Export output of a “for” loop to a file in python

Question

I have a text file (b.txt) like the following:

SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PLEHP20                                   
KEYWDS   2 METHODS, IRON-SULPHUR CLUSTER, METALLOPROTEIN                        
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    E.PARISINI,F.CAPOZZI,P.LUBINI,V.LAMZIN,C.LUCHINAT,                    
REVDAT   4   24-FEB-09 1CKU    1       VERSN                                    
JRNL        PMID   10531472                                                     
REMARK   1 REFERENCE 1         
ATOM      1  N   SER A   1      -8.686  33.363  10.216  1.00 33.39           N  
ANISOU    1  N   SER A   1     2884   4416   5388   1179  -1154   1000       N  
HETATM 1565  O   HOH B 350       7.855  16.938  27.107  1.00 34.27           O  
ANISOU 1565  O   HOH B 350     3399   5455   4168    135   -563    -23       O

I have a python code (see below) that reads only the lines that start with “ATOM” or “HETATOM”.

pdb_text = open("b.txt","r")
# read contents of the file to string
data = ""
data = pdb_text.read()
for line in data.split('\n'):
    if line.startswith("ATOM") or line.startswith("HETATM"):
        print(line)

The code works well and generates an output as the following.

ATOM      1  N   SER A   1      -8.686  33.363  10.216  1.00 33.39           N  
HETATM 1565  O   HOH B 350       7.855  16.938  27.107  1.00 34.27           O

However, I want to export the output to a new file. How should I change the last line of the code to do this?

Pablo Santa Cruz · Accepted Answer · 2022-08-06 12:56:51Z

1

Try this:

pdb_text = open("b.txt","r")
out = open("out.txt", "w")
# read contents of the file to string
data = ""
data = pdb_text.read()
for line in data.split('\n'):
    if line.startswith("ATOM") or line.startswith("HETATM"):
        out.write(line)
out.close()
pdb_text.close()

This is basically the same python code with but a little bit more pythonic:

with open("b.txt","r") as pdb_text:
    with open("out.txt", "w") as ouy:
        for line in pdb_text:
            if line.startswith("ATOM") or line.startswith("HETATM"):
                out.write(line)

Otherwise, you could just use your shell's redirection capabilities like this:

python your_program.py > out.txt

You even could have accomplished what you have with the python program by running (if you're on macOS, Linux or other UNIX flavor) with this one liner:

cat b.txt | egrep "^ATOM|^HETATM" > out.txt

edited Aug 6, 2022 at 12:56

answered Aug 6, 2022 at 12:50

Pablo Santa Cruz

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Chels · Accepted Answer · 2022-08-06 13:31:34Z

1

You could try this (similar to a previous answer but "a"ppending to the file and not "w"ritting):

pdb_text = open("b.txt","r")
out = open("b.txt", "a")
# read contents of the file to string
data = ""
data = pdb_text.read()
for line in data.split('\n'):
    if line.startswith("ATOM") or line.startswith("HETATM"):
        out.write(line + '\n')
out.close()
pdb_text.close()

edited Aug 6, 2022 at 13:31

answered Aug 6, 2022 at 12:55

Chels

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2 Comments

Mehdi Irani Over a year ago

Thank you for your response. The code now generates a file. In the output, I expected two lines (one that begins with "ATOM" and one that begins with "HETATM"); however, the code prints the entire output on a single line. What can I do to resolve this issue?

Chels Over a year ago

You can change: out.write(line) to out.write(line + "\n") so it will break-line. Hope it helps :)

hengrv · Accepted Answer · 2022-08-06 13:52:51Z

1

a more concise and pythonic answer would be to use context managers.

this outputs the selected lines to a new file called out.txt

data = ""
with open("b.txt", "r") as pdb_text:
    data = pdb_text.read()

with open("out.txt", "w") as output:

    for line in data.split("\n"):
        if line.startswith("ATOM") or line.startswith("HETATM"):
            output.write(line + "\n")

edited Aug 6, 2022 at 13:52

answered Aug 6, 2022 at 13:03

hengrv

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