#!/usr/bin/env python
"""
snippet.py
Author: Tony Papenfuss
Date: Mon Jun 23 23:32:21 EST 2008
"""
import os, sys
from alchemy import *
from blast import BlastFile, HSP
tableName = 'Devil454' # Devil454, Platy454, PlatySolexa
dsn = 'sqlite:///test.db'
metadata = MetaData()
# Create the table and define the mapping
h = HSP()
hsps_table = createTable(tableName, metadata, h.attributes, h.converters)
mapper(HSP, hsps_table)
# Start a session & initialize database
session = startSession(dsn, metadata)
for h in session.query(HSP).filter(HSP.subjectId == '3'):
print dir(h)
print h
tableName = 'Devil454_alt'
iFilename = os.path.join(
homeDir,
'databases/devil/transcriptome/reads/blast_results/blastn_tumour_v_opossum2.txt'
)
n = 472244
elif case == 3:
tableName = 'Platy454'
iFilename = os.path.join(
homeDir, 'databases/platypus/venom/454/blat_platy_venom_reads.txt')
n = 208523
metadata = MetaData()
# 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])
elif case==2:
tableName = 'Devil454_alt'
iFilename = os.path.join(homeDir,
'databases/devil/transcriptome/reads/blast_results/blastn_tumour_v_opossum2.txt')
n = 472244
elif case==3:
tableName = 'Platy454'
iFilename = os.path.join(homeDir,
'databases/platypus/venom/454/blat_platy_venom_reads.txt')
n = 208523
metadata = MetaData()
# 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:
"""
import os, sys
from alchemy import *
from blast import BlastFile, HSP
tableName = "Devil454" # Devil454, Platy454, PlatySolexa
dsn = "sqlite:///test.db"
metadata = MetaData()
# Create the table and define the mapping
h = HSP()
hsps_table = createTable(tableName, metadata, h.attributes, h.converters)
mapper(HSP, hsps_table)
# Start a session & initialize database
session = startSession(dsn, metadata)
# Load data
filename = "/Users/papenfuss/databases/devil/transcriptome/reads/blast_results/blastn_tumour_v_opossum.txt"
for i, h in enumerate(BlastFile(filename)):
h.convertBlockToGenomeCoords()
session.save(h)
if i == 10:
break
session.commit()
