MGT::Db::DbSeqSource Class Reference

Inherits MGT::Options::Options.

List of all members.

Public Member Functions
def	loadTaxNames
def	reportStat
	save gis only into a file to be used as gi list for NCBI alias db
Static Public Attributes
string	table = "all_src"
	in MySQL computation of acc_no_ver (ACC w/o '.X' suffix) would be just SUBSTRING_INDEX( a.acc , '.
list	dropList = ["table seq_sel_del"]
	Proved to be essential in MySQL for efficient planning of queries.

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Detailed Description

Database of sequence source for training the classifier

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Member Function Documentation

def MGT::Db::DbSeqSource::loadTaxNames

(

self )

We load only 'scientific name' entries.

def MGT::Db::DbSeqSource::reportStat

(

self )

save gis only into a file to be used as gi list for NCBI alias db

save all importand fields for selected seq records into a flat file to be merged with fasta sequence data extracted from blast databases through just created gi list the order must match the preceding 'select' for gis Full csv format will have something like OPTIONALLY ENCLOSED BY '"'

Output a report that shows a high-level overview of data.

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Member Data Documentation

list MGT::Db::DbSeqSource::dropList = ["table seq_sel_del"] [static]

Proved to be essential in MySQL for efficient planning of queries.

Backup all records from seq_sel that are to be discarded in case we want to analyze them later

string MGT::Db::DbSeqSource::table = "all_src" [static]

in MySQL computation of acc_no_ver (ACC w/o '.X' suffix) would be just SUBSTRING_INDEX( a.acc , '.

', 1 ) AS acc_no_ver, but we use SQL standard conforming expression

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The documentation for this class was generated from the following file:

• mgtaxa/MGT/Db.py