def __init__(self,
db=None,
tempfilepath=None,
pathtoblast=None,
pathtocddDatabase=None,
PhageIDs=None):
#password = getpass.getpass()
self.username = raw_input("Database Username: "******"Database Password: "******"Database Server: ")
self.database = raw_input("Database Name: ")
print 'using databse: %s' % self.database
self.c = db_conf(username=self.username,
password=self.password,
server=self.server,
db=self.database).get_cursor()
if not PhageIDs:
PhageIDs = phamerator_manage_db.get_PhageIDs(self.c)
self.PhageIDs = list(PhageIDs)
#errorHandler = pham.errorHandler()
self.dbase = pham.db(self.c)
if pathtocddDatabase == None:
self.rpsblast_db = os.path.join(os.environ['HOME'], 'Databases',
'Cdd', 'Cdd')
else:
self.rpsblast_db = pathtocddDatabase
if tempfilepath == None:
self.query_filename = "/tmp/query.fasta"
else:
self.query_filename = tempfilepath
if pathtoblast == None:
try:
import ConfigParser
cfg = ConfigParser.RawConfigParser()
cfg.read(
os.path.join(os.environ['HOME'], '.phamerator',
'phamerator.conf'))
blast_dir = cfg.get('Phamerator', 'BLAST_dir')
self.rpsblast_exe = os.path.join(blast_dir, 'bin', 'rpsblast')
print 'path to rpsblast: %s' % self.rpsblast_exe
except:
print "BLAST not found, Exiting"
sys.exit()
else:
self.rpsblast_exe = pathtoblast
def main():
cfg = ConfigParser.RawConfigParser()
cfg.read(os.path.join(os.environ['HOME'], '.my.cnf'))
import sys
db = sys.argv[1]
try:
username = cfg.get('client', 'user')
except ConfigParser.NoOptionError:
username = raw_input('database username: '******'client', 'password')
except ConfigParser.NoOptionError:
import getpass
password = getpass.getpass('database password: '******'root', password=password, server='localhost',
db=db).get_cursor()
phams = get_all_pham_names(c)
for phamName in phams:
print phamName
phamMembers = get_pham_members(c, phamName)
#for phamMember in phamMembers:
# relatives = [phamMember]
# #relatives = get_all_relatives(c, phamMember)
# #print 'seed: %s' % phamMember
# relatives = list(set(relatives) | set(follow_rel_chain2(c, phamMember, relatives)))
phamMember = phamMembers[0]
relatives = [phamMember]
# #relatives = get_all_relatives(c, phamMember)
# #print 'seed: %s' % phamMember
relatives = list(
set(relatives) | set(
follow_rel_chain2(c,
phamMember,
relatives,
cthreshold=0.325,
bthreshold=1e-50)))
phamMembers.sort()
relatives.sort()
if relatives != phamMembers:
print '%s cannot account for all genes in pham %s' % (phamMember,
phamName)
print 'relatives: %s\nphamMembers: %s' % (relatives, phamMembers)
print '%s : %s : %s' % (phamName, phamMembers, relatives)
print 'mercifully exiting after one mismatch'
sys.exit()
print '%s database is OK' % db
def main():
cfg = ConfigParser.RawConfigParser()
cfg.read(os.path.join(os.environ['HOME'], '.my.cnf'))
import sys
db = sys.argv[1]
try:
username = cfg.get('client','user')
except ConfigParser.NoOptionError:
username = raw_input('database username: '******'client','password')
except ConfigParser.NoOptionError:
import getpass
password = getpass.getpass('database password: '******'root', password=password, server='localhost', db=db).get_cursor()
phams = get_all_pham_names(c)
for phamName in phams:
print phamName
phamMembers = get_pham_members(c, phamName)
#for phamMember in phamMembers:
# relatives = [phamMember]
# #relatives = get_all_relatives(c, phamMember)
# #print 'seed: %s' % phamMember
# relatives = list(set(relatives) | set(follow_rel_chain2(c, phamMember, relatives)))
phamMember = phamMembers[0]
