String Replacement

[moconno5]

Hello everyone, I've got a simple one today. I have a string and I want to remove all carriage returns ('\n') between the characters [ACGU] and [ACGU] and preserve the other ones. For example:

'Musmusculuslet-7gstem-loop\nCCAGGCUGA GGUAGUAGUUUGUAC AGUUUGAGGGUCUAU GAUACCACCCGGUAC AGGAGA\nUAACUGU ACAGGCCACUGCCUU GCCAGG\n
Musmusculuslet-7istem-loop\nCUGGCUGAG GUAGUAGUUUGUGCU GUUGGUCGGGUUGUG ACAUUGCCCGCUGUG GAGAUA\nACUGCGC AAGCUACUGCCUUGC UAG\n'

editted string:

'Musmusculuslet-7gstem-loop\nCCAGGCUGA GGUAGUAGUUUGUAC AGUUUGAGGGUCUAU GAUACCACCCGGUAC AGGAGAUAACUGUAC AGGCCACUGCCUUGC CAGG\n
Musmusculuslet-7istem-loop\nCUGGCUGAG GUAGUAGUUUGUGCU GUUGGUCGGGUUGUG ACAUUGCCCGCUGUG GAGAUAACUGCGCAA GCUACUGCCUUGCUA G\n'

I tried the following code but I got a syntax error:

for a in chunk3:
	if ([ACGU]'\n'[ACGU]):
               chunk3 = chunk3.replace('\n','')

Thanks,

Mark

[ilikepython]

Hello everyone, I've got a simple one today. I have a string and I want to remove all carriage returns ('\n') between the characters [ACGU] and [ACGU] and preserve the other ones. For example:

'Musmusculuslet-7gstem-loop\nCCAGGCUGA GGUAGUAGUUUGUAC AGUUUGAGGGUCUAU GAUACCACCCGGUAC AGGAGA\nUAACUGU ACAGGCCACUGCCUU GCCAGG\n
Musmusculuslet-7istem-loop\nCUGGCUGAG GUAGUAGUUUGUGCU GUUGGUCGGGUUGUG ACAUUGCCCGCUGUG GAGAUA\nACUGCGC AAGCUACUGCCUUGC UAG\n'

editted string:

'Musmusculuslet-7gstem-loop\nCCAGGCUGA GGUAGUAGUUUGUAC AGUUUGAGGGUCUAU GAUACCACCCGGUAC AGGAGAUAACUGUAC AGGCCACUGCCUUGC CAGG\n
Musmusculuslet-7istem-loop\nCUGGCUGAG GUAGUAGUUUGUGCU GUUGGUCGGGUUGUG ACAUUGCCCGCUGUG GAGAUAACUGCGCAA GCUACUGCCUUGCUA G\n'

I tried the following code but I got a syntax error:

for a in chunk3:
	if ([ACGU]'\n'[ACGU]):
               chunk3 = chunk3.replace('\n','')

Thanks,

Mark

Try this:
[code=python]
import re

s = "Musmusculu slet-7gstem-loop\nCCAGGCUGA GGUAGUAGUUUGUAC AGUUUGAGGGUCUAU GAUACCACCCGGUAC AGGAGA\nUAACUGU ACAGGCCACUGCCUU GCCAGG\n"

patt = re.compile(r"[ACGU]\n[ACGU]")
matches = patt.findall(s)

for m in matches:
s = s.replace(m, m[0] + m[2])
[/code]

[bvdet]

Hello everyone, I've got a simple one today. I have a string and I want to remove all carriage returns ('\n') between the characters [ACGU] and [ACGU] and preserve the other ones. For example:

'Musmusculuslet-7gstem-loop\nCCAGGCUGA GGUAGUAGUUUGUAC AGUUUGAGGGUCUAU GAUACCACCCGGUAC AGGAGA\nUAACUGU ACAGGCCACUGCCUU GCCAGG\n
Musmusculuslet-7istem-loop\nCUGGCUGAG GUAGUAGUUUGUGCU GUUGGUCGGGUUGUG ACAUUGCCCGCUGUG GAGAUA\nACUGCGC AAGCUACUGCCUUGC UAG\n'

editted string:

'Musmusculuslet-7gstem-loop\nCCAGGCUGA GGUAGUAGUUUGUAC AGUUUGAGGGUCUAU GAUACCACCCGGUAC AGGAGAUAACUGUAC AGGCCACUGCCUUGC CAGG\n
Musmusculuslet-7istem-loop\nCUGGCUGAG GUAGUAGUUUGUGCU GUUGGUCGGGUUGUG ACAUUGCCCGCUGUG GAGAUAACUGCGCAA GCUACUGCCUUGCUA G\n'

I tried the following code but I got a syntax error:

for a in chunk3:
	if ([ACGU]'\n'[ACGU]):
               chunk3 = chunk3.replace('\n','')

Thanks,

Mark

It looks like you are trying to implement a regex solution without understanding how it works. This seems to do what you want:[code=Python]import re
patt = re.compile(r'[ACGU]\n[ACGU]')
s = 'Musmusculuslet-7gstem-loop\nCCAGGCUGA GGUAGUAGUUUGUAC AGUUUGAGGGUCUAU GAUACCACCCGGUAC AGGAGA\nUAACUGU ACAGGCCACUGCCUU GCCAGG\nMusmusc uluslet-7istem-loop\nCUGGCUGAG GUAGUAGUUUGUGCU GUUGGUCGGGUUGUG ACAUUGCCCGCUGUG GAGAUA\nACUGCGC AAGCUACUGCCUUGC UAG\n'
s1 = s
for item in patt.findall(s) :
s1 = s1.replace(item , (item.replace(' \n', '')))[/code]Output:

>>> Musmusculuslet-7gstem-loop
CCAGGCUGAGGUAGUAGUUUGUACAGUUUGAGGGUCUAUGAUACCACCCGGUACAGGAGAUAACUGUACAGGCCACUGCCUUGCCAGG
Musmusculuslet-7istem-loop
CUGGCUGAGGUAGUAGUUUGUGCUGUUGGUCGGGUUGUGACAUUGCCCGCUGUGGAGAUAACUGCGCAAGCUACUGCCUUGCUAG

>>>

Step by step:

1. Import the 're' module
2. Define and compile the pattern to match substrings in your string: a character in the set 'ACGU' followed by '\n' followed by a character in the set 'ACGU'.
3. Use the compiled pattern object to find all occurrences of the matched patterns.
>>> patt.findall(s)
['A\nU', 'A\nA']
>>>
4. Use string method replace to replace each '\n' with "".

HTH

[bvdet]

You beat me to it ilikepython! :(

[moconno5]

Thanks for the guidance. My question is why are you creating a second string (s1), and running the pattern and replacing in that string? I'm still working my way around understanding regex's.

Mark

[bvdet]

Thanks for the guidance. My question is why are you creating a second string (s1), and running the pattern and replacing in that string? I'm still working my way around understanding regex's.

Mark

No reason other that to do further manipulations at the interactive prompt.