[FIX] Redundant input files now auto-generated

Fixes #4. Both protein and exon input datasets now only require a FASTA
file with all sequences, and a txt file with the IDs of target
sequences. Other necessary files are generated within the output
directory.

Note/possible bug: ENSACAP00000005077 now successfully assembles with
velvet using the 100K read dataset due to some yet unknown change.
Previously, cap3 tended to throw an error (see Issue #7) due to an empty
velvet assembly.