Question

My Friends,

I spent quite some time on this one… but cannot yet figure out a better way to do it. I am coding in python, by the way.

So, here is a line of text in a file I am working with, for example:

“>ref|ZP_01631227.1| 3-dehydroquinate synthase [Nodularia spumigena CCY9414]…”

How can I extract the two strings “ZP_01631227.1” and “Nodularia spumigena CCY9414” from the line?

The pairs of “| |” and brackets are like markers so we know we want to get the strings in between the two…

I guess I can probably loop over all the characters in the line and do it the hard way. It just takes so much time… Wondering if there is a python library or other smart ways to do it nicely?

Thanks to all!

Answer 1

>>> for line in open("file"):
...     if "|" in line:
...         whatiwant_1=line.split("|")[1]
...         if "[" in line:
...             whatiwant_2=line.split("[")[1].split("]")[0]
...
>>> print whatiwant_1 , whatiwant_2
ZP_01631227.1 Nodularia spumigena CCY9414