def setUp(self):
'''
@param mock_db_fpath (str) path to syntheticaly created CDSs which serves
to fill up mock database of records
@param input_aln_fpath (str) path to input alignment file
@param results_fpath (str) path to file with generated correct results
greedy solver should generate
'''
self.mock_db_fpath = './test/solver/read2cds/.test_data/cds.fa'
self.input_aln_fpath = './test/solver/read2cds/.test_data/lisa.in'
self.results_fpath = './test/solver/read2cds/.test_data/cds_ordering.txt'
# Initialize read container
self.read_cont = ReadContainer()
self.read_cont.populate_from_aln_file(self.input_aln_fpath)
# Initialize and fill record container
self.db_query = MockDbQuery(self.mock_db_fpath)
self.record_cont = RecordContainer()
self.record_cont.set_db_access(self.db_query)
self.record_cont.populate(self.read_cont.fetch_all_reads_versions())
self.read_cont.populate_cdss(self.record_cont)
# Initialize and fill up cds aln container
self.cds_aln_cont = CdsAlnContainer()
self.cds_aln_cont.populate(self.read_cont.fetch_all_reads())
self.greedy_solver = GreedySolver()
self.greedy_solver.map_reads_2_cdss(self.cds_aln_cont)
def fill_containers (alignment_file, db_access):
'''
Populates read, record and CDS alignment container.
@return tuple(ReadContainer, RecordContainer, CdsAlnContainer)
'''
read_cont = ReadContainer()
record_cont = RecordContainer()
record_cont.set_db_access(db_access)
cdsaln_cont = CdsAlnContainer()
# 1. Load all the information available in the alignment file
read_cont.populate_from_aln_file(alignment_file)
# 2. Fetch all the records reported in the alignment file from the database
record_cont.populate(read_cont.fetch_all_reads_versions())
# 3. Find to which coding sequences reads map
read_cont.populate_cdss(record_cont)
# 4. Populate Cds Alignment container
cdsaln_cont.populate(read_cont.fetch_all_reads())
return (read_cont, record_cont, cdsaln_cont)
def setUp(self):
self.read_container = ReadContainer()
self.record_container = RecordContainer()
def setUp(self):
self.read_cont = ReadContainer()
self.aln_file = './test/data/containers/.data/example.in'
from solver.read2cds.Read2CDSSolver import Read2CDSSolver
from data.containers.record import RecordContainer
from data.containers.read import ReadContainer
from data.containers.cdsaln import CdsAlnContainer
from utils.logger import Logger
Logger("log")
db_query = DbQuery()
# create containers
record_container = RecordContainer()
record_container.set_db_access(db_query)
read_container = ReadContainer()
read_container.populate_from_aln_file("example_data/2reads.in")
record_container.populate(read_container)
read_container.populate_cdss(record_container)
cds_aln_container = CdsAlnContainer()
cds_aln_container.populate(read_container)
print cds_aln_container
r2c_solver = BestScoreSolver()
r2c_solver.map_reads_2_cdss(cds_aln_container)
print "Consistency test result: ", Read2CDSSolver.test_cds_alignment_container_consistency(cds_aln_container)