def main():
'''
Script to perform LCA binning with a given read alignment file.
'''
# Input arguments
argparser = TestRunArgParser()
args = argparser.parse_args()
# Access database
dataAccess = DataAccess(args)
print '1. Loading tax tree...'
tax_tree = TaxTree()
print 'done.'
print '2. Loading alignment file...'
read_container = ReadContainer()
read_container.load_alignment_data(args.alignment_file)
#---SET TAXIDS FOR ALL ALIGNMENTS--#
read_container.set_taxids(dataAccess)
print 'done'
print '4. Creating LCA solution...'
lca_binner = LCABinner(tax_tree)
lca_sol = lca_binner.bin_reads(read_container)
print 'done'
print '5. Nice output of read assignment here'
lca_sol.print_nicely(tax_tree)
class RecordContainerTest (unittest.TestCase):
def setUp(self):
self.read_container = ReadContainer()
self.record_container = RecordContainer()
def tearUp(self):
pass
def testFillRecordContainer(self):
'''Method to test whether record container populating works.
Uses mock database access to test whether record container
has correct number of items.'''
aln_file = './test/solver/read2cds/.test_data/lisa.in'
cds_fasta = './test/solver/read2cds/.test_data/cds.fa'
db_access = MockDbQuery(cds_fasta)
self.record_container.set_db_access(db_access)
self.read_container.populate_from_aln_file(aln_file)
self.record_container.populate(
self.read_container.fetch_all_reads_versions())
records = self.record_container.fetch_all_records(format=list)
self.assertEqual (len(db_access.records), len(records))
def testReturnsNoneForNonexistentRecord(self):
record = self.record_container.fetch_existing_record("XXX")
self.assertIsNone(record, "No record with version XXX should be found")
class RecordContainerTest(unittest.TestCase):
def setUp(self):
self.read_container = ReadContainer()
self.record_container = RecordContainer()
def tearUp(self):
pass
def testFillRecordContainer(self):
'''Method to test whether record container populating works.
Uses mock database access to test whether record container
has correct number of items.'''
aln_file = './test/solver/read2cds/.test_data/lisa.in'
cds_fasta = './test/solver/read2cds/.test_data/cds.fa'
db_access = MockDbQuery(cds_fasta)
self.record_container.set_db_access(db_access)
self.read_container.populate_from_aln_file(aln_file)
self.record_container.populate(
self.read_container.fetch_all_reads_versions())
records = self.record_container.fetch_all_records(format=list)
self.assertEqual(len(db_access.records), len(records))
def testReturnsNoneForNonexistentRecord(self):
record = self.record_container.fetch_existing_record("XXX")
self.assertIsNone(record, "No record with version XXX should be found")
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 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)
class ReadContainerTest(unittest.TestCase):
def setUp(self):
self.read_cont = ReadContainer()
self.aln_file = './test/data/containers/.data/example.in'
def tearUp(self):
pass
def testReadCount(self):
'''
Tests whether the number of reads in the read container
is consistent with the number of reads in the
alignment file.
'''
self.read_cont.populate_from_aln_file(self.aln_file)
reads_cont = self.read_cont.read_repository.keys()
reads_from_file = self._load_read_ids()
for read_id in reads_from_file:
self.assertTrue(read_id in reads_cont, msg = "Read ID %s not in read container." % read_id)
self.assertEqual(len(reads_cont), 100)
def testCorrectAlignmentNumber (self):
'''
Test the loader for correct number of alignments.
Test file organized so that read ID specifies number
of alignments.
'''
aln_file = './test/data/containers/.data/aln_num.in'
self.read_cont.populate_from_aln_file(aln_file)
for (read_id, read) in self.read_cont.read_repository.items():
self.assertEqual(int(read_id), len(read.get_alignments()))
def _load_read_ids (self):
aln_fhandle = open(self.aln_file, 'r')
nextline = aln_fhandle.readline
read_ids = []
while(True):
line = nextline()
if not line: break
read_id = line.split(',')[0]
if read_id.startswith('@'):
read_id = read_id[1:]
read_ids.append(read_id)
aln_fhandle.close()
return read_ids
class ReadContainerTest(unittest.TestCase):
def setUp(self):
self.read_cont = ReadContainer()
self.aln_file = './test/data/containers/.data/example.in'
def tearUp(self):
pass
def testReadCount(self):
'''
Tests whether the number of reads in the read container
is consistent with the number of reads in the
alignment file.
'''
self.read_cont.populate_from_aln_file(self.aln_file)
reads_cont = self.read_cont.read_repository.keys()
reads_from_file = self._load_read_ids()
for read_id in reads_from_file:
self.assertTrue(read_id in reads_cont,
msg="Read ID %s not in read container." % read_id)
self.assertEqual(len(reads_cont), 100)
def testCorrectAlignmentNumber(self):
'''
Test the loader for correct number of alignments.
Test file organized so that read ID specifies number
of alignments.
