def trim(run):
# (re) create the trim status file
run.trim_status_file_h = open(run.trim_status_file_name, "w")
# do the trim work
mytrim = TrimRun(run)
# pass True to write out the straight fasta file of all trimmed non-deleted seqs
# Remember: this is before chimera checking
trim_codes = mytrim.trimrun(True)
trim_results_dict = {}
if trim_codes[0] == 'SUCCESS':
# setup to write the status
new_lane_keys = trim_codes[2]
trim_results_dict['status'] = "success"
trim_results_dict['new_lane_keys'] = new_lane_keys
logger.debug("Trimming finished successfully")
# write the data files
mytrim.write_data_files(new_lane_keys)
run.trim_status_file_h.write(json.dumps(trim_results_dict))
run.trim_status_file_h.close()
else:
logger.debug("Trimming finished ERROR")
trim_results_dict['status'] = "error"
trim_results_dict['code1'] = trim_codes[1]
trim_results_dict['code2'] = trim_codes[2]
run.trim_status_file_h.write(json.dumps(trim_results_dict))
run.trim_status_file_h.close()
sys.exit()
def trim(runobj):
# def is in utils.py
# open_zipped_directory(runobj.run_date, runobj.output_dir)
# (re) create the trim status file
runobj.trim_status_file_h = open(runobj.trim_status_file_name, "w")
idx_keys = get_keys(runobj)
# do the trim work
mytrim = TrimRun(runobj, idx_keys)
# pass True to write out the straight fasta file of all trimmed non-deleted seqs
# Remember: this is before chimera checking
# trim_codes should alwas be a tuple with 3 elements!
if runobj.vamps_user_upload:
trim_codes = mytrim.trimrun_vamps(True)
else:
if runobj.platform == 'illumina':
trim_codes = mytrim.filter_illumina()
# trim_codes = mytrim.trim_illumina(file_list = trim_codes[2])
elif runobj.platform == '454':
trim_codes = mytrim.trimrun_454(True)
elif runobj.platform == 'ion-torrent':
trim_codes = mytrim.trimrun_ion_torrent(True)
else:
trim_codes = ('ERROR', 'No Platform Found', '')
trim_results_dict = {}
if trim_codes[0] == 'SUCCESS':
# setup to write the status
new_lane_keys = trim_codes[2]
trimmed_seq_count = trim_codes[1]
if trimmed_seq_count == 0 or trimmed_seq_count == '0':
trim_results_dict['status'] = "ERROR"
logger.debug("Trimming finished: ERROR: no seqs passed trim")
else:
trim_results_dict['status'] = "success"
logger.debug("Trimming finished successfully")
trim_results_dict['new_lane_keys'] = new_lane_keys
trim_results_dict['trimmed_seq_count'] = trimmed_seq_count
# write the data files
mytrim.write_data_files(new_lane_keys)
runobj.trim_status_file_h.write(json.dumps(trim_results_dict) + "\n")
runobj.trim_status_file_h.close()
runobj.run_status_file_h.write(json.dumps(trim_results_dict) + "\n")
runobj.run_status_file_h.close()
else:
logger.debug("Trimming finished ERROR")
trim_results_dict['status'] = "ERROR"
trim_results_dict['code1'] = trim_codes[1]
trim_results_dict['code2'] = trim_codes[2]
runobj.trim_status_file_h.write(json.dumps(trim_results_dict) + "\n")
runobj.trim_status_file_h.close()
runobj.run_status_file_h.write(json.dumps(trim_results_dict) + "\n")
runobj.run_status_file_h.close()
sys.exit("Trim Error")
def trim(runobj):
# def is in utils.py
#open_zipped_directory(runobj.run_date, runobj.output_dir)
# (re) create the trim status file
runobj.trim_status_file_h = open(runobj.trim_status_file_name, "w")
idx_keys = get_keys(runobj)
# do the trim work
mytrim = TrimRun(runobj, idx_keys)
