NCBI-Companion 2.1.1

NCBI_Companion assists you to build a reference database with a fasta and a mapping file through Genbank

NCBI_Companion

Introduction

NCBI_Companion targets to construct databases, generate a fasta file and a taxonomy mappingusing by using Genbank Entrez utilities.

Biopython copyright belongs to Biopython teams Entrez copyright belongs to NCBI entrez teams

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Contents

class LoadSpecies

This class is to used fetch species name contains in csv file, text file, excel or fasta file.

Functions

function names	parameters	Return
LoadSpecies	species_input, species_output, ifout	initialize
ReadSpeciesFile_text	None	a list (if specified, a table in local directory)
ReadSpeciesFile_excel	sp_col, sheetname, header, fullname	a list (or a local file)
ReadSpeciesFile_csv	sp_col, header, fullname	a list (or a local file )
ExtractSpeciesFromFasta	ranges, delimiter	a list (or a local file)

all those functions return a list of species names or ID list

Usage

species = LoadSpecies(input_file, output_file, ifout = True)
species.ReadSpeciesFile_excel(sp_col='act_sym_fullname', sheetname = 0, header = 0,  fullname = False)

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class NCBI_Tools

This class implements Biopython Entrez to interact with NCBI/Genbank API to either get accession id, taxonomy id, sequences or taxonomy ranking, or converting them. Some of core functions return a tracker flag that can trace which functions have been called. This order will be used by Sqlite_Dumps class to generate fasta file and mapping file

Functions

Functions	parameters	return	database table name	Tracker Flag
NCBI_Tools	ncbi_key, ncbi_email, sqlite_db, ncbi_db, idtype	initialize	None	None
Update_API	key, email	updated key and email	None	None
getTracker	None	a tracker list	None	None
ncbi_Species2Genome	species list	accession ID list	Sp2Genome	P9
ncbi_Search2Acc	search terms, howmany to quire	Search2AccIDs	Tracker	P1
ncbi_Species2Acc	species list, more terms (optional)	Sp2AccIDs	Tracker	P2
ncbi_GetSeqsFromAcc	table_name, column_name	Acc2Seq	Tracker	P3
ncbi_GetTaxIdFromAcc	table_name, column_name	Uid2TaxIDs	Tracker	P4
ncbi_eAcc2Seq	accession ID	Tracker	Acc2Seq	P5
ncbi_eAcc2TaxID	accession ID	Tracker	Uid2TaxIDs	P6
ncbi_Species2Taxa	species list, style, levels_n	Tracker	Sp2Taxa	P7
ncbi_Id2Taxa	style, levels_n	Tracker	TaxId2Ranking	P8

Usage

Example 1: Known species list and search for its trnL gene

Tracker Flag: P2---> P3 / P4 ---> P4 / P3 ---> P8

from NCBI_Companion import NCBI_Companion
companion = NCBI_Companion.NCBI_Tools(key, email, 'databasename', 'nuccore', 'acc')
companion.ncbi_Species2Acc(species_list, 'trnL')
companion.ncbi_GetSeqsFromAcc('Sp2AccIDs', 'acc_id')
companion.ncbi_GetTaxIdFromAcc('Sp2AccIDs', 'acc_id')
companion.ncbi_Id2Taxa(style = 'qiime', levels_n = 7) # 7 levels of taxonomy ranking qiime style D_0_..;

class Sqlite_Dumps

Functions

functions	parameters	return
Sqlite_Dumps	sqlite_db, output_prefix, tracker, header_type = 'acc'	initialize
sqlite_dump	None	a fasta and a mapping file in local

Usage

# get tracker
tracker = companion.getTracker()
dump = Sqlite_Dumps('database constructed by NCBI_Tools', 'fasta and mapping file name, not extension', tracker, header_type = 'acc')