'''
aln_file = './test/data/containers/.data/aln_num.in'
self.read_cont.populate_from_aln_file(aln_file)
for (read_id, read) in self.read_cont.read_repository.items():
self.assertEqual(int(read_id), len(read.get_alignments()))
def _load_read_ids(self):
aln_fhandle = open(self.aln_file, 'r')
nextline = aln_fhandle.readline
read_ids = []
while (True):
line = nextline()
if not line: break
read_id = line.split(',')[0]
if read_id.startswith('@'):
read_id = read_id[1:]
read_ids.append(read_id)
aln_fhandle.close()
return read_ids
class BestScoreSolverTest(unittest.TestCase):
# setUp is executed before each test method
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.bs_solver = BestScoreSolver()
self.bs_solver.map_reads_2_cdss(self.cds_aln_cont)
def testCdsAlignmentContainerConsistency(self):
assert (Read2CDSSolver.test_cds_alignment_container_consistency(
self.cds_aln_cont) == True)
def main():
'''
Script to extract reads without any alignments
'''
# Input arguments
argparser = ArgParser()
args = argparser.parse_args()
# Access database
dataAccess = DataAccess(args)
# ------------------ #
print '1. Loading tax tree...'
start = time.time()
tax_tree = TaxTree()
end = time.time()
print("done: {0:.2f} sec".format(end - start))
# ------------------ #
print '2. Loading alignment file...'
start = time.time()
read_container = ReadContainer()
read_container.load_alignment_data(args.alignment_file)
#---SET TAXIDS FOR ALL ALIGNMENTS--#
read_container.set_taxids(dataAccess)
end = time.time()
print("done: {0:.2f} sec".format(end - start))
# ------------------ #
# Loop through reads and take those with no alignments
out_file = open(args.read_ids_out, 'w')
no_aln_count = 0
for read in read_container.fetch_all_reads(format=list):
if not read.has_alignments():
out_file.write("{0}\n".format(read.id))
no_aln_count += 1
out_file.close()
total_read_count = read_container.get_read_count()
print("total number of reads : {0}".format( total_read_count ))
print("reads without alignments: {0}".format(no_aln_count))
print
print("no aln percentage: {0:.2f}%".format(no_aln_count * 100 / float(total_read_count)))
def main():
'''
Script to experiment with binner.
'''
print "Hello world!"
# Input arguments
argparser = TestRunArgParser()
args = argparser.parse_args()
# Access database
dataAccess = DataAccess(args)
print '1. Loading tax tree...'
tax_tree = TaxTree()
print 'done.'
print '2. Loading alignment file...'
read_container = ReadContainer()
read_container.load_alignment_data(args.input)
#---SET TAXIDS FOR ALL ALIGNMENTS--#
read_container.set_taxids(dataAccess)
print 'done'
print '3. Loading correct solution from FASTA with reads produced by metasim...'
sol = Solution.from_metasim_fasta(args.metasim_fasta, dataAccess)
print 'done'
print '4. Creating LCA solution...'
lca_binner = LCABinner(tax_tree)
lca_sol = lca_binner.bin_reads(read_container)
print 'done'
print '5. Evaluating LCA solution...'
rankAcc = RankAccuracy(tax_tree, sol, lca_sol)
print 'done'
# Print test results
rankAcc.print_data()
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)
class StatisticsTest(unittest.TestCase):
# setUp is executed before each test method
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/statistics/.test_data/cds.fa'
self.input_aln_fpath = './test/statistics/.test_data/lisa.in'
# 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())
def testStatistics(self):
assert (num_read_alns(self.read_cont) == 22)
assert (num_active_aligned_regions(self.cds_aln_cont) == 22)
assert (num_inactive_read_alns(self.read_cont) == 0)
self.bs_solver = BestScoreSolver()
self.bs_solver.map_reads_2_cdss(self.cds_aln_cont)
records_stats = count_alns_to_record_and_cds(self.read_cont)
print "Number of records for which we have stats: %d\n" % len(
records_stats)
for rec_stat in records_stats.values():
rec_stat.print_data()
assert (num_active_aligned_regions(self.cds_aln_cont) == 16)
assert (num_cdss(self.cds_aln_cont) == 4)
assert (num_cdss_with_no_alns(self.cds_aln_cont) == 0)
class StatisticsTest (unittest.TestCase):
# setUp is executed before each test method
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/statistics/.test_data/cds.fa'
self.input_aln_fpath = './test/statistics/.test_data/lisa.in'
# 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())
def testStatistics(self):
assert(num_read_alns(self.read_cont) == 22)
assert(num_active_aligned_regions(self.cds_aln_cont) == 22)
assert(num_inactive_read_alns(self.read_cont) == 0)
self.bs_solver = BestScoreSolver()
self.bs_solver.map_reads_2_cdss(self.cds_aln_cont)
records_stats = count_alns_to_record_and_cds(self.read_cont)
print "Number of records for which we have stats: %d\n" % len(records_stats)
for rec_stat in records_stats.values():
rec_stat.print_data()
assert(num_active_aligned_regions(self.cds_aln_cont) == 16)
assert(num_cdss(self.cds_aln_cont) == 4)
assert(num_cdss_with_no_alns(self.cds_aln_cont) == 0)
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)
class GreedySolverTest(unittest.TestCase):
# setUp is executed before each test method
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 testAlignmentsCorrectlyInactivated(self):
'''
Loads correct results from results file and checks whether
all the reads for a CDS listed in the file are active and
whether all the other reads are inactive.
