Groups | Search | Server Info | Keyboard shortcuts | Login | Register [http] [https] [nntp] [nntps]

Groups > comp.lang.python > #36173

Re: Need a specific sort of string modification. Can someone help?

Show all headers | View raw

In article <e480480d-f3b4-4491-969c-7d1843bf9e33@googlegroups.com>,
 Sia <hossein.asgharian@gmail.com> wrote:

> I have strings such as:
> 
> tA.-2AG.-2AG,-2ag
> or
> .+3ACG.+5CAACG.+3ACG.+3ACG

Some kind of DNA binding site?

A couple of questions.  Are the numbers always single digits?  How much 
data is there?  Are we talking a few hundred 20-character strings, or 
all of Genbank?

> The plus and minus signs are always followed by a number (say, i). I want 
> python to find each single plus or minus, remove the sign, the number after 
> it and remove i characters after that. So the two strings above become:
> 
> tA..,
> and
> ...

If I follow your description properly, the last output should be "...." 
(4 dots), right?  This looks like it should work.  I'm sure there's more 
efficient ways to do it, but for small inputs, this should be ok.˜

The general pattern here is a state machine.  It's a good pattern to 
learn if you're going to be doing any kind of sequence analysis.  See, 
for example, http://en.wikipedia.org/wiki/State_machine.

# Build up the new string as a list (for efficiency)                                                
new = []

# Keep track of what state we're in.  The three possible states                                     
# are 1) scanning for a region to be deleted, 2) looking for the                                    
# number, and 3) reading past the letters to be deleted.                                            
SCANNING = 1
NUMBER = 2
DROPPING = 3
state = SCANNING

# If we are in state DROPPING, dropcount is the number of                                           
# letters remaining to be dropped.                                                                  
dropcount = 0

old = '.+3ACG.+5CAACG.+3ACG.+3ACG'
for c in old:
    if state == SCANNING:
        if c in '+-':
            state = NUMBER
        else:
            new.append(c)

    elif state == NUMBER:
        # Assume the counts are all single digits.  If not, then
        # we'll need a 4th state for accumulating the digits.  
        dropcount = int(c)
        state = DROPPING

    else:
        assert state == DROPPING
        dropcount -= 1
        if dropcount == 0:
            state = SCANNING

print ''.join(new)

Back to comp.lang.python | Previous | Next — Previous in thread | Next in thread | Find similar | Unroll thread

Thread

Need a specific sort of string modification. Can someone help? Sia <hossein.asgharian@gmail.com> - 2013-01-05 00:35 -0800
  Re: Need a specific sort of string modification. Can someone help? Frank Millman <frank@chagford.com> - 2013-01-05 11:15 +0200
  Re: Need a specific sort of string modification. Can someone help? Chris Angelico <rosuav@gmail.com> - 2013-01-05 20:27 +1100
    Re: Need a specific sort of string modification. Can someone help? Roy Smith <roy@panix.com> - 2013-01-05 09:30 -0500
      Re: Need a specific sort of string modification. Can someone help? Chris Angelico <rosuav@gmail.com> - 2013-01-06 01:47 +1100
        Re: Need a specific sort of string modification. Can someone help? Roy Smith <roy@panix.com> - 2013-01-05 10:03 -0500
          Re: Need a specific sort of string modification. Can someone help? Chris Angelico <rosuav@gmail.com> - 2013-01-06 02:09 +1100
            Re: Need a specific sort of string modification. Can someone help? Roy Smith <roy@panix.com> - 2013-01-05 10:38 -0500
              Re: Need a specific sort of string modification. Can someone help? Chris Angelico <rosuav@gmail.com> - 2013-01-06 02:57 +1100
              Re: Need a specific sort of string modification. Can someone help? Ian Kelly <ian.g.kelly@gmail.com> - 2013-01-05 13:04 -0700
              Re: Need a specific sort of string modification. Can someone help? Chris Angelico <rosuav@gmail.com> - 2013-01-06 07:32 +1100
                Re: Need a specific sort of string modification. Can someone help? Roy Smith <roy@panix.com> - 2013-01-05 15:47 -0500
                Re: Need a specific sort of string modification. Can someone help? Roy Smith <roy@panix.com> - 2013-01-06 12:28 -0500
                Re: Need a specific sort of string modification. Can someone help? Steven D'Aprano <steve+comp.lang.python@pearwood.info> - 2013-01-06 23:19 +0000
  Re: Need a specific sort of string modification. Can someone help? Roy Smith <roy@panix.com> - 2013-01-05 09:12 -0500
  Re: Need a specific sort of string modification. Can someone help? Tim Chase <python.list@tim.thechases.com> - 2013-01-05 11:24 -0600
  Re: Need a specific sort of string modification. Can someone help? Tim Chase <python.list@tim.thechases.com> - 2013-01-05 12:49 -0600
  Re: Need a specific sort of string modification. Can someone help? Mitya Sirenef <msirenef@lightbird.net> - 2013-01-06 01:32 -0500
  Re: Need a specific sort of string modification. Can someone help? Mitya Sirenef <msirenef@lightbird.net> - 2013-01-06 14:53 -0500
  Re: Need a specific sort of string modification. Can someone help? Nick Mellor <thebalancepro@gmail.com> - 2013-01-06 18:48 -0800
  Re: Need a specific sort of string modification. Can someone help? Nick Mellor <thebalancepro@gmail.com> - 2013-01-06 19:40 -0800
    Re: Need a specific sort of string modification. Can someone help? Nick Mellor <thebalancepro@gmail.com> - 2013-01-06 21:28 -0800
  Re: Need a specific sort of string modification. Can someone help? Nick Mellor <thebalancepro@gmail.com> - 2013-01-06 21:30 -0800
  Re: Need a specific sort of string modification. Can someone help? John Ladasky <john_ladasky@sbcglobal.net> - 2013-01-06 21:39 -0800
  Re: Need a specific sort of string modification. Can someone help? Nick Mellor <thebalancepro@gmail.com> - 2013-01-06 23:07 -0800

csiph-web