Closed hannesbecher closed 5 years ago
I added a small note to the docstrings for each script stating that more details for the arguments, including short vs. long forms and hyphenation, can be found by reading the help message:
For more details on script arguments, type: run_hyde.py -h
This is the help message I get for the run_hyde.py
script:
usage: run_hyde.py [-h] -i -m -o -n -t -s [-tr] [-p]
[--prefix] [-q] [--ignore_amb_sites]
Options for run_hyde.py
optional arguments:
-h, --help show this help message and exit
required arguments:
-i, --infile name of the data input file
-m, --map map of individuals to taxa
-o, --outgroup name of the outgroup (only one accepted)
-n, --num_ind number of individuals in data matrix
-t, --num_taxa number of taxa (species, OTUs)
-s, --num_sites number of sites in the data matrix
additional arguments:
-tr, --triples table of triples to be analyzed
-p, --pvalue p-value cutoff for test of significance [default=0.05]
--prefix prefix appended to output files [default=hyde]
-q, --quiet suppress printing to stdout
--ignore_amb_sites ignore missing/ambiguous sites
Looks great, thank you!
Hi Paul, For me, the docstring of
run_hyde.py
looks like this:This is not very helpful if one wants to figure out the one-letter names of the arguments. They could be stated, too, I think (in particular as they are used in the examples). Also, it would be helpful to remind the user that when using the full-lengh argument names, two hyphens are needed. Thanks, Hannes