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Search found 5 results on 1 pages for 'chavanak'.

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• Calling gawk from python

  - by chavanak

  Hi, I am trying to call gawk from python in this manner. import os import string import codecs ligand_file=open( "2WTKA_ab.txt", "r" ) #Open the receptor.txt file ligand_lines=ligand_file.readlines() # Read all the lines into the array ligand_lines=map( string.strip, ligand_lines ) ligand_file.close() for i in ligand_lines: os.system ( " gawk %s %s"%( "'{if ($2==""i"") print $0}'", 'unique_count_a_from_ac.txt' ) ) My problem is that "i" is not being replaced by the value it represent. The value "i" represents is an integer and not a string. Can anyone help me out? Cheers, Chavanak

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• Printing elements out of list

  - by chavanak

  Hi, I have a certain check to be done and if the check satisfies, I want the result to be printed. Below is the code: import string import codecs import sys y=sys.argv[1] list_1=[] f=1.0 x=0.05 write_in = open ("new_file.txt", "w") write_in_1 = open ("new_file_1.txt", "w") ligand_file=open( y, "r" ) #Open the receptor.txt file ligand_lines=ligand_file.readlines() # Read all the lines into the array ligand_lines=map( string.strip, ligand_lines ) #Remove the newline character from all the pdb file names ligand_file.close() ligand_file=open( "unique_count_c_from_ac.txt", "r" ) #Open the receptor.txt file ligand_lines_1=ligand_file.readlines() # Read all the lines into the array ligand_lines_1=map( string.strip, ligand_lines_1 ) #Remove the newline character from all the pdb file names ligand_file.close() s=[] for i in ligand_lines: for j in ligand_lines_1: j = j.split() if i == j[1]: print j The above code works great but when I print j, it prints like ['351', '342'] but I am expecting to get 351 342 (with one space in between). Since it is more of a python question, I have not included the input files (basically they are just numbers). Can anyone help me? Cheers, Chavanak

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• Avoiding nesting two for loops

  - by chavanak

  Hi, Please have a look at the code below: import string from collections import defaultdict first_complex=open( "residue_a_chain_a_b_backup.txt", "r" ) first_complex_lines=first_complex.readlines() first_complex_lines=map( string.strip, first_complex_lines ) first_complex.close() second_complex=open( "residue_a_chain_a_c_backup.txt", "r" ) second_complex_lines=second_complex.readlines() second_complex_lines=map( string.strip, second_complex_lines ) second_complex.close() list_1=[] list_2=[] for x in first_complex_lines: if x[0]!="d": list_1.append( x ) for y in second_complex_lines: if y[0]!="d": list_2.append( y ) j=0 list_3=[] list_4=[] for a in list_1: pass for b in list_2: pass if a==b: list_3.append( a ) kvmap=defaultdict( int ) for k in list_3: kvmap[k]+=1 print kvmap Normally I use izip or izip_longest to club two for loops, but this time the length of the files are different. I don't want a None entry. If I use the above method, the run time becomes incremental and useless. How am I supposed to get the two for loops going? Cheers, Chavanak

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• Merging contents of two lists based on a if-loop

  - by chavanak

  I have a minor problem while checking for elements in a list: I have two files with contents something like this file 1: file2: 47 358 47 48 450 49 49 56 50 I parsed both files into two lists and used the following code to check for i in file_1: for j in file_2: j = j.split() if i == j[1]: x=' '.join(j) I am now trying to get a "0" if the value of file_1 is not there in file_2 for example, value "48" is not there is file_2 so I need to get the output like (with only one space in between the two numbers): output_file: 358 47 0 48 450 49 56 50 I tried using the dictionary approach but I didn't quite get what I wanted (actually I don't know how to use dictionary in python correctly ;)). Any help will be great.

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• Unable to get set intersection to work

  - by chavanak

  Sorry for the double post, I will update this question if I can't get things to work :) I am trying to compare two files. I will list the two file content: File 1 File 2 "d.complex.1" "d.complex.1" 1 4 5 5 48 47 65 21 d.complex.10 d.complex.10 46 6 21 46 109 121 192 192 TI am trying to compare the contents of the two file but not in a trivial way. I will explain what I want with an example. If you observe the file content I have typed above, the d.complex.1 of file_1 has "5" similar to d.complex.1 in file_2; the same d.complex.1 in file_1 has nothing similar to d.complex.10 in file_2. What I am trying to do is just to print out those d.complex. which has nothing in similar with the other d.complex. Consider the d.complex. as a heading if you want. But all I am trying is compare the numbers below each d.complex. and if nothing matches, I want that particular d.complex. from both files to be printed. If even one number is present in both d.complex. of both files, I want it to be rejected. My Code: The method I chose to achieve this was to use sets and then do a difference. Code I wrote was: first_complex=open( "file1.txt", "r" ) first_complex_lines=first_complex.readlines() first_complex_lines=map( string.strip, first_complex_lines ) first_complex.close() second_complex=open( "file2.txt", "r" ) second_complex_lines=second_complex.readlines() second_complex_lines=map( string.strip, second_complex_lines ) second_complex.close() list_1=[] list_2=[] res_1=[] for line in first_complex_lines: if line.startswith( "d.complex" ): res_1.append( [] ) res_1[-1].append( line ) res_2=[] for line in second_complex_lines: if line.startswith( "d.complex" ): res_2.append( [] ) res_2[-1].append( line ) h=len( res_1 ) k=len( res_2 ) for i in res_1: for j in res_2: print i[0] print j[0] target_set=set ( i ) target_set_1=set( j ) for s in target_set: if s not in target_set_1: if s[0] != "d": print s The above code is giving an output like this (just an example): d.complex.1.dssp d.complex.1.dssp 1 48 65 d.complex.1.dssp d.complex.10.dssp 46 21 109 What I would like to have is: d.complex.1 d.complex.1 (name from file2) d.complex.1 d.complex.10 (name from file2) I am sorry for confusing you guys, but this is all that is required. I am so new to python so my concept above might be flawed. Also I have never used sets before :(. Can someone give me a hand here?

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