# 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()
