Just to answer your question about sorting a long file that doesn't fit into the memory - you'll need to use some external sorting algorithm such as Merge sort. The process is roughly following:
Partition the input into several parts that fit into memory and can be sorted using standard in-memory sorting algorithms (e.g. 100 MB or larger - you'll need to keep ~4 parts in memory at once). Sort all the parts and write them back to disk.
Read two parts from the disk (they are both sorted) and merge them, which can be done just by simultaneously iterating over the two inputs. Write the merged data set to another place in the disk. Note that you don't need to read the whole part into memory - just read it/write it in blocks as you go.
Repeat merging of parts until you have only a single part (which will be sorted file with all the data from your original input data set).
You mentioned that the data is partially sorted already, so it would be a good idea to pick some algorithm for in-memory sorting (in the first phase) that is efficient in this case. You can see some suggestions in this question (though I'm not sure if the answer will be the same for very large data sets - and it depends on how much partially sorted the input is).
