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