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.
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