# Create the table and define the mapping h = HSP() hsps_table = createTable(tableName, metadata, h.attributes, h.converters, indexedAttributes=['subjectId', 'sStart', 'sEnd']) mapper(HSP, hsps_table) # Start a session & initialize database session = createSession(dsn, metadata) if case in [1,2]: # Devil 454 reads for i,line in enumerate(open(iFilename)): tokens = line.strip().split('\t') h = HSP(tokens[0:-2]) h.convertBlockToGenomeCoords() session.save(h) if (i % 5000)==0: progressMessage("# HSPs %s", i, n) session.commit() progressMessage("# HSPs %s\n", i, n) session.commit() elif case==3: # Platypus 454 reads for i,h in enumerate(BlastFile(iFilename)): h.subjectId = h.subjectId.split('|')[1] h.convertBlockToGenomeCoords() session.save(h) if (i % 5000)==0: progressMessage("# HSPs %s", i, n) session.commit()
hsps_table = createTable(tableName, metadata, h.attributes, h.converters, indexedAttributes=['subjectId', 'sStart', 'sEnd']) mapper(HSP, hsps_table) # Start a session & initialize database session = createSession(dsn, metadata) if case in [1, 2]: # Devil 454 reads for i, line in enumerate(open(iFilename)): tokens = line.strip().split('\t') h = HSP(tokens[0:-2]) h.convertBlockToGenomeCoords() session.save(h) if (i % 5000) == 0: progressMessage("# HSPs %s", i, n) session.commit() progressMessage("# HSPs %s\n", i, n) session.commit() elif case == 3: # Platypus 454 reads for i, h in enumerate(BlastFile(iFilename)): h.subjectId = h.subjectId.split('|')[1] h.convertBlockToGenomeCoords() session.save(h) if (i % 5000) == 0: progressMessage("# HSPs %s", i, n) session.commit()