'''
cds2read = self._load_active_reads()
for (cds, cds_aln) in self.cds_aln_cont.cds_repository.items():
accession = cds.record_id
mapped_reads = cds2read[accession]
for cds_aln_subloc in cds_aln.aligned_regions.values():
if cds_aln_subloc.active:
assert (cds_aln_subloc.read_id in mapped_reads)
else:
assert (cds_aln_subloc.read_id not in mapped_reads)
def testCdsAlignmentContainerConsistency(self):
assert (Read2CDSSolver.test_cds_alignment_container_consistency(
self.cds_aln_cont) == True)
def _load_active_reads(self):
results_fhandle = open(self.results_fpath)
lines = iter(results_fhandle.readlines())
cds2read_map = {}
while (True):
cds_id = next(lines, None)
read_ids = next(lines, None)
if not cds_id: break
cds2read_map[cds_id.strip()] = read_ids.strip().split(';')
results_fhandle.close()
return cds2read_map
def main():
'''
Script to analyse genes expressed for given tax id.
'''
# Input arguments
argparser = ArgParser()
args = argparser.parse_args()
# Access database
dataAccess = DataAccess(args)
print '1. Loading tax tree...'
tax_tree = TaxTree()
print 'done.'
print '2. Loading alignment file...'
read_container = ReadContainer()
read_container.load_alignment_data(args.alignment_file)
#---SET TAXIDS FOR ALL ALIGNMENTS--#
read_container.set_taxids(dataAccess)
print 'done'
# TODO: Here i should recognize host reads!
# ------------------------------------- #
#----------------------------------#
#------- LOAD ALL RECORDS -------#
print '4. Loading referenced records...'
record_container = RecordContainer()
record_container.set_db_access(dataAccess)
record_container.populate(read_container.fetch_all_reads_versions(), table='cds')
print 'done'
#----------------------------------#
#-- MAP ALIGNMENTS TO GENES -----#
print '5. Mapping alignments to genes...'
read_container.populate_cdss(record_container)
#----------------------------------#
#- RECORD ALL ALIGNEMENTS TO GENE -#
print '6. Populating CDS container...'
cds_aln_container = CdsAlnContainer()
cds_aln_container.populate(read_container.fetch_all_reads(format=list))
print 'done'
print("Loaded CDS container")
# Take only CDSs of given tax_id
# Remove CDSs with too low mean coverage value
min_mean_coverage = 10
min_length = 20
cds_alns = cds_aln_container.fetch_all_cds_alns(format=list)
print ( "All CDSs (all organisms): " + str(len(cds_alns)) )
cds_alns_targeted = [cds_aln for cds_aln in cds_alns
if cds_aln.get_tax_id() == args.tax_id
# Filters
and cds_aln.get_cds_length() > min_length
and cds_aln.get_mean_coverage() > min_mean_coverage]
# Remove CDSs with no gene/product
cds_alns_targeted = [cds_aln for cds_aln in cds_alns_targeted
if cds_aln.cds.gene != None
and cds_aln.cds.product != None]
# ------------------- CDSs filtered and ready to be analyzed ------------------- #
# Number of targeted CDSs
print ( "Targeted CDSs: " + str(len(cds_alns_targeted)) )
'''
print ("Sorting CDSs: stddev/mean")
cds_alns_sorted = sorted(cds_alns_targeted,
key=lambda cds_aln: cds_aln.get_std_over_mean(),
reverse=False)
# TODO: Here I should somehow determine which CDSs are "expressed", and which are not?
# Write to file stuff(gene, protein_id) for each cds_aln
print("Writing data to file")
path = args.export_path
f = open(path, 'w')
for cds_aln in cds_alns_targeted:
gene = cds_aln.cds.gene
product = cds_aln.cds.product
protein_id = cds_aln.cds.protein_id
f.write("{0} {1}\n".format(gene, protein_id))
f.close()
print("Done")
'''
# -------------------- #
'''
# Analyse those CDSs
print ( "Targeted CDSs: " + str(len(cds_alns_targeted)) )
# See the mean length of CDS
mean_cds_length = 0
no_locs_num = 0
for cds_aln in cds_alns_targeted:
try:
loc_length = cds_aln.get_cds_length()
mean_cds_length += loc_length
except:
no_locs_num += 1
# Get mean
mean_cds_length /= float(len(cds_alns_targeted))
print("---------------------------------------------")
print("Mean CDS length: " + str(mean_cds_length))
print("Nones: " + str(no_locs_num))
print("---------------------------------------------")
'''
'''
# Create folder where data about CDSs will be stored
if not os.path.exists(args.export_path):
os.makedirs(args.export_path)
# Export some amount of best CDSs
i = 1
for cds_aln in cds_alns_sorted:
filename = "cds_" + str(i) + ".txt"
coverage_path = os.path.join(args.export_path, filename)
print(str(i) + ": " + str(cds_aln.get_std_over_mean()))
cds_aln.coverage_to_file(coverage_path)
if i == 50: # TODO: Define this somehow as parameter
break
i += 1
# Load CDS container
'''
