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Subject: [Tutor] raw_input()

Dear group:
I have a large file 3GB. Each line is a tab delim file. 

example lines of it:

585     chr1    433     433     rs56289060      0       +       -       -       -/C     genomic insertion       unknown 0       0       unknown between 1
585     chr1    491     492     rs55998931      0       +       C       C       C/T     genomic single  unknown 0       0       unknown exact   1
585     chr1    518     519     rs62636508      0       +       G       G       C/G     genomic single  unknown 0       0       unknown exact   1
585     chr1    582     583     rs58108140      0       +       G       G       A/G     genomic single  unknown 0       0       unknown exact   1

Now I dont want to load this entire file. I want to give each line as an input and print selective lines. 

For example:

x1.py  = 

second = raw_input()
x =  second.split('\t')
y = x[1:]
print '\t'.join(y)


%cat mybigfile.rod | python x1.py
chr1    433     433     rs56289060      0       +       -       -       -/C     genomic insertion       unknown 0       0       unknown between 1


My question:

this program is only printing first line. It is not processing every line that cat spits to x1.py. 
how do I print every line. 

Subject: Re: [Tutor] raw_input()

Here it worked after trying a while loop:


x1.py  = 

while True:
         second = raw_input()
         x =  second.split('\t')
         y = x[1:]
         print '\t'.join(y)




%cat mybigfile.rod | python x1.py
Traceback (most recent call last):
  File "x1.py", line 2, in <module>
    second = raw_input()
EOFError: EOF when reading a line



How to notify that at EOF break and suppress exception.

Subject: Re: [Tutor] raw_input()

> I have a large file 3GB. Each line is a tab delim file.
[...]
> Now I dont want to load this entire file. I want to give each line as
> an input and print selective lines.

datafile = open("somefile.data", "r")
for line in datafile:
    print line

will print each line. If you want to print selected lines, you have to 
explain what the condition is that decides whether to print it or not. 
I'm going to make something up: suppose you want the line to only print 
if the eighth column is "A":

def condition(line):
    line = line.strip()
    fields = line.split('\t')
    return fields[7].strip().upper() == "A"


datafile = open("somefile.data", "r")
for line in datafile:
    if condition(line):
        print line

will print only the lines where column 8 is the letter A.


Subject: Re: [Tutor] raw_input()

> x1.py  =
>
> second = raw_input()
> x =  second.split('\t')
> y = x[1:]
> print '\t'.join(y)
>
>
> %cat mybigfile.rod | python x1.py
> chr1    433     433     rs56289060      0 
> +       -       -       -/C     genomic insertion       unknown 0       0 
> unknown between 1
>
>
> My question:
>
> this program is only printing first line. It is not processing every line 
> that cat spits to x1.py.
> how do I print every line.

You need to read every line.

But since you appear to be on Unix have you looked at the cut command
which would appear to do what you want directly?

Unless you just want the learning experience.

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