seqsql2fa.py

#!/usr/bin/env python
# Copyright (C) 2015,2016 Mohammad Alanjary
# University of Tuebingen
# Interfaculty Institute of Microbiology and Infection Medicine
# Lab of Nadine Ziemert, Div. of Microbiology/Biotechnology
# Funding by the German Centre for Infection Research (DZIF)
#
# This file is part of ARTS
# ARTS is free software. you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version
#
# License: You should have received a copy of the GNU General Public License v3 with ARTS
# A copy of the GPLv3 can also be found at: <http://www.gnu.org/licenses/>.

import argparse, setlog, os, sqlalchemy as sql

global log
log = setlog.init(toconsole=True)

def writefasta(db,outfile,nuc=False,idprfx="",latest=False):
    if not db.lower().startswith("sqlite://") and not db.lower().startswith("postgresql://"):
        db = "sqlite:///"+os.path.realpath(db)
    eng = sql.create_engine(db)
    cur = eng.connect()
    result = cur.execute('SELECT * FROM "Seqs"')
    if latest:
        result = cur.execute('SELECT * FROM "Seqs" WHERE lastscan >= (SELECT Max(lastscan) from "Seqs")')
    log.info("Writing sequences to disk...")
    with open(outfile,"w") as ofil:
        for r in result:
            ofil.write(">%s|%s%s %s|source|%s|loc|%s %s %s\n%s\n" % (r[1], idprfx, r[0],r[2],r[4],r[5],r[6],r[7],r[-1-int(nuc)]))
    cur.close()

# Commandline Execution
if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="Write fasta file of sequence DB with format >ORG|dbkey")
    parser.add_argument("input", help="sequence database sqlite file or postgre db connection: 'postgresql://user:pass@host:5432/dbname' ")
    parser.add_argument("outfile", help="Filename of for saved files. Number extension will be added for split files.")
    parser.add_argument("-n","--nuc", help="Write DNA sequences instead of protein",action='store_true')
    parser.add_argument("-l","--latest", help="Only write latest sequences added to database",action='store_true')
    args = parser.parse_args()
    writefasta(args.input,args.outfile,args.nuc,latest=args.latest)