# Analyse stuff
# print("Analysing stuff!")
'''
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'
class GreedySolverTest (unittest.TestCase):
# setUp is executed before each test method
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 testAlignmentsCorrectlyInactivated(self):
'''
Loads correct results from results file and checks whether
all the reads for a CDS listed in the file are active and
whether all the other reads are inactive.
'''
cds2read = self._load_active_reads()
for (cds, cds_aln) in self.cds_aln_cont.cds_repository.items():
accession = cds.record_id
mapped_reads = cds2read[accession]
for cds_aln_subloc in cds_aln.aligned_regions.values():
if cds_aln_subloc.active:
assert (cds_aln_subloc.read_id in mapped_reads)
else:
assert (cds_aln_subloc.read_id not in mapped_reads)
def testCdsAlignmentContainerConsistency(self):
assert(Read2CDSSolver.test_cds_alignment_container_consistency(self.cds_aln_cont) == True)
def _load_active_reads (self):
results_fhandle = open(self.results_fpath)
lines = iter(results_fhandle.readlines())
cds2read_map = {}
while (True):
cds_id = next(lines, None)
read_ids = next(lines, None)
if not cds_id: break
cds2read_map[cds_id.strip()] = read_ids.strip().split(';')
results_fhandle.close()
return cds2read_map
def setUp(self):
self.read_container = ReadContainer()
self.record_container = RecordContainer()
# Create database access
db_access = DbQuery()
tax_tree = TaxTree(args.tax_tree)
host_determinator = HostDeterminator(dbquery=db_access,
tax_tree=tax_tree)
log.info("Started.")
processing_start = timing.start()
solver = Solver(host_determinator, read2cds_solver, tax_solver)
# Populate read container
# The read container type can now be determined from the input parameters
# and injected into the Solver
start = timing.start()
read_container = ReadContainer()
read_container.populate_from_aln_file(read_alignment_file=args.input)
elapsed_time = timing.end(start)
log.info("Populate read container - elapsed time: %s",
timing.humanize(elapsed_time))
# Populate record container
# The record container type can now be determine from the input parameters
# and injected into the Solver
start = timing.start()
record_container = RecordContainer()
record_container.set_db_access(db_access)
# Extract all records from database
record_container.populate(read_container.fetch_all_reads_versions())
elapsed_time = timing.end(start)
log.info("Populate record container - elapsed time: %s",
def main():
'''
Script to run binner in one of the most common
usage scenarios.
* load alignment data
* load taxonomy data
* do basic alignment data filtering (remove host reads ecc)
'''
#----------------------------------#
#------ INPUT ARGUMENTS -----------#
argparser = TestRunArgParser()
args = argparser.parse_args()
#----------------------------------#
#------- STATIC DATA SOURCE -------#
# CDS - GI2TAXID -- NAMES -- NODES #
dataAccess = DataAccess(args)
#raw_input('Data access created')
#----------------------------------#
#-------- TAXONOMY TREE -----------#
print '1. Loading tax tree...'
tax_tree = TaxTree()
# tax_tree.load_taxonomy_data(dataAccess)
print 'done.'
#----------------------------------#
#------- ALIGNMENT DATA SOURCE ----#
print '2. Loading alignment file...'
read_container = ReadContainer()
read_container.load_alignment_data(args.input)
#---SET TAXIDS FOR ALL ALIGNMENTS--#
read_container.set_taxids(dataAccess)
# Remember total number of reads
total_read_num = read_container.get_read_count()
print 'done'
#------- FILTER HOST READS -------#
print '3. Filtering host reads & alignments...'
new_reads = host_filter.filter_potential_host_reads(
read_container.fetch_all_reads(format=list),
tax_tree.tax2relevantTax,
tax_tree.potential_hosts,
#delete_host_alignments =
True,
#filter_unassigned =
True,
#unassigned_taxid=
-1,
host_filter.perc_of_host_alignments_larger_than)
dataAccess.clear_cache() # deletes gi2taxid cache
reads_with_no_host_alignments = host_filter.filter_potential_hosts_alignments(
new_reads,
tax_tree.tax2relevantTax,
tax_tree.potential_hosts,
True, # delete host alignments
True, # filter unassigned
-1) # unassigned taxid
host_read_count = len(read_container.fetch_all_reads(format=list)) - len(reads_with_no_host_alignments)
read_container.set_new_reads(reads_with_no_host_alignments)
print 'done'
#----------------------------------#
#------- LOAD ALL RECORDS -------#
print '4. Loading referenced records...'
