hmmfetch: conflicting documentation

[nick-youngblut]

The hmmfetch docs state:

  -O     Output  HMM(s)  to  individual file(s) named <key> instead of standard output. With
              the -f option, this can result in many files being created.

Specifically:

With the -f option

indicates that -f can be used with -O, but when used together:

$ hmmfetch -O -f Pfam-A.hmm domain_keys.txt
Error in configuration: Option -O is incompatible with option(s) -o,-f,--index
Usage: hmmfetch [options] <hmmfile> <key>         (retrieves HMM named <key>)
Usage: hmmfetch [options] -f <hmmfile> <keyfile>  (retrieves all HMMs in <keyfile>)
Usage: hmmfetch [options] --index <hmmfile>       (indexes <hmmfile>)

To see more help on available options, do hmmfetch -h

...so it appears that -O cannot actually be used with -f. Either the error message is incorrect or the script docs are incorrect. It seems like -O should be compatible with -f, since I don't see the use of -O outside of usage with -f.

I'm using hmmer 3.3.2 bioconda

[cryptogenomicon]

That documentation error was fixed back in Sept 2019 and is not actually present in the 3.3.2 HMMER release.

(-O is not compatible with -f, currently; the error message is correct and the man page was wrong.)