Added function get_hash to parse a csv and return a hash of IDs from the specified column
first commit
Modified get_hash to use the python csv parser

This meant rewriting the function (and tests) to work with files rather than with
file handles

I also added functionality to guess the delimiter character if it is not specified
Added a function to remove dots from sequence alignments
fixed bug causing remove_dots to also remove seq ids
added additional test for sequence ids

I also added additional assertions to the tests for each sequence and moved the alignment
specification out of the individual tests