# pass True to write out the straight fasta file of all trimmed non-deleted seqs
# Remember: this is before chimera checking
# trim_codes should alwas be a tuple with 3 elements!
if runobj.vamps_user_upload:
trim_codes = mytrim.trimrun_vamps(True)
else:
if runobj.platform == 'illumina':
trim_codes = mytrim.filter_illumina()
# trim_codes = mytrim.trim_illumina(file_list = trim_codes[2])
elif runobj.platform == '454':
trim_codes = mytrim.trimrun_454(True)
elif runobj.platform == 'ion-torrent':
trim_codes = mytrim.trimrun_ion_torrent(True)
else:
trim_codes = ('ERROR','No Platform Found','')
trim_results_dict = {}
if trim_codes[0] == 'SUCCESS':
# setup to write the status
new_lane_keys = trim_codes[2]
trimmed_seq_count = trim_codes[1]
if trimmed_seq_count == 0 or trimmed_seq_count == '0':
trim_results_dict['status'] = "ERROR"
logger.debug("Trimming finished: ERROR: no seqs passed trim")
else:
trim_results_dict['status'] = "success"
logger.debug("Trimming finished successfully")
trim_results_dict['new_lane_keys'] = new_lane_keys
trim_results_dict['trimmed_seq_count'] = trimmed_seq_count
# write the data files
mytrim.write_data_files(new_lane_keys)
runobj.trim_status_file_h.write(json.dumps(trim_results_dict)+"\n")
runobj.trim_status_file_h.close()
runobj.run_status_file_h.write(json.dumps(trim_results_dict)+"\n")
runobj.run_status_file_h.close()
else:
logger.debug("Trimming finished ERROR")
trim_results_dict['status'] = "ERROR"
trim_results_dict['code1'] = trim_codes[1]
trim_results_dict['code2'] = trim_codes[2]
runobj.trim_status_file_h.write(json.dumps(trim_results_dict)+"\n")
runobj.trim_status_file_h.close()
runobj.run_status_file_h.write(json.dumps(trim_results_dict)+"\n")
runobj.run_status_file_h.close()
sys.exit("Trim Error")
def setUp(self):
"""
set up data used in the tests.
setUp is called before each test function execution.
"""
args = unittestargs()
run = Run('./unittesting/unittest10.ini')
self.unittest_trimrun = TrimRun(run,'./unittesting',args)
trim_code = self.unittest_trimrun.trimrun()
self.id1 = 'GFADN4I02JYSYM'
self.seq1 = 'CGTGATGGGCGTAAAGTGGGTTTAAAGGGTGCGTAGGCGGATTTATAAGTCAGTGGTGAAAGCCTGCGGCTCAACCGTAG\
AATTGCCATTGATACTGTAGATCTTGAGTGCAATCGAGGTGGTTGGAATACGTAGTGTAGCTGTGAAATGCATAGATATTACGTAGAACACC\
AATTGCGAAGGCAGATCACTAGATTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCG\
TAAACGATGGATACTAGGTGTTCGGGATAATTGAGTCCTGAGTGCCCAAGCGAAAGCGATAAGTATCCCACCTGGGGAGTACGTCCGCAAGG\
ATGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCTGGGCTAAAT\
GTTAGTGACGTACCGTGAAAGCGGTATTTCTTCGGACACGAAACA'
self.trim_info1 = self.unittest_trimrun.do_trim(self.id1,self.seq1)
# proximal deleted:
self.id2 = 'GFADN4I02HD8KF'
self.seq2 = 'TGGGCCAACGCGAAAAACCTTACCTCGGAGGTTACCCCCTTCGGTGCCGCAGCTAACGCATTAAGTACTCCG\
CCTGGGGAGTACGCACGCAAGTGTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGTAGCGGAGCATGTGGTTTAATTCGAAGCAACGCGAA\
GAACCTTACCTAGGCTTGACATCCTTCTGACCGAGGATTAATCTCCTCAGGTGGTGCATGGGCTGTCG'
self.trim_info2 = self.unittest_trimrun.do_trim(self.id2,self.seq2)
# deleted for key:
self.id3 = 'GFADN4I02HD8KF'
self.seq3 = 'TGGCCAACGCGAAAAACCTTACCTCGGAGGTTACCCCCTTCGGTGCCGCAGCTAACGCATTAAGTACTCCG\
