Iterating over a file in python

[moconno5]

Hello everyone, I wrote a post awhile ago about automating a local client to access a BLAT webserver, but today I have a much easier one. I want to take a batch file and delete every odd line. See below:

Sample File:
>MusmusculusmiR-344
UGAUCUAGCCAAAGCCUGACUGU
>MusmusculusmiR-345
UGCUGACCCCUAGUCCAGUGC
>MusmusculusmiR-346
UGUCUGCCCGAGUGCCUGCCUCU
>MusmusculusmiR-350
UUCACAAAGCCCAUACACUUUCA

I need to delete all the lines that start with '>' and end with a '\n'. I have some code below, but it just isolates the part of the string I want to delete. I need to do the reverse... I know there is some easy way that I am totally missing here!

#!/usr/bin/env python
# written 7/28/2007
# by Mark O'Connor
 
def Resize( filename ):
    line = 0
    collect = []
    fp = file( filename )
    data = fp.read()
    fp.close()
    #print data
    while line != -1:
        start = data.find('>', line+1)
        end = data.find ('/n', start)
        chunk = data[start:end]
    return chunk
 
 

Thanks,

Mark

[bartonc]

Hello everyone, I wrote a post awhile ago about automating a local client to access a BLAT webserver, but today I have a much easier one. I want to take a batch file and delete every odd line. See below:

Sample File:
>MusmusculusmiR-344
UGAUCUAGCCAAAGCCUGACUGU
>MusmusculusmiR-345
UGCUGACCCCUAGUCCAGUGC
>MusmusculusmiR-346
UGUCUGCCCGAGUGCCUGCCUCU
>MusmusculusmiR-350
UUCACAAAGCCCAUACACUUUCA

I need to delete all the lines that start with '>' and end with a '\n'. I have some code below, but it just isolates the part of the string I want to delete. I need to do the reverse... I know there is some easy way that I am totally missing here!

#!/usr/bin/env python
# written 7/28/2007
# by Mark O'Connor
 
def Resize( filename ):
    line = 0
    collect = []
    fp = file( filename )
    data = fp.read()
    fp.close()
    #print data
    while line != -1:
        start = data.find('>', line+1)
        end = data.find ('/n', start)
        chunk = data[start:end]
    return chunk
 
 

Thanks,

Mark

Hey Mark...
I'd use something like this:

outList = []
f = open(fileName)
for line in f:
    if line.startswith('>'):
        continue
    outList.append(line)
f.close()
f = open(newFileName, 'w') # or old one to replace it
f.writelines(outLIst)
f.close()

Untested, but generally sound.

[moconno5]

Thanks! That did the trick

Mark

[bartonc]

Thanks! That did the trick

Mark

Files, like all iterators have some pretty cool methods hung on them. That example just scratches the surface.

Any time,
Barton

[robin746]

Or even:

out = []
with open(fileName) as f:
    for line in f:
        if line.startswith('>'):
            continue
        out.append(line)
 
with open(newFileName, 'w') as f:
    f.writelines(out)
 

[twohot]

@ bartonc

Files, like all iterators have some pretty cool methods hung on them. That example just scratches the surface.

Now I'm listening. What are those cool methods?

[Michael Colon]

Personally, I love python for many reasons, especially when it comes to parsing things and shifting things. This next piece of code should take you to the next level in python development.

input = open("inputfile.txt")
output = open("outputfile.txt", 'w')
 
output.writelines([(line) for line in input if not line.startswith('>')])
 

And thats it!