Get SMARTER samples list

This notebook is used to get the list of samples that are used in the SMARTER dataset. Here’s another example of how to use the SheepEndPoints class to get the list of samples:

import pandas as pd

from tskitetude import get_data_dir
from tskitetude.smarterapi import SheepEndpoint

Collecting all samples (no parameters are provided using the SheepEndPoints.get_samples() method:

sheep_api = SheepEndpoint()

data = sheep_api.get_samples()
page = 1
sheep = pd.DataFrame(data["items"])

while data["next"] is not None:
    data = sheep_api.get_samples(page=page+1,)
    df_page = pd.DataFrame(data["items"])
    page = data["page"]
    sheep = pd.concat([sheep, df_page], ignore_index=True)

sheep.info()

<class 'pandas.core.frame.DataFrame'>
RangeIndex: 11837 entries, 0 to 11836
Data columns (total 17 columns):
 #   Column       Non-Null Count  Dtype  
---  ------       --------------  -----  
 0   _id          11837 non-null  object 
 1   breed        11837 non-null  object 
 2   breed_code   11837 non-null  object 
 3   chip_name    11837 non-null  object 
 4   country      11837 non-null  object 
 5   dataset_id   11837 non-null  object 
 6   locations    9295 non-null   object 
 7   metadata     9298 non-null   object 
 8   original_id  11837 non-null  object 
 9   phenotype    1582 non-null   object 
 10  smarter_id   11837 non-null  object 
 11  species      11837 non-null  object 
 12  type         11837 non-null  object 
 13  father_id    279 non-null    object 
 14  mother_id    63 non-null     object 
 15  sex          3054 non-null   float64
 16  alias        2059 non-null   object 
dtypes: float64(1), object(16)
memory usage: 1.5+ MB

Inspecting the first 5 samples of the dataframe:

sheep.head()

	_id	breed	breed_code	chip_name	country	dataset_id	locations	metadata	original_id	phenotype	smarter_id	species	type	father_id	mother_id	sex	alias
0	{'$oid': '66544dd515d202ad5f28dc8e'}	Texel	TEX	IlluminaOvineSNP50	Uruguay	{'$oid': '604f75a61a08c53cebd09b67'}	{'coordinates': [[-54.79980235632396, -32.8596...	{'gps_2': 'https://www.google.com/maps/place/E...	20181210002	{'purpose': 'Meat'}	UYOA-TEX-000000001	Ovis aries	background	NaN	NaN	NaN	NaN
1	{'$oid': '66544dd615d202ad5f28dc8f'}	Texel	TEX	IlluminaOvineSNP50	Uruguay	{'$oid': '604f75a61a08c53cebd09b67'}	{'coordinates': [[-54.79980235632396, -32.8596...	{'gps_2': 'https://www.google.com/maps/place/E...	20181210003	{'purpose': 'Meat'}	UYOA-TEX-000000002	Ovis aries	background	NaN	NaN	NaN	NaN
2	{'$oid': '66544dd615d202ad5f28dc90'}	Texel	TEX	IlluminaOvineSNP50	Uruguay	{'$oid': '604f75a61a08c53cebd09b67'}	{'coordinates': [[-54.79980235632396, -32.8596...	{'gps_2': 'https://www.google.com/maps/place/E...	20181210005	{'purpose': 'Meat'}	UYOA-TEX-000000003	Ovis aries	background	NaN	NaN	NaN	NaN
3	{'$oid': '66544dd715d202ad5f28dc91'}	Texel	TEX	IlluminaOvineSNP50	Uruguay	{'$oid': '604f75a61a08c53cebd09b67'}	{'coordinates': [[-54.79980235632396, -32.8596...	{'gps_2': 'https://www.google.com/maps/place/E...	20181210006	{'purpose': 'Meat'}	UYOA-TEX-000000004	Ovis aries	background	NaN	NaN	NaN	NaN
4	{'$oid': '66544dd715d202ad5f28dc92'}	Texel	TEX	IlluminaOvineSNP50	Uruguay	{'$oid': '604f75a61a08c53cebd09b67'}	{'coordinates': [[-54.79980235632396, -32.8596...	{'gps_2': 'https://www.google.com/maps/place/E...	20181210008	{'purpose': 'Meat'}	UYOA-TEX-000000005	Ovis aries	background	NaN	NaN	NaN	NaN

Collect some useful information about the samples into a CSV file:

sheep[["smarter_id", "breed", "breed_code", "phenotype"]].to_csv(
    get_data_dir() / "smarter_sheep_list.csv", index=False)