Thanks for all the help, Peter's and Hugo's methods worked well in
concatenating multiple lines into a single data structure!
S
On Fri, Feb 10, 2012 at 5:30 PM, Mark Lawrence <breamore...@yahoo.co.uk>wrote:
> On 10/02/2012 17:08, Peter Otten wrote:
>
>> Spyros Charonis wrote:
>>
>> Dear python community,
>>>
>>> I have a file where I store sequences that each have a header. The
>>> structure of the file is as such:
>>>
>>> sp|(some code) =>1st header
>>>>
>>> ATTTTGGCGG
>>> MNKPLOI
>>> .....
>>> .....
>>>
>>> sp|(some code) => 2nd header
>>>>
>>> AAAAAA
>>> GGGG ...
>>> .........
>>>
>>> ......
>>>
>>> I am looking to implement a logical structure that would allow me to
>>> group
>>> each of the sequences (spread on multiple lines) into a single string. So
>>> instead of having the letters spread on multiple lines I would be able to
>>> have 'ATTTTGGCGGMNKP....' as a single string that could be indexed.
>>>
>>> This snipped is good for isolating the sequences (=stripping headers and
>>> skipping blank lines) but how could I concatenate each sequence in order
>>> to get one string per sequence?
>>>
>>> for line in align_file:
>>>>>>
>>>>> ... if line.startswith('>sp'):
>>> ... continue
>>> ... elif not line.strip():
>>> ... continue
>>> ... else:
>>> ... print line
>>>
>>> (... is just OS X terminal notation, nothing programmatic)
>>>
>>> Many thanks in advance.
>>>
>>
>> Instead of printing the line directly collect it in a list (without
>> trailing
>> "\n"). When you encounter a line starting with">sp" check if that list is
>> non-empty, and if so print "".join(parts), assuming the list is called
>> parts, and start with a fresh list. Don't forget to print any leftover
>> data
>> in the list once the for loop has terminated.
>>
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>>
> The advice from Peter is sound if the strings could grow very large but
> you can simply concatenate the parts if they are not. For the indexing
> simply store your data in a dict.
>
> --
> Cheers.
>
> Mark Lawrence.
>
>
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> Tutor maillist - Tutor@python.org
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