NCBI_Companion
version: 1.0.8
installation:
pip3 install NCBI-Companion --userload module:
from NCBI_Companion import NCBI_CompanionIntroduction
NCBI_Companion targets to construct databases, generate a fasta file and a taxonomy mappingusing by using Genbank Entrez utilities.
Current Supported Database: nuccore, nucleotide, genome
Please also follow NCBI E-utitlites rules rules
Biopython copyright belongs to Biopython teams E-Utitlites copyright belongs to NCBI teams
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)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 | Used For |
|---|---|---|---|---|---|
| NCBI_Tools | ncbi_key, ncbi_email, sqlite_db, ncbi_db, idtype | initialize | None | None | Initialize |
| Update_API | key, email | updated key and email | None | None | update your key and email |
| getTracker | None | a tracker list | None | None | get all the tracker ID |
| ncbi_Species2Genome | species list | accession ID list | Sp2Genome | P9 | convert species to accession IDs |
| ncbi_Search2Acc | search terms, howmany to quire | Tracker | Search2AccIDs | P1 | search term to get accession number |
| ncbi_Species2Acc | species list, more terms (optional) | Tracker | Sp2AccIDs | P2 | convert species and with extra terms to get accession id |
| ncbi_GetSeqsFromAcc | table_name, column_name | Tracker | Acc2Seq | P3 | from accession ID to get sequences for each |
| ncbi_GetTaxIdFromAcc | table_name, column_name | Tracker | Uid2TaxIDs | P4 | from accession ID to get tax ID for each |
| ncbi_eAcc2Seq | accession ID | Tracker | Acc2Seq | P5 | search accession list to get sequences |
| ncbi_eAcc2TaxID | accession ID | Tracker | Uid2TaxIDs | P6 | search accesson list to get tax id |
| ncbi_Species2Taxa | species list, style, levels_n | Tracker | Sp2Taxa | P7 | search species to get taxonomy ranking |
| ncbi_Id2Taxa | style, levels_n | Tracker | TaxId2Ranking | P8 | from accession and tax id to get taxonomy ranking |
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')
