biopython / biopython/biopython

Bio.Emboss.Applications-module: FProtDistCommandline has wrong options

Open
#2,069 1 comment 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
5.2k
Forks
1.9k
Avg merge
2d 6h
Merged PRs (30d)
11

Description

### Setup
```python
[GCC 7.3.0]
CPython
Linux-4.4.0.17134-Microsoft-x86_64-with-debian-stretch-sid
1.70
```

when trying to run fprotdist via the [Bio.Emboss.Applications-module](https://biopython.org/DIST/docs/api/Bio.Emboss.Applications-module.html) as follows:
`cline = FProtDistCommandline(sequence = "example.phy", model = "s", gamma = "g")`
, I keep getting the error `ValueError: Option name model was not found`, even though this "model" is definitively an (important) [option for this tool](http://bioinfo.nhri.org.tw/cgi-bin/emboss/help/fprotdist).

Looking into the [source code of FProtDdistCommandLine](https://biopython.org/DIST/docs/api/Bio.Emboss.Applications-pysrc.html#FProtDistCommandline.__init__), it seems clear that this was copy-pasted from FDnaDistCommandline at some point, but then forgotten and not adjusted (also i am pretty sure the option "catergories", found there, must be a typo). The options are all suitable for DNA sequences and NOT for proteinsequences.

I guess this should either be corrected, or the function should be deleted in order to avoid confusion.

### Expected behaviour

FProtDistCommandline recognizes all options for fprotdist

### Actual behaviour

Instead, FprotDistCommandline recognizes only the options for fdnadist (Not suitable)

### Steps to reproduce

Try using FProtDistCommandline and specifying the model to use as per [these instructions](http://bioinfo.nhri.org.tw/cgi-bin/emboss/help/fprotdist)

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.