Skip to content

Latest commit

 

History

History
245 lines (144 loc) · 6.26 KB

file_generators.rst

File metadata and controls

245 lines (144 loc) · 6.26 KB

File Generators

.. toctree::
   :maxdepth: 2
   :caption: gen

This page shows how a generator function might be applied when reading information from files. Specifically, we will use the PDB file 1yuw.pdb in these examples.

Before we begin

Just a quick note: You can loop through a file without calling the readlines() method. A file is an iterable object in Python, meaning you can loop through it as you would loop through a list. You cannot, however, index it like a list or loop through it twice as you would a list, e.g.

new_file = open('1yuw.pdb', 'r')

for i in new_file:
    print i.strip()

output:

>>> run_demo_script.py

HEADER    CHAPERONE                               14-FEB-05   1YUW
TITLE     CRYSTAL STRUCTURE OF BOVINE HSC70(AA1-554)E213A/D214A MUTANT
COMPND    MOL_ID: 1;

... (etc) ...

HETATM 4402  O   HOH A 673     -25.597  -7.669  -1.875  1.00 42.36           O
HETATM 4403  O   HOH A 674     -30.646  29.519  28.046  1.00 33.50           O
HETATM 4404  O   HOH A 675     -11.236  31.946  24.433  1.00 42.17           O
MASTER      292    0    0   19   29    0    0    6 4403    1    0   43
END

Now if we try run this same for-loop again

#second attempt
print "\n\nSecond looping attempt"

for i in new_file:
    print i.strip()

#Note, nothing is printed because we have reached the end of the file...

print "\nOne more looping attempt...\n"

for i in new_file:
    print i.strip()

output:

>>> run_demo_script.py

Second looping attempt

One more looping attempt...

(*crickets*)

Just out of interest; the file object has a seek() method to allow you to move back to the beginning of the file. (or anywhere in the file really).

seek(0) will go to the beginning, though...

print 'resetting using seek()'
new_file.seek(0)

print("\nLast try...\n")

for i in new_file:
    print i.strip()

output:

>>> run_demo_script.py

resetting using seek()

Last try...


HEADER    CHAPERONE                               14-FEB-05   1YUW
TITLE     CRYSTAL STRUCTURE OF BOVINE HSC70(AA1-554)E213A/D214A MUTANT
COMPND    MOL_ID: 1;

... (etc) ...

HETATM 4402  O   HOH A 673     -25.597  -7.669  -1.875  1.00 42.36           O
HETATM 4403  O   HOH A 674     -30.646  29.519  28.046  1.00 33.50           O
HETATM 4404  O   HOH A 675     -11.236  31.946  24.433  1.00 42.17           O
MASTER      292    0    0   19   29    0    0    6 4403    1    0   43
END

Writing generators for file reading

Using our generator logic, we can write a generator that yields values as it reads through a file. More importantly, it can do this when specific conditions are met, e.g.

SEQRES example

def get_seqres(f):

    print '\nSeqres Extraction:\nOpening file %s' % f.name

    for line in f:
        if line.startswith('SEQRES'):
            yield line


with open('1yuw.pdb', 'r') as new_file:

    for line in get_seqres(new_file):

        print line.strip()

output:

>>> run_demo_script.py

Seqres Extraction:
Opening file 1yuw.pdb

SEQRES   1 A  554  MET SER LYS GLY PRO ALA VAL GLY ILE ASP LEU GLY THR
SEQRES   2 A  554  THR TYR SER CYS VAL GLY VAL PHE GLN HIS GLY LYS VAL

... (etc) ...

SEQRES  42 A  554  ASP LYS VAL SER SER LYS ASN SER LEU GLU SER TYR ALA
SEQRES  43 A  554  PHE ASN MET LYS ALA THR VAL GLU

A more generalized example

This can be further generalized to loop through specific parts of a PDB file.

def get_lines(file_obj, identifier):

    print '\nGeneral Extraction:\nOpening file %s' % file_obj.name
    print 'Extracting %s information' % identifier

    for line in file_obj:
        if line.startswith(identifier):
            yield line

Obviously the two print-statements are not strictly necessary. They are only included to help show what the function is doing. Now let us test it out...

First let's see what happens if we set the identifier as 'ATOM'

with open('1yuw.pdb', 'r') as new_file:

    for line in get_lines(new_file, 'ATOM'):

        print line.strip()

output:

>>> run_demo_script.py

General Extraction:
Opening file 1yuw.pdb
Extracting ATOM information

ATOM      1  N   MET A   1      -0.688  28.039  -8.659  1.00108.11           N
ATOM      2  CA  MET A   1      -0.686  27.081  -7.519  1.00108.04           C
ATOM      3  C   MET A   1      -2.028  27.143  -6.792  1.00107.64           C

... (etc) ...

ATOM   4280  OE1 GLU A 554       6.939  -5.505  33.720  1.00137.66           O
ATOM   4281  OE2 GLU A 554       7.065  -5.945  31.577  1.00137.69           O
ATOM   4282  OXT GLU A 554       9.455  -3.863  36.636  1.00136.09           O

Now we set the identifier as 'HETATM':

with open('1yuw.pdb', 'r') as new_file:

    for line in get_lines(new_file, 'HETATM'):

        print line.strip()

output:

>>> run_demo_script.py

General Extraction:
Opening file 1yuw.pdb
Extracting HETATM information

HETATM 4284  O   HOH A 555     -26.474   8.773  -1.079  1.00 10.89           O
HETATM 4285  O   HOH A 556     -14.802  13.650  13.146  1.00  9.28           O
HETATM 4286  O   HOH A 557      25.036  -0.072  31.041  1.00 16.67           O

... (etc) ...

HETATM 4402  O   HOH A 673     -25.597  -7.669  -1.875  1.00 42.36           O
HETATM 4403  O   HOH A 674     -30.646  29.519  28.046  1.00 33.50           O
HETATM 4404  O   HOH A 675     -11.236  31.946  24.433  1.00 42.17           O