def main():
logger = init_logging_console_only(logging.INFO)
try:
logger.info('Starting.')
fname = 'censored1.fastq'
bad_cycles_filename = 'bad_cycles.csv'
dd = MicallDD(fname, bad_cycles_filename)
read_indexes = range(len(dd.reads))
run_test = True
if run_test:
min_indexes = dd.ddmin(read_indexes)
else:
min_indexes = read_indexes
dd._test(min_indexes, debug_file_prefix='micall_debug')
# dd.write_simple_fastq(fname + '_min.fastq', min_indexes)
logger.info('Done.')
except Exception as ex:
logger.error('Failed.', exc_info=ex)
from micall.utils.externals import Bowtie2, Bowtie2Build, LineCounter
from micall.utils.translation import reverse_and_complement
CONSENSUS_Q_CUTOFF = 20 # Min Q for base to contribute to conseq (pileup2conseq)
MIN_MAPPING_EFFICIENCY = 0.95 # Fraction of fastq reads mapped needed
MAX_REMAPS = 3 # Number of remapping attempts if mapping efficiency unsatisfied
# SAM file format
fieldnames = [
'qname', 'flag', 'rname', 'pos', 'mapq', 'cigar', 'rnext', 'pnext', 'tlen',
'seq', 'qual'
]
cigar_re = re.compile('[0-9]+[MIDNSHPX=]') # CIGAR token
logger = miseq_logging.init_logging_console_only(logging.DEBUG)
indel_re = re.compile('[+-][0-9]+')
line_counter = LineCounter()
def is_first_read(flag):
"""
Interpret bitwise flag from SAM field.
Returns True or False indicating whether the read is the first read in a pair.
"""
IS_FIRST_SEGMENT = 0x40
return (int(flag) & IS_FIRST_SEGMENT) != 0
def is_unmapped_read(flag):
"""
simple_prefix,
pssm,
ruby_script,
delete_results=False)
if not txtfilename.endswith('.txt'):
with open(simple_prefix + '.txt', 'w') as simplefile:
for line in simple_remap_lines:
simplefile.write(line)
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description='Find the simplest test failure by trimming SAM files.')
parser.add_argument('workdir', help='path to folder holding SAM files')
parser.add_argument('ruby_script', help='path to Ruby version of G2P')
parser.add_argument('--pattern',
default='*.remap.csv',
help='File name pattern to match SAM files')
args = parser.parse_args()
logger = init_logging_console_only(logging.INFO)
pssm = Pssm(path_to_lookup='../g2p/g2p_fpr.txt',
path_to_matrix='../g2p/g2p.matrix')
for txtfilename in sorted(
glob.glob(os.path.join(args.workdir, args.pattern))):
logger.info(os.path.basename(txtfilename))
compare_conseqs(txtfilename, args.ruby_script, pssm)
logger.info('Done.')
parser.add_argument('coord_ins_csv',
type=argparse.FileType('w'),
help='CSV containing insertions relative to coordinate reference')
parser.add_argument('conseq_csv',
type=argparse.FileType('w'),
help='CSV containing consensus sequences')
parser.add_argument('failed_align_csv',
type=argparse.FileType('w'),
help='CSV containing any consensus that failed to align')
parser.add_argument('nuc_variants_csv',
type=argparse.FileType('w'),
help='CSV containing top nucleotide variants')
return parser.parse_args()
logger = miseq_logging.init_logging_console_only(logging.DEBUG)
MAX_CUTOFF = 'MAX'
class SequenceReport(object):
""" Hold the data for several reports related to a sample's genetic sequence.
To use a report object, read a group of aligned reads that mapped to a
single region, and then write out all the reports for that region.
"""
def __init__(self,
insert_writer,
projects,
conseq_mixture_cutoffs):
""" Create an object instance.
print 'Simplifying sample {}'.format(txtfilename)
reads = defaultdict(list)
read_fastq(txtfilename, reads)
read_count = len(reads)
read_fastq(get_reverse_filename(txtfilename), reads)
added_count = len(reads) - read_count
if added_count > 0:
raise RuntimeError('Found {} new reads.'.format(added_count))
reads = reads.values()
simple_filename = txtfilename.replace('censored1.fastq',
'simple_censored1.fastq')
simple_fastq_lines = ddmin(reads, simple_filename)
write_simple_fastq(simple_filename, simple_fastq_lines)
if __name__ == '__main__':
logger = init_logging_console_only(logging.INFO)
test_file('/home/don/git/MiCall/micall/tests/working/61515A-HCV_S1_uncensored1.fastq')
exit()
parser = argparse.ArgumentParser(
description='Find the simplest test failure by trimming FASTQ files.')
parser.add_argument('workdir', help='path to folder holding FASTQ files')
parser.add_argument('--pattern',
default='*censored1.fastq',
help='File name pattern to match FASTQ files')
args = parser.parse_args()
filenames = glob.glob(os.path.join(args.workdir, args.pattern))
filenames.sort()
