opened
trvinh
username_0
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## Description
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The previous rank indexing function did not work correctly while sorting the noranks (undefined ranks). This has been fixed now.

## Related Issue
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## Example
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improve taxonomy rank indexing
issue
created
trvinh
username_0
Hi @username_1 
sorry, but I don't know how to solve the issue with `vcr`. I tested the function `class2tree` using the test file `test-class2tree.R`, it worked fine by commenting out the `vcr::use_cassette` function.
comment
created
trvinh
username_0
@username_1 removing the cassette files solved the issue, the test for `class2tree` passed. But the travis-ci has another error: `The command "sudo add-apt-repository -y "ppa:marutter/rrutter3.5"" failed and exited with 1 during .` . I think it has nothing to do with the taxize package, right?
comment
created
sckott
username_1
thanks for fixing cassettes 

for the travis failure, i restarted it, its a server system dependency problem - probably intermittent

please answer the above too: Can you please explain the problem in more detail? I'm not sure what problem this is solving.
comment
created
trvinh
username_0
$`Streptomyces coelicolor`
                              name          rank      id
1               cellular organisms       no rank  131567
2                         Bacteria  superkingdom       2
3              Terrabacteria group       no rank 1783272
4                   Actinobacteria        phylum  201174
5                   Actinobacteria         class    1760
6                 Streptomycetales         order   85011
7                Streptomycetaceae        family    2062
8                     Streptomyces         genus    1883
9  Streptomyces albidoflavus group species group 1477431
10         Streptomyces coelicolor       species    1902
```

However, the old `rank_indexing` places it way before **phylum** (pos 26 vs 34). With the new function, **norank_1783272** (pos 35) can be placed correctly between **phylum**  and **superkingdom** (pos 34 and 40). 

P.S.: the changes in other functions (`get_rank`, `get_name` and `taxonomy_table_creator`) are just code formatting :)

P.P.S.: the travis-ci still failed because of other cassettes, should I also removed them and run the test agains for the whole package?
comment
created
sckott
username_1
- okay, thanks for the explanation of the issue. makes sense now. 
- okay on formatting changes
- don't worry about tests for other fxns

Looks good to me, thanks for the fix!
comment