Standard input incorrect when including subcommand flags

[btski]

I tried to use cat test.fasta | smof grep -f test.txt and got a "ShitInput" error. This only occurs when a subcommand flag is invoked when trying to pipe from standard input. I added default=sys.stdin to all file arguments. I then encountered TypeError: can only concatenate list (not "_io.TextIOWrapper") to list in the main function. This was simply resolved by overwriting fh entirely instead of appending. Since the default value of fh is now standard input, appending text is not compatible. I also considered the additional conditionals to be unnecessary.

Created pull request #5 with proposed solution. Tested with the following:
cat test.fasta | smof grep -f test.txt
smof grep -f test.txt test.fasta

[arendsee]

Ah, quite right. I'll accept the pull request. Thanks!

I should probably remove that shit also.