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Output FASTA sequence headers throw away some information

Right now, the headers look like this:
>7SLRNA;DF0000016.4;35.5;3e-10;+

In other words, you're only keeping family name ("target name"), accession number ("acc"), bitscore ("bits"), e-value ("e-value"), and strand ("+"). However, I would recommend also saving "ali-st" (the position in the query sequence at which the hit starts), "ali-en" (the position in the query sequence at which the hit ends, and "description of target"

File Not Found: ./Test/family

Dfam running... (this may take a while)
nhmmscan not found in $PATH at dfamscan.pl line 85.
Dfam finished!
Family Screen running...
Traceback (most recent call last):
  File "main.py", line 157, in <module>
    main()
  File "main.py", line 95, in main
    familyScreener(famFile, dfamRaw, dfamScreen1)
  File "/Users/niema/Desktop/TErex1.0/familyScreener.py", line 4, in familyScreener
    with open(family, 'r') as family:
IOError: [Errno 2] No such file or directory: './Test/family'

Probably exit with an error message if nhmmscan wasn't found in $PATH

Dfam running... (this may take a while)
**nhmmscan not found in $PATH at dfamscan.pl line 85.**
Dfam finished!
Bitscore Screen running...
Traceback (most recent call last):
  File "main.py", line 157, in <module>
    main()
  File "main.py", line 103, in main
    bitscore(dfamScreen1, bst, dfamScreen2)
  File "/Users/niema/Desktop/TErex1.0/bitscore.py", line 9, in bitscore
    with open(file) as dfamfile:
IOError: [Errno 2] No such file or directory: './Test/Output/Internal_Files/dfamRaw.out'