIS+B0370 0.01
HIS+B0372 0.01
ASP-B0380 2.097
LYS+B0382 11.693
LYS+B0393 11.693
ASP-B0394 0.473
TYR-B0402 14
GLU-B0406 2.85
GLU-B0407 4.328
ASP-B0408 2.562
GLU-B0411 5.428
HIS+B0412 2.554
ARG+B0418 14
TYR-B0422 14
HIS+B0425 7.15
ASP-B0434 0.01
ASP-B0437 0.01
TYR-B0440 10.199
LYS+B0443 12.693
LYS+B0449 12.693
CTR-B0449 3.18
_MG+B0452 8.86
pattern2
pKaRes NTR 1 A,value=  0.01
pKaRes GLU 3 A,value= 8.21

pKaRes GLU 8 A,value= 3.619
pKaRes ARG 10 A,value= 14

mycode1
from __future__ import with_statement
import  re
dict={"NTR":"NTR","CTR":"CTR","_MG":"_MG","PHE":"PHE",
"LEU":"LEU","SER":"SER","TYR":"TYR","CYS":"CYS",
"TRP":"TRP","LEU":"LEU","PRO":"PRO","HIS":"HIS",
"GLN":"GLN","ARG":"ARG","ILE":"ILE","MET":"MET",
"THR":"THR","ASN":"ASN","LYS":"LYS","SER":"SER",
"ARG":"ARG","VAL":"VAL","ALA":"ALA","ASP":"ASP",
"GLU":"GLU","GLY":"GLY"}

# in google search for '''re python search print pattern'''
def  new1():
#this takes...#
with  open('C:/Documents and  
Settings/Administrator/Desktop/Northeastern/Research2/python/E341K.txt') as  fil:
print  fil
contents =  fil.read()
letter =  contents
letter=str(letter)
#list1=list(letter)
x=  len(contents)
#''.join(contents)
#splitted=letter.split("-")
AA='AA'
xx=dict.keys()
NTR1='NTR1'
#for B in letter and  dict.keys():
for A in  letter:
if  re.sub(' ',' ',  letter):
letter=re.sub('\t','\t',letter) #'value=  '
#print  letter
#print re.sub('\t' and r'\+','',letter), re.sub(r'\+',' ',letter),  
re.sub('A0','A',letter)
break
for A in  letter:
if  re.sub(r'\+','  ',letter):
letter=re.sub(r'\+','  ',letter)
#print  letter
break
for A in  letter:
if  re.sub(r'\-','  ',letter):
letter=re.sub(r'\-','  ',letter)
#print  letter
break
for A in  letter:
if  re.sub('[0-9]','',letter):
letter2=re.sub('[0-9]','',letter)
#print letter2,  'letter2'
break
for A in  letter2:
if  re.sub(r'\.','',letter2):
letter1=re.sub(r'\.','',letter2)
#print letter1,  'letter1'
break
for A in  letter:
if  re.sub('A000?', 'A',  letter):
letter3=re.sub('A000?', 'A',  letter)
#print  letter3
break
for A in  letter:
if  re.sub('A010?','A',letter3):
letter4=re.sub('A010?','A',letter3)
print  letter4
break

re.purge()

#digs=re.compile(r'\+A')
#for line  in letter:
#if  digs.search(line):
#splitted=line.split(' ') #print  line
#line=list(line)
#print line

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