Extract-ORFs.py mistranslates lowercase letters

[Tali]

In a sequence with mixed uppercase and lowercase letters, extract-ORFs.py output has incorrect translations only for the sites of lowercase letters. (Even though the translations function of dark/reads.py translate a sequence with mixed upper and lower case letters correctly)

[Tali]

The issue was in the reverseComplemented method in reads.py, where lower case letters were not found in the complement table. So instead of translation of the lower case letters to the values in the table, the python string translation method leaves these strings untouched, and the reverse complement is incorrect where there are lower case letters.