record_container = RecordContainer()
record_container.set_db_access(dataAccess)
record_container.populate(read_container.fetch_all_reads_versions(), table='cds')
print 'done'
#----------------------------------#
#-- MAP ALIGNMENTS TO GENES -----#
print '5. Mapping alignments to genes...'
read_container.populate_cdss(record_container)
#----------------------------------#
#- RECORD ALL ALIGNEMENTS TO GENE -#
cds_aln_container = CdsAlnContainer()
cds_aln_container.populate(read_container.fetch_all_reads(format=list))
print 'done'
print '6. Estimating organisms present in sample...'
target_organisms = [633, 632, 263, 543, 86661, 1392, 55080, 1386] # What is this part?
print 'done.'
print '7. Annotating reads...'
annotated_reads = rstate.annotate_reads(
read_container.fetch_all_reads(format=list),
cds_aln_container.read2cds,
tax_tree,
target_organisms)
read_container.set_new_reads(annotated_reads)
print 'done'
print '8. Binning reads...'
orgs = bin_reads(
read_container.fetch_all_reads(format=list),
cds_aln_container.cds_repository,
cds_aln_container.read2cds,
tax_tree,
target_organisms,
None,
None,
False)
'''
for org in orgs.values():
print org.name
print len(set(org.get_reads()))
print len(org.identified_coding_regions)
print 'done.'
'''
print ("total_read_num: " + str(total_read_num))
print '9. Generating XML...'
dataset = Dataset(args.xml_description_file)
xml_organisms = []
host = Organism (host_read_count, host_read_count/float(total_read_num), None, None, "Host",
None, None, [], [], [], is_host=True)
xml_organisms.append(host)
for org in orgs.values():
xml_organisms.append(org.to_xml_organism(tax_tree, total_read_num))
xml_organisms.sort(key=operator.attrgetter("amount_count"), reverse=True)
xml = XMLOutput(dataset, xml_organisms, args.output)
xml.xml_output();
def main():
# Input arguments
argparser = ArgParser()
args = argparser.parse_args()
# Access database
dataAccess = DataAccess(args)
# ------------------ #
print '1. Loading tax tree...'
start = time.time()
tax_tree = TaxTree()
end = time.time()
print("done: {0:.2f} sec".format(end - start))
# ------------------ #
print '2. Loading alignment file...'
start = time.time()
read_container = ReadContainer()
read_container.load_alignment_data(args.alignment_file)
#---SET TAXIDS FOR ALL ALIGNMENTS--#
read_container.set_taxids(dataAccess)
end = time.time()
print("done: {0:.2f} sec".format(end - start))
# ------------------ #
# Create folder if does not exist
if not os.path.exists(args.export_folder):
os.makedirs(args.export_folder)
# File for data analysis summary
summary_path = os.path.join(args.export_folder, "CDSs_summary.txt")
cds_summary = open(summary_path, 'w')
if args.remove_host:
print "Removing host..."
start = time.time()
#------- FILTER HOST READS -------#
#print '3. Filtering host reads & alignments...'
new_reads = host_filter.filter_potential_host_reads(
read_container.fetch_all_reads(format=list),
tax_tree.tax2relevantTax,
tax_tree.potential_hosts,
#delete_host_alignments =
True,
#filter_unassigned =
True,
#unassigned_taxid=
-1,
host_filter.perc_of_host_alignments_larger_than)
dataAccess.clear_cache() # deletes gi2taxid cache
reads_with_no_host_alignments = host_filter.filter_potential_hosts_alignments(
new_reads,
tax_tree.tax2relevantTax,
tax_tree.potential_hosts,
True, # delete host alignments
True, # filter unassigned
-1) # unassigned taxid
read_count = len(read_container.fetch_all_reads(format=list))
host_read_count = read_count - len(reads_with_no_host_alignments)
non_host_read_count = read_count - host_read_count
cds_summary.write("total : {0:8d}\n".format(read_count))
cds_summary.write("host : {0:8d} {1:.2f}\n".format(host_read_count,
host_read_count / float(read_count)
))
cds_summary.write("non-host: {0:8d} {1:.2f}\n".format(non_host_read_count,
non_host_read_count / float(read_count)
))
# Set host-free reads
read_container.set_new_reads(reads_with_no_host_alignments)
end = time.time()
print("done: {0:.2f} sec".format(end - start))
#------- LOAD ALL RECORDS -------#
print '4. Loading referenced records...'
start = time.time()
record_container = RecordContainer()
record_container.set_db_access(dataAccess)
record_container.populate(read_container.fetch_all_reads_versions(), table='cds')
end = time.time()
print("done: {0:.2f} sec".format(end - start))
#-- MAP ALIGNMENTS TO GENES -----#
print '5. Mapping alignments to genes...'
