Closed nhartwic closed 10 months ago
Noted.
To be clear, I'm referring to the output that is already tabular, available from "--tblout" or "--domtblout". Is there any reason why these tables use inconsistent field separators?
Yes, there is. The reasons have been discussed at length already elsewhere. So has the ease of parsing these files with pandas, python, perl, awk, or whatever. I won't have anything else to say about it here, sorry; this is not the place for the discussion.
Fair enough. See you around.
If you're space-delimiting output and claiming it's parser friendly while neither quoting multi-word column names nor replacing their internal spaces with hyphens or underscores, I find it hard to believe your stance "I still stubbornly feel that space-delimited files are just as easily parsed as tab-delimited files." is well thought-out.
Noted.
hmmscan output is needlessly annoying to parse. It is whitespace delimited, but some whitespace, particularly whitespace in "description of target" does not act as a delimiter. While proper escaping or quoting could resolve this, a practical sollution would involve just switching to tab as a separator.
For backwards compatibility, outputting tsv may need to be enabled via a flag.