`numberAntibodySeq`: support reading from STDIN

[merkys]

As is usual in command-line world, command-line tools should be able to read from STDIN. It would be nice if numberAntibodySeq could read from STDIN as well. I think --input command-line option could be removed altogether (since it is always needed), and numberAntibodySeq could just open and read all files given on the command line:

$ numberAntibodySeq light.fa # processes light.fa
$ numberAntibodySeq # reads from standard input

This is a wishlist item though, implementation of it can wait.

[Wolchear]

In the latest commit, I added the ability to use STDIN. So far, it has been tested only with manual input of a single sequence. I will close the issue later after conducting some additional tests. However, in theory, it should already work as expected

[merkys]

Thanks, the script now reads STDIN. However, running the script with file names (without STDIN redirection) does not work:

$ numberAntibodySeq tests/data/light/fasta91.fasta

If there are files given on the command line, STDIN should be ignored and the files should be processed instead. I am not sure if Getopt::Long leaves the file names in @ARGV, but at least Getopt::Long::Descriptive does so, thus it should be enough to check for empty @ARGV to decide whether STDIN or files in @ARGV need to be processed.