start = time.time()
read_container.populate_cdss(record_container)
end = time.time()
print("done: {0:.2f} sec".format(end - start))
#- RECORD ALL ALIGNEMENTS TO GENE -#
print '6. Populating CDS container...'
start = time.time()
cds_aln_container = CdsAlnContainer()
cds_aln_container.populate(read_container.fetch_all_reads(format=list))
end = time.time()
print("done: {0:.2f} sec".format(end - start))
# ------------------------------- #
print 'Sorting CDSs ...DISABLED'
start = time.time()
# Sort CDSs by their "good looks"!
cds_alns = cds_aln_container.fetch_all_cds_alns(format=list)
'''
cds_alns = sorted(cds_alns,
key=lambda cds_aln: cds_aln.get_std_over_mean(),
reverse=False)
'''
end = time.time()
print("done: {0:.2f} sec".format(end - start))
# ------------------------------- #
'''
print "Exporting phase 0 - all CDSs..."
export_CDS_stats_data(cds_alns, args.export_folder, "0_all_CDSs.txt")
print "done"
'''
# Count Nones in cds_alns
nones = count_nones(cds_alns)
cds_summary.write("\n")
cds_summary.write("gene None : {0}\n".format(nones['gene']))
cds_summary.write("protein_id None: {0}\n".format(nones['protein_id']))
cds_summary.write("product None : {0}\n".format(nones['product']))
cds_summary.write("\n")
cds_summary.write("CDSs all: {0}\n".format(len(cds_alns)))
print 'Filtering valid CDSs...'
start = time.time()
# Remove CDSs with too low mean coverage value or length
min_mean_coverage = 0
min_length = 0
cds_alns_targeted = [cds_aln for cds_aln in cds_alns
# Filters
if cds_aln.get_cds_length() > min_length
and cds_aln.get_mean_coverage() > min_mean_coverage]
# Remove CDSs with no gene/product
cds_alns_targeted = [cds_aln for cds_aln in cds_alns_targeted
if cds_aln.cds.product is not None]
#if cds_aln.cds.gene != None
#and cds_aln.cds.product != None]
end = time.time()
print("done: {0:.2f} sec".format(end - start))
# All valid CDSs - Output coverage/length histogram data
print "Exporting phase 1 - all CDSs..."
start = time.time()
export_CDS_stats_data(cds_alns_targeted, args.export_folder, "1_all_valid_CDSs.txt")
end = time.time()
print("done: {0:.2f} sec".format(end - start))
# ------------------- CDSs filtered and ready to be analyzed ------------------- #
print 'Extracting ribosomal CDSs...'
# Number of targeted CDSs
cds_summary.write("CDSs valid: {0}\n".format(len(cds_alns_targeted)))
cds_alns_ribosomal = []
for cds_aln in cds_alns_targeted:
# If has word "ribosomal" in name, store coverage data for graph
gene = cds_aln.cds.gene
product = cds_aln.cds.product
protein_id = cds_aln.cds.protein_id
if is_ribosomal(product):
#print("{0} {1} {2}\n".format(gene, protein_id, product))
cds_alns_ribosomal.append(cds_aln)
print 'done'
# ------------------- Ribosomal CDSs acquired! --------------------- #
print 'Analysing ribosomals...'
# Extract interesting data
# Mean coverage, max coverage
mm_cov = 0
max_cov = 0
for cds_aln in cds_alns_ribosomal:
mean_cov = cds_aln.get_mean_coverage()
mm_cov += mean_cov
max_cov = max(max_cov, mean_cov)
if mm_cov > 0:
mm_cov /= len(cds_alns_ribosomal)
cds_summary.write("ribosomals all {0}\n".format(len(cds_alns_ribosomal)))
cds_summary.write("mean coverage: {0}\n".format(mm_cov))
cds_summary.write("max coverage : {0}\n".format(max_cov))
print 'done'
# Ribosomal CDSs only - Output coverage/length histogram
print "Exporting phase 2 - ribosomal CDSs only..."
export_CDS_stats_data(cds_alns_ribosomal, args.export_folder, "2_ribosomal_CDSs.txt")
print "done"
# ------------------- Making biological sense - choosing CDSs -------------------- #
print 'Filtering under-average ribosomals...'
# NOTE: take length into consideration?
cds_alns_ribosomal = [cds_aln for cds_aln in cds_alns_ribosomal
# Filters
if cds_aln.get_mean_coverage() > mm_cov]
print 'done'
cds_summary.write("ribosomals over-mean: {0}\n".format(len(cds_alns_ribosomal)))
cds_summary.close()
print 'Phase 3 - filtered ribosomal CDSs...'
export_CDS_stats_data(cds_alns_ribosomal, args.export_folder, "3_ribosomal_CDSs_filtered.txt")
print 'done'
# Store charts cov data - if selected so
if args.export_charts:
print "Exporting chart coverage data..."
export_CDS_graph_data(cds_alns_ribosomal, args.export_charts)
print "done."
