{ "info": { "author": "Pierre Larmande, Quan Do", "author_email": "pierre.larmande@ird.fr, dohongquan1612@gmail.com", "bugtrack_url": null, "classifiers": [ "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.6" ], "description": "\n# Python query engine for PyRice package\n\n## Instruction for install package on git (on products branch only)\n\n- Clone project on PyRice `master` branch\n ```\n git clone https://github.com/SouthGreenPlatform/PyRice.git\n ```\n## Instruction for install package on pypi\n\n- Use pip to install package PyRice\n ```\n pip install pyrice\n ```\n\n ## Instruction \n\n### Example of system search_gene\n\n```py\nfrom pyrice.multi_query import MultiQuery\n\nquery = MultiQuery()\nresult = query.search_on_chromosome(chro=\"chr01\", start_pos=\"1\", end_pos=\"20000\",\n number_process = 4, dbs=\"all\", save_path=\"./result/\")\nprint(\"Output database:\", result)\n```\n```bash\nOutput database:\n{'OsNippo01g010050': {\n 'msu7Name': {'LOC_Os01g01010'},\n 'raprepName': {'Os01g0100100'},\n 'contig': 'chr01', 'fmin': 2982,\n 'fmax': 10815},\n'OsNippo01g010150': {\n 'msu7Name': {'LOC_Os01g01019'},\n 'raprepName': {'Os01g0100200'},\n 'contig': 'chr01',\n 'fmin': 11217,\n 'fmax': 12435},\n...\n'OsNippo01g010300': {\n 'msu7Name': {'LOC_Os01g01040'},\n 'raprepName': {'Os01g0100500'},\n 'contig': 'chr01',\n 'fmin': 16398,\n 'fmax': 20144}\n}\n```\n\n### Example of system query_by_chromosome\n\n```py\nfrom pyrice.multi_query import MultiQuery\n\nquery = MultiQuery()\nresult = query.query_by_chromosome(chro=\"chr01\", start_pos=\"1\", end_pos=\"20000\", \n number_process = 4, multi_processing=True,\n multi_threading=True, dbs=\"all\")\n\nquery.save(result, save_path=\"./result/\",\n format=[\"csv\", \"html\", \"json\", \"pkl\"], hyper_link=False)\nprint(\"Output database:\", db)\n```\n```bash\nOutput database:\n{'OsNippo01g010050': {\n 'rapdb': {\n 'Locus_ID': 'Os01g0100100',\n 'Description': 'RabGAP/TBC domain containing protein.',\n 'Oryzabase Gene Name Synonym(s)': 'Molecular Function: Rab GTPase activator activity (GO:0005097)',\n ...},\n 'gramene': {\n '_id': 'Os01g0100100',\n 'name': 'Os01g0100100',\n 'biotype': 'protein_coding',\n ...},\n ...},\n 'OsNippo01g010150': {\n 'rapdb': {...},\n 'gramene': {...},\n ...},\n ...\n}\n```\n\n### Example of system query_by_ids\n```py\nfrom pyrice.multi_query import MultiQuery\n\nquery = MultiQuery()\nresult = query.query_by_ids(ids=[\"Os08g0164400\", \"Os07g0586200\"],\n locs=[\"LOC_Os10g01006\", \"LOC_Os07g39750\"],\n irics=[\"OsNippo01g010050\", \"OsNippo01g010300\"],\n number_process = 4, multi_processing=True, multi_threading=True, dbs=\"all\")\nquery.save(result, save_path = \"./result/\",\n\t format=[\"csv\", \"html\", \"json\", \"pkl\"], hyper_link=False) \nprint(\"Output database:\",result) \n```\n```bash\nOutput database:\n{'OsNippo01g010050': {\n 'rapdb': {\n 'Locus_ID': 'Os01g0100100',\n 'Description': 'RabGAP/TBC domain containing protein.',\n 'Position': '',\n ...},\n 'ic4r': {\n 'Anther_Normal': {'expression_value': '0.699962'},\n 'Anther_WT': {'expression_value': '13.9268'},\n ...},\n ...},\n 'OsNippo01g010300': {\n 'rapdb': {...},\n 'ic4r': {...},\n ...},\n ...\n} \n```\n### Example of system query_new_database\n```py\nfrom pyrice.multi_query import MultiQuery\n\nquery = MultiQuery()\nresult = query.query_new_database(atts=['TRAES3BF001000010CFD'], number_process= 4,\n multi_processing=True,multi_threading=True,dbs=['urgi'])\nquery.save(result, save_path=\"./result/\",\n format=[\"csv\", \"html\", \"json\", \"pkl\"], hyper_link=False) \nprint(\"Output database:\",result) \n```\n```bash\nOutput database:\n{'TRAES3BF001000010CFD':\n {'urgi':{\n 'recordsTotal': 1177800,\n 'recordsFiltered': 1177800,\n 'draw': None,\n ...}\n }\n}\n```\n### Example of Build Dictinary Module\n```py\nfrom pyrice.build_dictionary import update_gene_dictionary,update_rapdb_oryzabase\n\nupdate_gene_dictionary()\nupdate_rapdb_oryzabase(rapdb_url, oryzabase_url)\n```\n\n### Example of Search Module\nYou have to save file as .pkl and re-load it again to use search function.\n\n```py\nfrom pyrice.utils import search\nimport pandas as pd\n\ndf1 = pd.read_pickle(\"./result1/data/db.pkl\")\ndf2 = pd.read_pickle(\"./result2/data/db.pkl\")\ndf = pd.concat([df1,df2])\nresult = search(df,\"Amino acid \")\n```\n\n## List of supported database\n\n* Oryzabase\n* RapDB\n* Gramene\n* IC4R\n* SNP-Seek\n* Funricegene\n* MSU\n\n## List of exception\n\n* Server Exception\n\n Throw when server response code is not 200.\n\n Throw with the corresponding server response code.\n* Internet Connection Exceptioin\n\n Throw requests.exceptions.RequestException\n\n *requests* module exception.\n* Timeout Exception\n\n Throw requests.exceptions.Timeout\n\n *requests* module exception.\n* Database Exception\n\n Throw when database description is not 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