def createdb(self, inname, outname, force):
"""Create the database
Args:
inname (str): Path to human genome reference file
outname (str): Name of sqlite3 database
force (bool): If True overwrite existing database even if it
is newer than `inname`
"""
if os.path.exists(outname):
if fileutils.file_newer(inname, outname) or \
fileutils.file_newer(dbconfig.DBCONFIG['REFGENE']['name'],\
outname):
newer = True
else:
newer = False
else:
newer = True
self.logger = fileconfig.getlogger()
if not newer and not force:
self.logger.info('Not Updating. REFMRNA database already uptodate')
else:
self.inname = inname
self.outname = outname
t1 = time.time()
self._makedb()
time_taken = (time.time() - t1) / 60
self.logger.info("Time Taken for creating %s is %f min" \
% (self.outname, time_taken))
return
def createdb(self, inname, outname, force):
"""Create the database
Args:
inname (str): Swissprot file. Note - The trEMBL file does not
contain OMIM annotation and even if it exists
the information is partial like only mimid is
specified but does not say anything is the id
is gene omim id or phenotype omim id.
outname (str): Name of sqlite3 database
force (bool): If True overwrite existing database even if it
is newer than any of `inname`
"""
self.logger = fileconfig.getlogger()
if os.path.exists(outname):
newer = fileutils.file_newer(inname, outname)
else:
newer = True
if not newer and not force:
self.logger.info('Not Updating. OMIM database already uptodate')
else:
self.inname = inname
self.outname = outname
t1 = time.time()
self._makedb()
time_taken = (time.time() - t1) / 60
self.logger.info("Time Taken for creating %s is %f min" %
(self.outname, time_taken))
return
def createdb(self, inname, outname, force):
"""Create the database
Args:
inname (str): Name of the csv file containing utr data
outname (str): Name of sqlite3 database
force (bool): If True overwrite existing database even if it
is newer than `inname`
"""
newfiles = []
self.inname = inname
if os.path.exists(outname):
for fn in os.listdir(inname):
infile = os.path.join(inname, fn)
newer = fileutils.file_newer(infile, outname)
if newer is True:
break
else:
newer = True
self.logger = fileconfig.getlogger()
if not newer and not force:
self.logger.info('Not Updating. UTRdb' +
'database already uptodate')
else:
self.inname = inname
self.outname = outname
t1 = time.time()
self._makedb()
time_taken = (time.time() - t1) / 60
self.logger.info("Time Taken for creating %s is %f min"
% (self.outname, time_taken))
return
def createdb(self, inname, outname, force):
"""Create the database
Args:
inname (str): Name of the csv file containing mirna data
outname (str): Name of sqlite3 database
force (bool): If True overwrite existing database even if it
is newer than `inname`
"""
if os.path.exists(outname):
newer = fileutils.file_newer(inname, outname)
else:
newer = True
self.logger = fileconfig.getlogger()
if not newer and not force:
self.logger.info('Not Updating. MIRNA database already uptodate')
else:
self.inname = inname
self.outname = outname
t1 = time.time()
self._makedb()
time_taken = (time.time() - t1) / 60
self.logger.info("Time Taken for creating %s is %f min" \
% (self.outname, time_taken))
return
def createdb(self, inname, outname, force, hgmd_on=0):
"""Create the database
Args:
inname (str): interpro file name from ucsc SQL results
outname (str): Name of sqlite3 database
force (bool): If True overwrite existing database even if it
is newer than any of `inname`
"""
self.logger = fileconfig.getlogger()
if os.path.exists(outname):
newer = fileutils.file_newer(inname, outname)
else:
newer = True
if not newer and not force:
self.logger.info(
'Not Updating. INTERPRO database already uptodate')
else:
self.inname = inname
self.outname = outname
self.hgmd_on = hgmd_on
t1 = time.time()
self._makedb()
time_taken = (time.time() - t1) / 60
self.logger.info("Time Taken for creating %s is %f min" %
(self.outname, time_taken))
return
def createdb(self, inname, outname, force):
"""Create the database
Args:
inname (str): Name of the directory containing NSFP Database files
outname (str): Name of sqlite3 database
force (bool): If True overwrite existing database even if it
is newer than `inname`
"""
self.indir = os.path.dirname(inname)
if os.path.exists(outname):
newer = False
for filename in os.listdir(self.indir):
if 'chr' in os.path.splitext(filename)[1]:
infile = os.path.join(self.indir, filename)
newer = fileutils.file_newer(infile, outname)
if newer:
break
else:
newer = True
self.logger = fileconfig.getlogger()
if not newer and not force:
self.logger.info('Not Updating. NSFP database already uptodate')
else:
self.outname = outname
t1 = time.time()
self._makedb()
time_taken = (time.time() - t1) / 60
self.logger.info("Time Taken for creating %s is %f min" %
(self.outname, time_taken))
return
def createdb(self, inname, goaname, outname, force):
'''
Args:
-inname (str): Name of gene ontology similarity tab delimited file generated by app_build_go.py
-outname (str): Name of sqlite3 database
-force (bool): If True overwrite existing database even if it is newer than *ism_prefix
'''
if os.path.exists(outname):
#TODO: to handle more than two files or pick one of them
newer = fileutils.file_newer(inname, outname)
else:
newer = True
self.logger = fileconfig.getlogger()
if not newer and not force:
self.logger.info('Not Updating. GO database already update')
else:
self.inname = inname
self.goaname = goaname
self.outname = outname
self.uni2gene = {}
t1 = time.time()
# preprocessing (filtering and sorting)
self._preproces()
# -----------
self._makedb()
# -----------
time_taken = (time.time() - t1) / 60
self.logger.info("Time Taken for creating %s is %f min" % (self.outname, time_taken))
return