CCTGGGGAGTACGCACGCAAGTGTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGTAGCGGAGCATGTGGTTTAATTCGAAGCAACGCGAA\
GAACCTTACCTAGGCTTGACATCCTTCTGACCGAGGATTAATCTCCTCAGGTGGTGCATGGGCTGTCG'
self.trim_info3 = self.unittest_trimrun.do_trim(self.id3,self.seq3)
# deleted for N:
self.id4 = 'GFADN4I02JYSYM'
self.seq4 = 'CGTGATGGGCGTAAAGTGGGTTTAAAGGGTGCGTAGGCGGATTTATAAGTCAGTGGTGAAAGCCTGCGGCTCAACCGTAG\
AATTGCCATTGATACTGTAGATCTTGAGTGCAATCGAGGTGGTTGGAATACGTAGTGTAGCTGTGAAATGCATAGATATTACGTAGAACACC\
AATTGCGAAGGCAGATCACTAGATTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCG\
TAAACGATGGATACTAGGTGTTCGGGATAATTGAGTCCNTGAGTGCCCAAGCGAAAGCGATAAGTATCCCACCTGGGGAGTACGTCCGCAAGG\
ATGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCTGGGCTAAAT\
GTTAGTGACGTACCGTGAAAGCGGTATTTCTTCGGACACGAAACA'
self.trim_info4 = self.unittest_trimrun.do_trim(self.id4,self.seq4)
# deleted for distal:
self.id5 = 'GFADN4I02I64C9'
self.seq5 = 'TGGGCTGGGCGTAAAGCGAAGGGTGCGTAGGCGGATTTATAAGTCAGTGGTGAAAGCCTGCGGCTCAACCGTAGAATTG\
CCATTGATACTGTAGATCTTGAGTGCAATCGAGGTTTTGGTTGGAATACGTAGTGTAGCGGTGAAATGCATAGATATTACGTAGAACACCAATTGCGAAGGCA\
GATCACTAGATTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGATACTAGGTGT\
TCGGGATAATTGAGTCCTGAGTGCCCAAGCGAAAGCGATAAGTATCCCACCTGGGGAGTACGTCCGCAAGGATGAAACTCAAAGGAATTGACGGGGGCCC\
GCACAAGCGGTGGAGCATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCTGGGCTAAATGTTAGT'
self.trim_info5 = self.unittest_trimrun.do_trim(self.id5,self.seq5)
def trim(runobj):
# def is in utils.py
# open_zipped_directory(runobj.run_date, runobj.output_dir)
# (re) create the trim status file
runobj.trim_status_file_h = open(runobj.trim_status_file_name, "w")
# do the trim work
mytrim = TrimRun(runobj)
# pass True to write out the straight fasta file of all trimmed non-deleted seqs
# Remember: this is before chimera checking
if runobj.platform == "illumina":
trim_codes = mytrim.trimrun_illumina(True)
elif runobj.platform == "454":
trim_codes = mytrim.trimrun_454(True)
elif runobj.platform == "ion-torrent":
trim_codes = mytrim.trimrun_ion_torrent(True)
else:
trim_codes = ["ERROR", "No Platform Found"]
trim_results_dict = {}
if trim_codes[0] == "SUCCESS":
# setup to write the status
new_lane_keys = trim_codes[2]
trim_results_dict["status"] = "success"
trim_results_dict["new_lane_keys"] = new_lane_keys
logger.debug("Trimming finished successfully")
# write the data files
mytrim.write_data_files(new_lane_keys)
runobj.trim_status_file_h.write(json.dumps(trim_results_dict))
runobj.trim_status_file_h.close()
runobj.run_status_file_h.write(json.dumps(trim_results_dict) + "\n")
runobj.run_status_file_h.close()
else:
logger.debug("Trimming finished ERROR")
trim_results_dict["status"] = "error"
trim_results_dict["code1"] = trim_codes[1]
trim_results_dict["code2"] = trim_codes[2]
runobj.trim_status_file_h.write(json.dumps(trim_results_dict))
runobj.trim_status_file_h.close()
runobj.run_status_file_h.write(json.dumps(trim_results_dict) + "\n")
runobj.run_status_file_h.close()
sys.exit("Trim Error")
class TestTrimFunctions(unittest.TestCase):
def setUp(self):
"""
set up data used in the tests.
setUp is called before each test function execution.
