python - Regular expression matching a multiline block of text

Question

I'm having a bit of trouble getting a Python regex to work when matching against text that spans multiple lines. The example text is (' ' is a newline)

some Varying TEXT



DSJFKDAFJKDAFJDSAKFJADSFLKDLAFKDSAF

[more of the above, ending with a newline]

[yep, there is a variable number of lines here]



(repeat the above a few hundred times).

I'd like to capture two things: the 'some_Varying_TEXT' part, and all of the lines of uppercase text that comes two lines below it in one capture (i can strip out the newline characters later). I've tried with a few approaches:

re.compile(r"^>(w+)$$([.$]+)^$", re.MULTILINE) # try to capture both parts
re.compile(r"(^[^>][ws]+)$", re.MULTILINE|re.DOTALL) # just textlines

and a lot of variations hereof with no luck. The last one seems to match the lines of text one by one, which is not what I really want. I can catch the first part, no problem, but I can't seem to catch the 4-5 lines of uppercase text. I'd like match.group(1) to be some_Varying_Text and group(2) to be line1+line2+line3+etc until the empty line is encountered.

If anyone's curious, its supposed to be a sequence of aminoacids that make up a protein.

Answer 1

Try this:

re.compile(r"^(.+)
((?:
.+)+)", re.MULTILINE)

I think your biggest problem is that you're expecting the ^ and $ anchors to match linefeeds, but they don't. In multiline mode, ^ matches the position immediately following a newline and $ matches the position immediately preceding a newline.

Be aware, too, that a newline can consist of a linefeed ( ), a carriage-return ( ), or a carriage-return+linefeed ( ). If you aren't certain that your target text uses only linefeeds, you should use this more inclusive version of the regex:

re.compile(r"^(.+)(?:
|
?)((?:(?:
|
?).+)+)", re.MULTILINE)

BTW, you don't want to use the DOTALL modifier here; you're relying on the fact that the dot matches everything except newlines.