new user needs help!

[Mike Driscoll]

On Apr 8, 2:55 pm, drjekil <drjeki... at gmail.com> wrote:
> 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 Z-COORED 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.
> IF PRESENT IN THAT RANGE
> IF not PRESENT IN THAT RANGE then
> -1 1:0 2:0 so on,it should be 1 instead of 0 when it will find corresponding
> amino acid for that line.say here,for 2nd line it will be 16:1.
> true will represent 1,false -1.
> i have to cheek all the lins in the file and print it.
> u have to tell simply otherwise i cant understand even,so stupid am i!
> I will be really greatful!Thanks in advance
> --
> View this message in context:http://www.nabble.com/new--user-needs-help%21-tp16571823p16571823.html
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To read the file, do something like this:

<code>

f = open('path/to/filename')
for line in f.readlines():
    # do something
    print line

</code>

See http://docs.python.org/lib/bltin-file-objects.html for more
information.

You'll want to look at using "if" statements to do the various
conditions and you'll probably need to use string slicing/splitting to
get the correct part of the line to do the comparison.

So, something like

<code>

f = open('path/to/filename')
for line in f.readlines():
    parts = line.split()
    zcoord = parts[-1]
    if zcoord > 10 and zcoord < 22:
       # do something
       pass
    print line

</code>

Resources:

http://docs.python.org/ref/if.html
http://www.ibiblio.org/g2swap/byteofpython/read/if-statement.html
http://docs.python.org/lib/string-methods.html
http://www.diveintopython.org/native_data_types/joining_lists.html

Mike