"""
args = unittestargs()
run = Run('./unittesting/unittest10.ini')
self.unittest_trimrun = TrimRun(run,'./unittesting',args)
trim_code = self.unittest_trimrun.trimrun()
self.id1 = 'GFADN4I02JYSYM'
self.seq1 = 'CGTGATGGGCGTAAAGTGGGTTTAAAGGGTGCGTAGGCGGATTTATAAGTCAGTGGTGAAAGCCTGCGGCTCAACCGTAG\
AATTGCCATTGATACTGTAGATCTTGAGTGCAATCGAGGTGGTTGGAATACGTAGTGTAGCTGTGAAATGCATAGATATTACGTAGAACACC\
AATTGCGAAGGCAGATCACTAGATTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCG\
TAAACGATGGATACTAGGTGTTCGGGATAATTGAGTCCTGAGTGCCCAAGCGAAAGCGATAAGTATCCCACCTGGGGAGTACGTCCGCAAGG\
ATGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCTGGGCTAAAT\
GTTAGTGACGTACCGTGAAAGCGGTATTTCTTCGGACACGAAACA'
self.trim_info1 = self.unittest_trimrun.do_trim(self.id1,self.seq1)
# proximal deleted:
self.id2 = 'GFADN4I02HD8KF'
self.seq2 = 'TGGGCCAACGCGAAAAACCTTACCTCGGAGGTTACCCCCTTCGGTGCCGCAGCTAACGCATTAAGTACTCCG\
CCTGGGGAGTACGCACGCAAGTGTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGTAGCGGAGCATGTGGTTTAATTCGAAGCAACGCGAA\
GAACCTTACCTAGGCTTGACATCCTTCTGACCGAGGATTAATCTCCTCAGGTGGTGCATGGGCTGTCG'
self.trim_info2 = self.unittest_trimrun.do_trim(self.id2,self.seq2)
# deleted for key:
self.id3 = 'GFADN4I02HD8KF'
self.seq3 = 'TGGCCAACGCGAAAAACCTTACCTCGGAGGTTACCCCCTTCGGTGCCGCAGCTAACGCATTAAGTACTCCG\
CCTGGGGAGTACGCACGCAAGTGTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGTAGCGGAGCATGTGGTTTAATTCGAAGCAACGCGAA\
GAACCTTACCTAGGCTTGACATCCTTCTGACCGAGGATTAATCTCCTCAGGTGGTGCATGGGCTGTCG'
self.trim_info3 = self.unittest_trimrun.do_trim(self.id3,self.seq3)
# deleted for N:
self.id4 = 'GFADN4I02JYSYM'
self.seq4 = 'CGTGATGGGCGTAAAGTGGGTTTAAAGGGTGCGTAGGCGGATTTATAAGTCAGTGGTGAAAGCCTGCGGCTCAACCGTAG\
AATTGCCATTGATACTGTAGATCTTGAGTGCAATCGAGGTGGTTGGAATACGTAGTGTAGCTGTGAAATGCATAGATATTACGTAGAACACC\
AATTGCGAAGGCAGATCACTAGATTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCG\
TAAACGATGGATACTAGGTGTTCGGGATAATTGAGTCCNTGAGTGCCCAAGCGAAAGCGATAAGTATCCCACCTGGGGAGTACGTCCGCAAGG\
ATGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCTGGGCTAAAT\
GTTAGTGACGTACCGTGAAAGCGGTATTTCTTCGGACACGAAACA'
self.trim_info4 = self.unittest_trimrun.do_trim(self.id4,self.seq4)
# deleted for distal:
self.id5 = 'GFADN4I02I64C9'
self.seq5 = 'TGGGCTGGGCGTAAAGCGAAGGGTGCGTAGGCGGATTTATAAGTCAGTGGTGAAAGCCTGCGGCTCAACCGTAGAATTG\
CCATTGATACTGTAGATCTTGAGTGCAATCGAGGTTTTGGTTGGAATACGTAGTGTAGCGGTGAAATGCATAGATATTACGTAGAACACCAATTGCGAAGGCA\
GATCACTAGATTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGATACTAGGTGT\
TCGGGATAATTGAGTCCTGAGTGCCCAAGCGAAAGCGATAAGTATCCCACCTGGGGAGTACGTCCGCAAGGATGAAACTCAAAGGAATTGACGGGGGCCC\
GCACAAGCGGTGGAGCATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCTGGGCTAAATGTTAGT'
self.trim_info5 = self.unittest_trimrun.do_trim(self.id5,self.seq5)
def test_lane_key(self):
self.assertEqual(self.trim_info1['lane_key'],'1_CGTGA')
def test_primer_name(self):
self.assertEqual(self.trim_info1['primer_name'],'565F')
def test_eaxct_right(self):
self.assertEqual(self.trim_info1['exact_right'],'AGGTGGT')
def test_exact_left(self):
self.assertEqual(self.trim_info1['exact_left'],'TGGGCGTAAAG')
def test_deleted(self):
self.assertEqual(self.trim_info1['deleted'],False)
def test_orientation(self):
self.assertEqual(self.trim_info1['orientation'],'+')
####################################################################
def test_deleted_proximal(self):
self.assertEqual(self.trim_info2['deleted'],True)
self.assertEqual(self.trim_info2['delete_reason'],'proximal')
def test_deleted_key(self):
self.assertEqual(self.trim_info3['deleted'],True)
self.assertEqual(self.trim_info3['delete_reason'],'runkey')
def test_deleted_N(self):
self.assertEqual(self.trim_info4['deleted'],True)
self.assertEqual(self.trim_info4['delete_reason'],'N')
def test_deleted_distal(self):
print self.trim_info5
self.assertEqual(self.trim_info5['deleted'],True)
self.assertEqual(self.trim_info5['delete_reason'],'distal')
