parsing newlines together

[laver68xo]

I'm trying to take a file that looks like this:

taxon1
ACCGTGGATC
CCTATTGATT
GGATATTATC
taxon2
TTCATATGTA
GGATTTCATA
GATGGCCCCC

And get it to look like this
taxon1 ACCGTGGATCCCTATTGATTGGATATTATC

I'm using a python script, so far this is what I have:

#!/usr/bin/python

import sys

if len(sys.argv) < 2:
    print "usage: finalmyscript.py infile.txt"
    sys.exit(1)

fname = sys.argv[1]

handle = open(fname, "r")
list = handle.readlines()

for line in list:
    parts = line.rstrip('\n')
    linearr = parts.split()
    combine = ''.join(linearr[0])
    print combine

handle.close()

The script removes the '\n' at the end of each line, but it still won't join the lines all on a single line. Can anyone help with where I'm going wrong?
Thanks!

[vegaseat]

Hint ...

s = '''\
taxon1
ACCGTGGATC
CCTATTGATT
GGATATTATC
'''

s2 = ""
for ix, line in enumerate(s.split('\n')):
    line = line.rstrip()
    if ix == 0:
        # add a space
        line += ' '
    s2 += line

print(s2)

''' result ...
taxon1 ACCGTGGATCCCTATTGATTGGATATTATC
'''

[chris.stout]

If you get rid of lines 14 - 19 you can print the input file as one line with:

print ''.join(list).replace("\n", " ")

[laver68xo]

Vegaseat:
that would work if I wasn't pulling the input from a file. I can only use the input file as a command for running my file, I can't use any of the verbatim info from the file, like the actual DNA code.

Chris, I used a line like that before, it does bring them together, but the problem is that it then puts all the taxons on one line and I need to split them by taxon.

Thank you guys!

[woooee]

Does the file have more than one taxon? In the example you posted there is only one so all of the solutions are for one only. Try this as a hint, although there are other ways to do it.

handle = open(fname, "r")
all_data = handle.read()
print all_data.split("taxon")

[laver68xo]

There are 3 taxon total, but I just printed 2 of them.

taxon1
ACCGTGGATC
CCTATTGATT
GGATATTATC
taxon2
TTCATATGTA
GGATTTCATA
GATGGCCCCC

[laver68xo]

That last comment helped alot! Thank you! The all_data.split got all 3 taxon on one line for me.

[vegaseat]

You can do something like that ...

''' infile_test.py
data processing from a file

file infile.txt has content ...
taxon1
ACCGTGGATC
CCTATTGATT
GGATATTATC
taxon2
TTCATATGTA
GGATTTCATA
GATGGCCCCC 
'''

fname = "infile.txt"

with open(fname) as fin:
    s2 = ""
    for line in fin:
        line = line.rstrip()
        if "taxon" in line:
            # add a space
            line += ' '
            # might need to adjust this value
            if len(s2) > 10:
                s2 += '\n'
        s2 += line
    print(s2)

''' result ...
taxon1 ACCGTGGATCCCTATTGATTGGATATTATC
taxon2 TTCATATGTAGGATTTCATAGATGGCCCCC
'''

[HiHe]

At this point it would be nice to know what your input data is. And what you expect your output data to look like.