Alignment fails when transcript TSV has a final newline

[chrisbrickhouse]

Some programs add a newline to the end of a text file, meaning that some transcript files end with a blank line. Currently FAVE fails when these files are input because the blank line is seen as an error, but users may not find this easy to diagnose.

Current behavior

• main() in FAAValign.py calls aligner.check_transcript()
• aligner.check_transcript() calls aligner.TranscriptProcessor.check_transcription_file()
• for each line, L in the transcript file, ....check_transcription_file() calls ....check_transcription_format(L)
• if L contains only white space, that line is marked as needing deletion (ln 284)
• when aligner.align() is called, if there are any lines needing deletion, the alignment fails raising a ValueError (ln 164)

Desired behavior

• Ideally the alignment should not fail if the final line is a newline, if anything we may want to just (optionally?) remove lines containing only white space since they're already identified.
• The output should be more helpful in debugging what lines need to be removed. The program should at least give the (approx) line number to remove, and should be more helpful in its user-facing messaging. See Improve logging in TranscriptProcessor.check_transcription_file() #64