PyRice - a Python package for query rice gene information

PrePrint version of our paper
Online documentation
How to cite : Bioinformatics Application notes

Install from source:

Clone project from Github:

git clone https://github.com/SouthGreenPlatform/PyRice.git

Install from PyPI

If you install PyRice on your local machine:
```
pip install pyrice
```
Now there is only version available (should use the latest version):
- Verrsion 0.2.0: Update reference for gene from Oryzabase. Add 2 new databases PlantTFDB for PyRice
  - If you install PyRice on your local machine, please follow these steps:
    - Please check carefully the current version of Chrome on your computer before downloading
    - Download the Chrome driver.
    - After downloading, fill the file path lead to Chrome driver before querying:
```
from pyrice import utils
utils.chrome_path = "the path of your Chrome driver"
```
- Version 0.1.9: PyRice on Google Colab or other cloud platform. Updating the change output format.
- Version 0.1.8: Addition of crawling JavaScript data with Selenium.

IN PROCESS: If you want to install the newest demo of PyRice:

!pip install -i https://test.pypi.org/simple/ pyrice

To see demo of package: Demo_PyRice.ipynb

Instruction

Example of system search_gene

from pyrice.multi_query import MultiQuery

query = MultiQuery()
result = query.search_on_chromosome(chro="chr01", start_pos="1", end_pos="20000",
                                    number_process = 4, dbs="all", save_path="./result/")
print("Output database:", result)

Output database:
{'OsNippo01g010050': {
    'msu7Name': {'LOC_Os01g01010'},
    'raprepName': {'Os01g0100100'},
    'contig': 'chr01', 'fmin': 2982,
    'fmax': 10815},
'OsNippo01g010150': {
    'msu7Name': {'LOC_Os01g01019'},
    'raprepName': {'Os01g0100200'},
    'contig': 'chr01',
    'fmin': 11217,
    'fmax': 12435},
...
'OsNippo01g010300': {
    'msu7Name': {'LOC_Os01g01040'},
    'raprepName': {'Os01g0100500'},
    'contig': 'chr01',
    'fmin': 16398,
    'fmax': 20144}
}

Example of system query_by_chromosome

from pyrice.multi_query import MultiQuery

query = MultiQuery()
result = query.query_by_chromosome(chro="chr01", start_pos="1", end_pos="20000", 
                                   number_process = 4, multi_processing=True,
                                   multi_threading=True, dbs="all")

query.save(result, save_path="./result/",
           format=["csv", "html", "json", "pkl"], hyper_link=False)
print("Output database:", result)

Output database:
{'OsNippo01g010050': {
    'rapdb': {
        'Locus_ID': 'Os01g0100100',
        'Description': 'RabGAP/TBC domain containing protein.',
            'Oryzabase Gene Name Synonym(s)': 'Molecular Function: Rab GTPase activator activity (GO:0005097)',
            ...},
        'gramene': {
            '_id': 'Os01g0100100',
            'name': 'Os01g0100100',
            'biotype': 'protein_coding',
            ...},
        ...},
    'OsNippo01g010150': {
        'rapdb': {...},
        'gramene': {...},
        ...},
    ...
}

Example of system query_by_ids

from pyrice.multi_query import MultiQuery

query = MultiQuery()
result = query.query_by_ids(ids=["Os08g0164400", "Os07g0586200"],
                            locs=["LOC_Os10g01006", "LOC_Os07g39750"],
                            irics=["OsNippo01g010050", "OsNippo01g010300"],
                            number_process = 4, multi_processing=True, multi_threading=True, dbs="all")
query.save(result, save_path = "./result/",
           format=["csv", "html", "json", "pkl"], hyper_link=False)   
print("Output database:",result)

Output database:
{'OsNippo01g010050': {
        'rapdb': {
            'Locus_ID': 'Os01g0100100',
            'Description': 'RabGAP/TBC domain containing protein.',
            'Position': '',
            ...},
        'ic4r': {
            'Anther_Normal': {'expression_value': '0.699962'},
            'Anther_WT': {'expression_value': '13.9268'},
            ...},
        ...},
    'OsNippo01g010300': {
        'rapdb': {...},
        'ic4r': {...},
        ...},
    ...
}

Example of system query_new_database

from pyrice.multi_query import MultiQuery

query = MultiQuery()
result = query.query_new_database(atts=['AT4G32150'], number_process= 4,
                                  multi_processing=True,multi_threading=True,dbs=['planteome'])
query.save(result, save_path="./result/",
           format=["csv", "html", "json", "pkl"], hyper_link=False) 
print("Output database:",result)

Output database:
{'AT4G32150':
    {'planteome':{
        'service': '/api/search/annotation', 
        'status': 'success',
        'arguments': {},
        'comments': ['Results found for: annotation; queries: ; filters: '],
        'data': [{...}]
        ...
   }
   ...
}

Example of Build Dictinary Module

from pyrice.build_dictionary import update_gene_dictionary, update_rapdb_oryzabase

update_gene_dictionary()
update_local_database(rapdb_url, oryzabase_url)

Example of Search Module

You have to save file as .pkl and re-load it again to use search function.

from pyrice import utils 
import pandas as pd

df1 = pd.read_pickle("./result1/data/db.pkl")
df2 = pd.read_pickle("./result2/data/db.pkl")
df = pd.concat([df1,df2])
result = utils.search(df,"Amino acid ")

Example of SQL Query

You can execute a SQL query over a pandas dataframe. You have to install package Pandasql. The variable name is same with the table name in SQL query. Next, follow the code below to run SQL query:

import pandas as pd
from pandasql import sqldf

data = pd.read_pickle("./result/data/db.pkl")
data = data.astype(str)
sql = "SELECT * FROM data WHERE `oryzabase.CGSNL Gene Symbol` = 'TLP27' or `gramene.system_name` = 'oryza_sativa'"
pysqldf = lambda q: sqldf(q, globals())
print(pysqldf(sql))

The variable name must be same with the table name in SQL query.

List of supported databases

Database_name: keywords

Oryzabase : oryzabase
RapDB : rapdb
Gramene : gramene
IC4R : ic4r
SNP-Seek : snpseek
Funricegene : funricegene_genekeywords, funricegene_faminfo, funricegene_geneinfo
MSU : msu
EMBL-EBI Expression Atlas : embl_ebi
GWAS-ATLAS : gwas_atlas
Planteome : planteome
AgroLD : planttfdb_tf, planttfdb_target_gene

Keywords are value of arguments in query module.

List of exception

Server Exception

Throw when server response code is not 200.

Throw with the corresponding server response code.
Internet Connection Exceptioin

Throw requests.exceptions.RequestException

requests module exception.
Timeout Exception

Throw requests.exceptions.Timeout

requests module exception.
Database Exception

Throw when database description is not found.

SouthGreenPlatform / PyRice

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