# --------------------- I have chosen CDSs - determine species and analyse ------------------------ #
# Species level resolution
# See which species are present - dump ones with not enough CDSs
# NOTE: So far done in determine_species_by_ribosomals.py
CDS_count = {} # Count CDSs of each species
species_set = set() # Get estimated tax_ids
for cds_aln in cds_alns_ribosomal:
tax_id = cds_aln.cds.taxon
# Put each tax_id up to the "species" level
tax_id_species = tax_tree.get_parent_with_rank(tax_id, 'species')
species_set.add(tax_id_species)
CDS_count[tax_id_species] = CDS_count.get(tax_id_species, 0) + 1
# Get reported CDSs ids
reported_CDS_ids = set()
for cds_aln in cds_alns_ribosomal:
reported_CDS_ids.add(cds_aln.cds.id)
# ------------ Read assignment analysis -------------- #
print "Read assignment analysis..."
reads = read_container.fetch_all_reads(format=list)
assignment_analysis(species_set, reads, tax_tree, args.export_folder, CDS_count)
# Create database access
db_access = DbQuery()
tax_tree = TaxTree(args.tax_tree)
host_determinator = HostDeterminator(dbquery=db_access, tax_tree=tax_tree)
log.info("Started.")
processing_start = timing.start()
solver = Solver(host_determinator, read2cds_solver, tax_solver)
# Populate read container
# The read container type can now be determined from the input parameters
# and injected into the Solver
start = timing.start()
read_container = ReadContainer()
read_container.populate_from_aln_file(read_alignment_file=args.input)
elapsed_time = timing.end(start)
log.info("Populate read container - elapsed time: %s",
timing.humanize(elapsed_time))
# Populate record container
# The record container type can now be determine from the input parameters
# and injected into the Solver
start = timing.start()
record_container = RecordContainer()
record_container.set_db_access(db_access)
# Extract all records from database
record_container.populate(read_container.fetch_all_reads_versions())
elapsed_time = timing.end(start)
log.info("Populate record container - elapsed time: %s",
def main():
'''
Script to run binner in one of the most common
usage scenarios.
* load alignment data
* load taxonomy data
* do basic alignment data filtering (remove host reads ecc)
'''
#----------------------------------#
#------ INPUT ARGUMENTS -----------#
argparser = PickleParser()
args = argparser.parse_args()
#----------------------------------#
#------- STATIC DATA SOURCE -------#
# CDS - GI2TAXID -- NAMES -- NODES #
dataAccess = DataAccess(args)
#raw_input('Data access created')
#----------------------------------#
#-------- TAXONOMY TREE -----------#
print '1. Loading tax tree...'
tax_tree = TaxTree()
# tax_tree.load_taxonomy_data(dataAccess)
print 'done.'
#----------------------------------#
#------- ALIGNMENT DATA SOURCE ----#
print '2. Loading alignment file...'
read_container = ReadContainer()
read_container.load_alignment_data(args.input)
#---SET TAXIDS FOR ALL ALIGNMENTS--#
read_container.set_taxids(dataAccess)
print 'done'
#------- FILTER HOST READS -------#
print '3. Filtering host reads & alignments...'
new_reads = host_filter.filter_potential_host_reads(
read_container.fetch_all_reads(format=list),
tax_tree.tax2relevantTax,
tax_tree.potential_hosts,
#delete_host_alignments =
True,
#filter_unassigned =
True,
#unassigned_taxid=
-1,
host_filter.perc_of_host_alignments_larger_than)
dataAccess.clear_cache() # deletes gi2taxid cache
reads_with_no_host_alignments = host_filter.filter_potential_hosts_alignments(
new_reads,
tax_tree.tax2relevantTax,
tax_tree.potential_hosts,
True, # delete host alignments
True, # filter unassigned
-1) # unassigned taxid
host_read_count = len(read_container.fetch_all_reads(format=list)) - len(reads_with_no_host_alignments)
read_container.set_new_reads(reads_with_no_host_alignments)
print 'done'
#----------------------------------#
#------- LOAD ALL RECORDS -------#
print '4. Loading referenced records...'
record_container = RecordContainer()
record_container.set_db_access(dataAccess)
record_container.populate(read_container.fetch_all_reads_versions(), table='cds')
record_container.populate(read_container.fetch_all_reads_versions(), table='rrna')
print 'done'
#----------------------------------#
#-- MAP ALIGNMENTS TO GENES -----#
print '5. Mapping alignments to genes...'
read_container.populate_cdss(record_container)
#----------------------------------#
#- RECORD ALL ALIGNEMENTS TO GENE -#
cds_aln_container = CdsAlnContainer()
cds_aln_container.populate(read_container.fetch_all_reads(format=list))
print 'done'
def main():
'''
Script to identify analyse ribosomal genes expressed.
'''
# Input arguments
argparser = ArgParser()
args = argparser.parse_args()
# Access database
dataAccess = DataAccess(args)
#print '1. Loading tax tree...'
tax_tree = TaxTree()
#print 'done.'
