[Tutor] Concatenating multiple lines into one

[Spyros Charonis]

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.

S.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/tutor/attachments/20120210/32284f53/attachment-0001.html>