need help!

Question

drjekil 0 Newbie Poster

16 Years Ago

I am totally new in biopython and its my first program.so may be i am asking stupid question.

I am working with a text filelooks like this:
#NAME AA TOPO ACCESS DSSP STRIDE Z-COORD
1lghB A i 79.8 H H -24.58
1lghB V i 79.6 H H -22.06
1lghB H i 71.9 H H -19.94
i need to compare those lines which has a value between 10 to 22 and presents in the following way
True/false A C D E F G H I K L M N P Q R S T V X Y W(here alfabets represents amino acids)
1 1:1 2:0 3:0 and so on for rest of the amino acids.

I have given 2 examples below to make it clear a bit:

ex.1:
#NAME AA TOPO ACCESS DSSP STRIDE Z-COORD
1lghB A i 79.8 H H -24.58 #for that line amino acid is A and z-COORED value is more than 22,so output should be look like

True/false A C D E F G H I K L M N P Q R S T V X Y W(here alfabets represents amino acids)
-1 1:1 2:0 3:o 4:0 so on upto 20 bcz there r 20 amino acids.and A presents in the 1st position.every line represents one amino acid with value,so output will show in which position is it(here A is in 1st position thats why its value 1:1 and all the other position o like 2:0,3:0,4:0 and if its Z-COORED value between 10-22 then true false value 1,otherwise -1.

another ex:

1lghB H i 71.9 H H -19.94 # for that line amino acid is H and it has value between 10-22.so output should looks like:

True/false A C D E F G H I K L M N P Q R S T V X Y W(here alfabets represents 20 amino acids)

1 1:0 2:0 3:0 4:0 5:0 6:0 7:1 8:0,every position is zero up to 20 bcz H presents in the 7th position.so it will be 1.

so for every line, output will in 21 coulum,1st coulum for true false value,others r for 20 amino acids.true false value will be either 1 or -1,and within other 20 coulum one value will be n:1,others will be n:0.n=0,1,2,3..20.
its a bit tricky.
thank u so much for ur help in advance
waiting for ur opinion.

python

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jrcagle 77 Practically a Master Poster

16 Years Ago

It is a bit tricky. Can you explain the problem more precisely? For example, what do each of the fields in the string

"1lghB H i 71.9 H H -19.94"

mean?

Jeff

woooee 814 Nearly a Posting Maven

16 Years Ago

It's late and I'm tired but this is the general idea if I understand correctly

data=["1lghB A i 79.8 H H -24.58",
      "1lghB V i 79.6 H H -22.06",
      "1lghB H i 71.9 H H -19.94"]
for line in data:
     print "\nlooking at", line
     substrs=line.strip().split()
     print  "amino acid =", substrs[1], "and value =", substrs[-1]
     value = abs(float(substrs[-1]))
     if 9.99 < value < 22.01:
          print "greater than 10 and less than 22"
#
# And if you want to keep track of how many hits are found for each
# amino, I would suggest a dictionary with the amino acid symbol 
# as key, containing a simple integer counter, so adding to a
# dictionary the simplest way is:
# (This is still under the if statement)
          if substrs[1] in amino_dic:
               amino_dic += 1
          else:
               amino_dic[substrs[1]]=1

This is what doesn't make sense to me

## what is Z_CORRED
## and you don't define z
for i in Z-CORRED:
if 10.0 <= z <= 22.0:
matches.append([1,i])

And I don't understand all of the print statements. But first, verify that this is the correct way to split the data. Then figure how to store/print it. HTH.

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drjekil 0 Newbie Poster · Answer 1 · 2008-04-11T05:06:15+00:00

I am working with a text filelooks like this:
#NAME AA TOPO ACCESS DSSP STRIDE Z-COORD
1lghB A i 79.8 H H -24.58
1lghB V i 79.6 H H -22.06
1lghB H i 71.9 H H -19.94
i need to compare those lines which has a value between 10 to 22 and presents in the following way
True/false A C D E F G H I K L M N P Q R S T V X Y W(here alfabets represents amino acids)
1 1:1 2:0 3:0 and so on for rest of the amino acids.

I have given 2 examples below to make it clear a bit:

ex.1:
#NAME AA TOPO ACCESS DSSP STRIDE Z-COORD
1lghB A i 79.8 H H -24.58 #for that line amino acid is A and z-COORED value is more than 22,so output should be look like

True/false A C D E F G H I K L M N P Q R S T V X Y W(here alfabets represents amino acids)
-1 1:1 2:0 3:o 4:0 so on upto 20 bcz there r 20 amino acids.and A presents in the 1st position.every line represents one amino acid with value,so output will show in which position is it(here A is in 1st position thats why its value 1:1 and all the other position o like 2:0,3:0,4:0 and if its Z-COORED value between 10-22 then true false value 1,otherwise -1.

another ex:

1lghB H i 71.9 H H -19.94 # for that line amino acid is H and it has value between 10-22.so output should looks like:

True/false A C D E F G H I K L M N P Q R S T V X Y W(here alfabets represents 20 amino acids)

1 1:0 2:0 3:0 4:0 5:0 6:0 7:1 8:0,every position is zero up to 20 bcz H presents in the 7th position.so it will be 1.

so for every line, output will in 21 coulum,1st coulum for true false value,others r for 20 amino acids.true false value will be either 1 or -1,and within other 20 coulum one value will be n:1,others will be n:0.n=0,1,2,3..20.
its a bit tricky.
I have done something so far about that problem,but its not the good way to
do it

need ur comments about that....

from string import *;
import sys

myfile = open("/afs/pdc.kth.se/home/d/debnath/membrane/1a91A.txt")
a = myfile.readlines()
data = myfile.readlines()
for line in myfile.readlines():
fields = line.split('\t')

items=fields.strip()
list1.append(items[1])

for i in Z-CORRED:
if 10.0 <= z <= 22.0:
matches.append([1,i])

else:
matches.append([-1,i])

print "#T/F A C D E F G H I K L M N P Q R S T V W X Y
Z"

for a in range(0,len(matches),1):

if matches[a][0]==1:

if matches[a][1]=='A':
print "1 1:1 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0 13:0
14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
elif matches[a][1]=='C':
print "1 1:0 2:1 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0 13:0
14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
elif matches[a][1]=='D':

print " 1 1:0 2:0 3:1 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
""" if matches[a][1]=='E' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:1 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='F' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:1 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='G' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:1 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='H' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:1 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='I' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:1 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='K' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:1 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='L' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:1 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='M' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:1 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='N' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:1
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='P' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:1 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='Q' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:1 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='R' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:1 16:0 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='S' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:1 17:0 18:0 19:0 20:0 21:0"
if matches[a][1]=='T' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:1 18:0 19:0 20:0 21:0"
if matches[a][1]=='V' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:1 19:0 20:0 21:0"
if matches[a][1]=='X' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:1 20:0 21:0"
if matches[a][1]=='Y' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:1 21:0"
if matches[a][1]=='Z' and matches[a][0]==1:

print " 1 1:0 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:1"

"""
else:#here i have getting comments
if matches[a][1]=='A':
print "-1 1:1 2:0 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0 13:0
14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
elif matches[a][1]=='C':
print "-1 1:0 2:1 3:0 4:0 5:0 6:0 7:0 8:0 9:0 10:0 11:0 12:0
13:0 14:0 15:0 16:0 17:0 18:0 19:0 20:0 21:0"
elif matches[a][1]=='D':