#print '2. Loading alignment file...'
read_container = ReadContainer()
read_container.load_alignment_data(args.alignment_file)
#---SET TAXIDS FOR ALL ALIGNMENTS--#
read_container.set_taxids(dataAccess)
#print 'done'
'''
# TODO: Here i should recognize host reads!
#------- FILTER HOST READS -------#
#print '3. Filtering host reads & alignments...'
new_reads = host_filter.filter_potential_host_reads(
read_container.fetch_all_reads(format=list),
tax_tree.tax2relevantTax,
tax_tree.potential_hosts,
#delete_host_alignments =
True,
#filter_unassigned =
True,
#unassigned_taxid=
-1,
host_filter.perc_of_host_alignments_larger_than)
dataAccess.clear_cache() # deletes gi2taxid cache
reads_with_no_host_alignments = host_filter.filter_potential_hosts_alignments(
new_reads,
tax_tree.tax2relevantTax,
tax_tree.potential_hosts,
True, # delete host alignments
True, # filter unassigned
-1) # unassigned taxid
read_count = len(read_container.fetch_all_reads(format=list))
host_read_count = read_count - len(reads_with_no_host_alignments)
non_host_read_count = read_count - host_read_count
print ("total : {0:8d}".format(read_count))
print ("host : {0:8d} {1:.2f}".format(host_read_count,
host_read_count / float(read_count)
))
print ("non-host: {0:8d} {1:.2f}".format(non_host_read_count,
non_host_read_count / float(read_count)
))
print
read_container.set_new_reads(reads_with_no_host_alignments)
'''
# ------------------------------------- #
#----------------------------------#
#------- LOAD ALL RECORDS -------#
#print '4. Loading referenced records...'
record_container = RecordContainer()
record_container.set_db_access(dataAccess)
record_container.populate(read_container.fetch_all_reads_versions(), table='cds')
#print 'done'
#----------------------------------#
#-- MAP ALIGNMENTS TO GENES -----#
#print '5. Mapping alignments to genes...'
read_container.populate_cdss(record_container)
#----------------------------------#
#- RECORD ALL ALIGNEMENTS TO GENE -#
#print '6. Populating CDS container...'
cds_aln_container = CdsAlnContainer()
cds_aln_container.populate(read_container.fetch_all_reads(format=list))
#print 'done'
#print("Loaded CDS container")
# Take only CDSs of given tax_id
# Remove CDSs with too low mean coverage value
min_mean_coverage = 0
min_length = 0
cds_alns = cds_aln_container.fetch_all_cds_alns(format=list)
print ( "CDSs all : " + str(len(cds_alns)) )
cds_alns_targeted = [cds_aln for cds_aln in cds_alns
# Filters
if cds_aln.get_cds_length() > min_length
and cds_aln.get_mean_coverage() > min_mean_coverage]
# Remove CDSs with no gene/product
cds_alns_targeted = [cds_aln for cds_aln in cds_alns_targeted
if cds_aln.cds.gene != None
and cds_aln.cds.product != None]
# ------------------- CDSs filtered and ready to be analyzed ------------------- #
# Number of targeted CDSs
print ( "CDSs valid: " + str(len(cds_alns_targeted)) )
print
cds_alns_ribosomal = []
for cds_aln in cds_alns_targeted:
# If has word "ribosomal" in name, store coverage data for graph
gene = cds_aln.cds.gene
product = cds_aln.cds.product
protein_id = cds_aln.cds.protein_id
if "ribosomal" in product:
#print("{0} {1} {2}\n".format(gene, protein_id, product))
cds_alns_ribosomal.append(cds_aln)
# ------------------- Ribosomal CDSs acquired! --------------------- #
# Sort it!
cds_alns_ribosomal = sorted(cds_alns_ribosomal,
key=lambda cds_aln: cds_aln.get_std_over_mean(),
reverse=False)
# Extract interesting data
# Mean coverage, max coverage
mm_cov = 0
max_cov = 0
for cds_aln in cds_alns_ribosomal:
mean_cov = cds_aln.get_mean_coverage()
mm_cov += mean_cov
max_cov = max(max_cov, mean_cov)
if mm_cov > 0:
mm_cov /= len(cds_alns_ribosomal)
# Print
print("ribosomals: " + str(len(cds_alns_ribosomal)))
print("mean coverage: " + str(mm_cov))
print("max coverage : {0}".format(max_cov))
print
for cds_aln in cds_alns_ribosomal:
gene = cds_aln.cds.gene
product = cds_aln.cds.product
protein_id = cds_aln.cds.protein_id
taxon = cds_aln.cds.taxon
name = tax_tree.nodes[taxon].organism_name
print("{0:4} {1:10} {2:50} {3:10d} {4:60}".format(gene, protein_id, product, taxon, name))
# Store graph data
export_CDS_graph_data(cds_alns_ribosomal, args.export_path)
'''