relatives = [phamMember]
# #relatives = get_all_relatives(c, phamMember)
# #print 'seed: %s' % phamMember
relatives = list(set(relatives) | set(follow_rel_chain2(c, phamMember, relatives, cthreshold=0.325, bthreshold=1e-50)))
phamMembers.sort()
relatives.sort()
if relatives != phamMembers:
print '%s cannot account for all genes in pham %s' % (phamMember, phamName)
print 'relatives: %s\nphamMembers: %s' % (relatives, phamMembers)
print '%s : %s : %s' % (phamName, phamMembers, relatives)
print 'mercifully exiting after one mismatch'
sys.exit()
print '%s database is OK' % db
def __init__(self,db=None,tempfilepath=None,pathtoblast=None,pathtocddDatabase=None,PhageIDs=None):
#password = getpass.getpass()
self.username = raw_input("Database Username: "******"Database Password: "******"Database Server: ")
self.database = raw_input("Database Name: ")
print 'using databse: %s' % self.database
self.c = db_conf(username=self.username,password=self.password,server=self.server,db=self.database).get_cursor()
if not PhageIDs:
PhageIDs = phamerator_manage_db.get_PhageIDs(self.c)
self.PhageIDs = list(PhageIDs)
#errorHandler = pham.errorHandler()
self.dbase = pham.db(self.c)
if pathtocddDatabase == None:
self.rpsblast_db = os.path.join(os.environ['HOME'], 'Databases', 'Cdd', 'Cdd')
else:
self.rpsblast_db = pathtocddDatabase
if tempfilepath == None:
self.query_filename = "/tmp/query.fasta"
else:
self.query_filename = tempfilepath
if pathtoblast == None:
try:
import ConfigParser
cfg = ConfigParser.RawConfigParser()
cfg.read(os.path.join(os.environ['HOME'], '.phamerator', 'phamerator.conf'))
blast_dir = cfg.get('Phamerator','BLAST_dir')
self.rpsblast_exe = os.path.join(blast_dir,'bin','rpsblast')
print 'path to rpsblast: %s' % self.rpsblast_exe
except:
print "BLAST not found, Exiting"
sys.exit()
else:
self.rpsblast_exe = pathtoblast
def main():
cfg = ConfigParser.RawConfigParser()
cfg.read(os.path.join(os.environ['HOME'], '.my.cnf'))
import sys
db = sys.argv[1]
try:
username = cfg.get('client','user')
except ConfigParser.NoOptionError:
username = raw_input('database username: '******'client','password')
except ConfigParser.NoOptionError:
import getpass
password = getpass.getpass('database password: '******'root', password=password, server='localhost', db=db).get_cursor()
finals = get_finals(c)
print 'finals:', finals
drafts = get_drafts(c)
print 'drafts:', drafts
print 'removing the following phages:\n'
remove_drafts(c, drafts, finals)
def main():
cfg = ConfigParser.RawConfigParser()
cfg.read(os.path.join(os.environ['HOME'], '.my.cnf'))
import sys
db = sys.argv[1]
try:
username = cfg.get('client', 'user')
except ConfigParser.NoOptionError:
username = raw_input('database username: '******'client', 'password')
except ConfigParser.NoOptionError:
import getpass
password = getpass.getpass('database password: '******'root', password=password, server='localhost',
db=db).get_cursor()
finals = get_finals(c)
print 'finals:', finals
drafts = get_drafts(c)
print 'drafts:', drafts
print 'removing the following phages:\n'
remove_drafts(c, drafts, finals)
#!/usr/bin/env python
from phamerator import *
from phamerator.phamerator_manage_db import *
from phamerator.db_conf import db_conf
import sys, getpass
GeneID = sys.argv[1]
password = getpass.getpass()
db = raw_input('database: ')
c = db_conf(username='******', password=password, server='134.126.132.72', db=db).get_cursor()
print get_relatives(c, GeneID, alignmentType='both', clustalwThreshold=0.275, blastThreshold=0.0001)