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

Contents

class LoadSpecies

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

Functions

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)

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

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

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')