Re: [Tutor] Concatenating multiple lines into one
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 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
>>> AGGCGG
>>> MNKPLOI
>>> .
>>> .
>>>
>>> sp|(some code) => 2nd header
>>> AA
>>> ...
>>> .
>>>
>>> ..
>>>
>>> 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 'AGGCGGMNKP' 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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>
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Re: [Tutor] Concatenating multiple lines into one
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
AGGCGG
MNKPLOI
.
.
sp|(some code) => 2nd header
AA
...
.
..
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 'AGGCGGMNKP' 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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Re: [Tutor] Concatenating multiple lines into one
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
> AGGCGG
> MNKPLOI
> .
> .
>
>>sp|(some code) => 2nd header
> AA
> ...
> .
>
> ..
>
> 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 'AGGCGGMNKP' 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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Re: [Tutor] Concatenating multiple lines into one
On Fri, Feb 10, 2012 at 5:38 PM, 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
> AGGCGG
> MNKPLOI
> .
> .
>
>>sp|(some code) => 2nd header
> AA
> ...
> .
>
> ..
>
> 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 'AGGCGGMNKP' 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.
>
> S.
>
python has a simple method to do that, str.join. Let me demonstrate it:
>>> a = ['a', 'b', 'c', 'd', 'e']
>>> ''.join(a)
'abcde'
>>> ' '.join(a) # with a space
'a b c d e'
>>> ' hello '.join(a) # go crazy if you want
'a hello b hello c hello d hello e'
so, it takes a list as an argument and joins the elements together in
a string. the string that you call join on is used as a separator
between the arguments. Pretty simple.
HTH,
Hugo
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[Tutor] Concatenating multiple lines into one
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
AGGCGG
MNKPLOI
.
.
>sp|(some code) => 2nd header
AA
...
.
..
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 'AGGCGGMNKP' 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.
S.
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