Processing text using python

[nuttydevil]

Hey everyone! I'm hoping someone will be able to help me, cause I
haven't had success searching on the web so far... I have large chunks
of text ( all in a long string) that are currently all in separate
notebook files. I want to use python to read these strings of text,
THREE CHARACTERS AT A TIME. (I'm studying the genetic code you see, so
I need to read and analyse each sequence one codon at a time
effectively.) Does anyone have any idea of how to do this using python?
I'm going to be optimistic and thank you for your help in advance!
Samantha.

[Alex Martelli]

nuttydevil <sj***@sussex.ac.uk> wrote:

Hey everyone! I'm hoping someone will be able to help me, cause I
haven't had success searching on the web so far... I have large chunks
of text ( all in a long string) that are currently all in separate
notebook files. I want to use python to read these strings of text,
THREE CHARACTERS AT A TIME. (I'm studying the genetic code you see, so
I need to read and analyse each sequence one codon at a time
effectively.) Does anyone have any idea of how to do this using python?

Open each file and call thefile.read(3) in a loop, move to the next file
when the current one is exhausted. What part of this is giving you
problems?
Alex

[Xavier Morel]

nuttydevil wrote:

Hey everyone! I'm hoping someone will be able to help me, cause I
haven't had success searching on the web so far... I have large chunks
of text ( all in a long string) that are currently all in separate
notebook files. I want to use python to read these strings of text,
THREE CHARACTERS AT A TIME. (I'm studying the genetic code you see, so
I need to read and analyse each sequence one codon at a time
effectively.) Does anyone have any idea of how to do this using python?
I'm going to be optimistic and thank you for your help in advance!
Samantha.

Since you're reading from files, the "read" operation of file-like
objects takes an argument specifying the number of characters to read
from the stream e.g.

f = file("stuff.txt")
f.read(3) 'car' f.read(3) 'act' f.read()

'erization'

Would that be enough for what you need?

[Roy Smith]

In article <11*********************@g43g2000cwa.googlegroups. com>,
"nuttydevil" <sj***@sussex.ac.uk> wrote:

Hey everyone! I'm hoping someone will be able to help me, cause I
haven't had success searching on the web so far... I have large chunks
of text ( all in a long string) that are currently all in separate
notebook files. I want to use python to read these strings of text,
THREE CHARACTERS AT A TIME. (I'm studying the genetic code you see, so
I need to read and analyse each sequence one codon at a time
effectively.) Does anyone have any idea of how to do this using python?

Don't reinvent the wheel. Take a look at http://www.biopython.org/.

[danmcleran]

I think this is what you want:

file = open(r'c:/test.txt','r')

c = file.read(3)
while c:
print c
c = file.read(3)

file.close();

[Steven Bethard]

da********@yahoo.com wrote:

I think this is what you want:

file = open(r'c:/test.txt','r')

c = file.read(3)
while c:
print c
c = file.read(3)

file.close();

Or:

def read3():
return file.read(3)
for chars in iter(read3, ''):
... do something with chars ...

STeVe

[Fredrik Lundh]

"nuttydevil" <sj***@sussex.ac.uk> wrote:

Hey everyone! I'm hoping someone will be able to help me, cause I
haven't had success searching on the web so far... I have large chunks
of text ( all in a long string) that are currently all in separate
notebook files. I want to use python to read these strings of text,
THREE CHARACTERS AT A TIME. (I'm studying the genetic code you see, so
I need to read and analyse each sequence one codon at a time
effectively.) Does anyone have any idea of how to do this using python?

did you read the string chapter in the tutorial ?

http://docs.python.org/tut/node5.htm...00000000000000

around the middle of that chapter, there's a section on slicing:

"substrings can be specified with the slice notation: two indices
separated by a colon"

</F>

[John Zenger]

If you have already read the string into memory and want a convenient
way to loop through it 3 characters at a time, check out the "batch" recipe:

http://aspn.activestate.com/ASPN/Coo.../Recipe/303279

It uses itertools to make an iterator over the string, returning 3
characters at a time. Cool stuff.
nuttydevil wrote:

Hey everyone! I'm hoping someone will be able to help me, cause I
haven't had success searching on the web so far... I have large chunks
of text ( all in a long string) that are currently all in separate
notebook files. I want to use python to read these strings of text,
THREE CHARACTERS AT A TIME. (I'm studying the genetic code you see, so
I need to read and analyse each sequence one codon at a time
effectively.) Does anyone have any idea of how to do this using python?
I'm going to be optimistic and thank you for your help in advance!
Samantha.

[Gerard Flanagan]

nuttydevil wrote:

Hey everyone! I'm hoping someone will be able to help me, cause I
haven't had success searching on the web so far... I have large chunks
of text ( all in a long string) that are currently all in separate
notebook files. I want to use python to read these strings of text,
THREE CHARACTERS AT A TIME. (I'm studying the genetic code you see, so
I need to read and analyse each sequence one codon at a time
effectively.) Does anyone have any idea of how to do this using python?
I'm going to be optimistic and thank you for your help in advance!
Samantha.

data1 = '''FOOTFALLSECHOINTHEMEMORY
DOWNTHEPASSAGEWHICHWEDIDNOTTAKE
TOWARDSTHEDOORWENEVEROPENED'''

num_codons = len(data1) // 3

codons = [ data1[3*i:3*(i+1)] for i in range( num_codons ) ]

print codons

class Codon(object):
#__slots__ = ['alpha', 'beta', 'gamma']
def __init__(self, a, b, c):
self.alpha = a
self.beta = b
self.gamma = c

codons = [ Codon(*codon) for codon in codons ]

print codons[0].alpha, codons[0].beta, codons[0].gamma

###output####

['FOO', 'TFA', 'LLS', 'ECH', 'OIN', 'THE', 'MEM', 'ORY', '\nDO', 'WNT',
'HEP', 'ASS', 'AGE', 'WHI', 'CHW', 'EDI', 'DNO', 'TTA', 'KE\n', 'TOW',
'ARD', 'STH', 'EDO', 'ORW', 'ENE', 'VER', 'OPE', 'NED']
F O O
Gerard

[danmcleran]

Sure. There's probably a thousand ways to do this.

[plahey]

Hi,

you have plenty of good responses. I thought I would add one more:

def data_iter(file_name):
data = file(file_name)
while True:
value = data.read(3)
if not value:
break
yield value
data.close()

With the above, you can grab the entire data set (3 characters at a
time) like so:

data_set = [ d for d in data_iter('data') ]

Or iterate over it:

for d in data_iter('data'):
# do stuff

Enjoy!

[Xavier Morel]

Fredrik Lundh wrote:

did you read the string chapter in the tutorial ?

http://docs.python.org/tut/node5.htm...00000000000000

around the middle of that chapter, there's a section on slicing:

"substrings can be specified with the slice notation: two indices
separated by a colon"

Fredrik, how would you use slices to split a string by groups of 3
characters?

[Alex Martelli]

Xavier Morel <xa**********@masklinn.net> wrote:

Fredrik Lundh wrote:

did you read the string chapter in the tutorial ?

http://docs.python.org/tut/node5.htm...00000000000000

around the middle of that chapter, there's a section on slicing:

"substrings can be specified with the slice notation: two indices
separated by a colon"

Fredrik, how would you use slices to split a string by groups of 3
characters?

I can't answer for him, but maybe:

[s[i:i+3] for i in xrange(0, len(s), 3)]

....?
Alex