semvec/pypi-packages huggingface dataset:
buty-phyl 1.0.7
Inferring traits by 16S
License: MIT
Keywords: 16S,bacterial genomes,function,traits

# buty_phyl
## Introduction
* buty_phyl infers traits by 16S
* input: otu table (-t) and otu sequences (-s)
* requirement: mafft
* Optional: fasttree
![alt text](https://raw.githubusercontent.com/caozhichongchong/buty_phyl/master/Methodology.png)

## Install
`pip install buty_phyl`\
in preparation: `anaconda download caozhichongchong/buty_phyl`

## Availability
in preparation: https://anaconda.org/caozhichongchong/buty_phyl

https://pypi.org/project/buty_phyl

## How to use it
1. test the buty_phyl\
`buty_phyl --test`

2. try your data\
`buty_phyl -t your.otu.table -s your.otu.seqs`\
`buty_phyl -t your.otu.table -s your.otu.seqs -top 2000`

3. try different traits (default is butyrate production)\
predicting butyrate production\
`buty_phyl -t your.otu.table -s your.otu.seqs`\
or\
`buty_phyl -t your.otu.table -s your.otu.seqs --rt b`\
predicting sulfate reduction\
`buty_phyl -t your.otu.table -s your.otu.seqs --rt s`\
predicting nitrate reduction\
`buty_phyl -t your.otu.table -s your.otu.seqs --rt n`

4. use your own traits\
`buty_phyl -t your.otu.table -s your.otu.seqs --rs your.own.reference.16s --rt your.own.reference.traits`

* your.own.reference.16s is a fasta file containing the 16S sequences of your genomes\
\>Genome_ID1\
ATGC...\
\>Genome_ID2\
ATGC...

* your.own.reference.traits is a metadata of whether there's trait in your genomes (0 for no and 1 for yes)\
Genome_ID1   0\
Genome_ID1   1

## Results
The result dir of "Bayers_model":
* `filename.infertraits.txt`: the OTUs inferring as butyrate-producing bacteria (1.0), unknown bacteria (0.5), 
and non-butyrate-producing bacteria (0.0).
* `filename.infertraits.abu`: the total abundance of butyrate-producing bacteria.
* `filename.infertraits.commensal.abu`: the total abundance of commensal butyrate-producing bacteria.
* `filename.infertraits.pathogen.abu`: the total abundance of pathogenic butyrate-producing bacteria.
* `filename.infertraits.otu_table`: the otu_table of butyrate-producing bacteria.
* `filename.infertraits.commensal.otu_table`: the otu_table of commensal butyrate-producing bacteria.
* `filename.infertraits.pathogen.otu_table`: the otu_table of pathogenic butyrate-producing bacteria.
* `filename.bpbspecies.commensal.abu`: the abundance of commensal butyrate-producing species.
* `filename.bpbspecies.pathogen.abu`: the abundance of pathogenic butyrate-producing species.

The result dir of "Filtered_OTU":
* Some temp files of filtered OTUs, alignment, and tree.

## Copyright
Copyright: An Ni Zhang, Prof. Eric Alm, Alm Lab in MIT\
Citation: Not yet, coming soon!\
Contact: anniz44@mit.edu
metalparser 0.6.9b1
Python library for heavy metal song lyrics, albums, song titles and other info.
License: MIT
Requires Python: >=3.4.*, <=3.8
Keywords: heavy metal darklyrics lyrics song api

# metalparser

**metalparser** is a Python API for obtaining song lyrics from diverse lyrics websites.
At the moment there is only one supported website, which is [DarkLyrics](http://www.darklyrics.com/), an online database of lyrics for heavy metal music.


## Description

This library scrapes the corresponding website for the lyrics and returns results according to the used API.
**Kindly read the [disclaimer](https://github.com/lucone83/metal-parser/blob/master/DISCLAIMER.md) to ensure that your use complies with it**.


## Installation

_metalparser_ is distributed as a Python package, freely available on [PyPI](https://pypi.org/project/metalparser/) and can easily be installed via pip.
Given that you are using ```python >= 3.5```:

```
pip install metalparser
```

Alternatively, it can be manually installed by cloning this project on your local computer:

```
git clone https://github.com/lucone83/metal-parser.git
cd metal-parser
pip install .
```


## Documentation

The library comes (at the moment) with 6 APIs:

- get_artists_list()
- get_albums_info()
- get_songs_info()
- get_album_info_and_lyrics()
- get_albums_info_and_lyrics_by_artist()
- get_song_info_and_lyrics()

More complete docs regarding this project can be found on [readthedocs](https://metalparser.readthedocs.io/).

### Some examples

I recommend not to change the default settings regarding requests rate per minute and the wait time (3 secs) after each request.
DarkLyrics does not have a robots.txt, so they don't really like scraping. Be gentle! :)

```
from metalparser.darklyrics import DarkLyricsApi

api = DarkLyricsApi()
```

#### Retrieve the lyrics given a song and the corresponding artist:

```
song = 'under grey skies'
artist = 'kamelot'
lyrics = api.get_song_info_and_lyrics(song=song, artist=artist, lyrics_only=True)

print(lyrics)

```

#### Get all the songs of a specific album:

```
artist = 'pantera'
album = 'vulgar display of power'
songs_list = api.get_songs_info(artist, album=album, title_only=True)

print(songs_list)
```

#### Get all the albums of a specific artist:

```
artist = 'iron maiden'
albums_list = api.get_albums_info(artist=artist, title_only=True)

print(albums_list)
```


## Support

Currently the following python versions are supported:

- 3.4.*
- 3.5.*
- 3.6.*
- 3.7.*
- 3.8.*


## Thanks to

- res0nance and his [darklyrics project](https://github.com/res0nance/darklyrics) for inspiration;