Here are a few thoughts.

This algorithm sounds like a fold, i.e. a reduction.  You're iterating over 
a sequence while accumulating into a collection.  A collection of 
collections, in this case.

You're starting value for the fold might be this:

{:first {}, :second {}}

You're reducing function would consume each line, adding it into the above 
map of maps.  Updating the map-of-maps might be done through something like 
update or update-in:

(update-in maps [:first] add-by-key-and-value line)


Here add-by-key-and-value is a function that I've left undefined.  It takes 
a single map and a line and adds that line by key and value.  (Since the 
definition of key and value were omitted from the example, I've delegated 
them to said function.)

Hence, the whole thing might look like this (untested!):

(defn _______ [lines]
  (let [rf (fn [maps line]
             (condp re-matches line
               #"some-regex"    (update-in maps [:first] 
add-by-key-and-value line)
               #"another-regex" (update-in maps [:second] 
add-by-key-and-value key line)))]
    (reduce rf {:first {}, :second {}} lines)))


P.S.  I'm using update-in here a bit unnecessarily.  update would work 
perfectly fine, but I thought it would be better to show you the general 
form which can update maps to any depth.

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