def type_sequences( input, grouping=GROUPING,
exon_fofn=None,
genomic_reference=None,
cDNA_reference=None,
loci=None):
"""
Pick the top Amplicon Analysis consensus seqs from a Fasta by Nreads
"""
log_file = get_log_file( input )
initialize_logger( log, log_file=log_file )
# First, get any references not specified by the user
grouping = grouping or GROUPING
exon_fofn = exon_fofn or get_exon_reference()
genomic_reference = genomic_reference or get_genomic_reference()
cDNA_reference = cDNA_reference or get_cDNA_reference()
# Second, get the input file if a directory was specified
sequence_file = get_input_file( input )
# Finally, run the Typing procedure
renamed_file = rename_sequences( sequence_file )
raw_alignment = full_align_best_reference( renamed_file, genomic_reference )
reoriented = orient_sequences( renamed_file, alignment_file=raw_alignment )
selected = extract_alleles( reoriented, alignment_file=raw_alignment,
method=grouping,
loci=loci)
gDNA_alignment = full_align_best_reference( selected, genomic_reference )
cDNA_file = extract_cDNA( selected, exon_fofn, alignment_file=gDNA_alignment )
cDNA_alignment = align_by_identity( cDNA_file, cDNA_reference )
typing = summarize_typing( gDNA_alignment, cDNA_alignment )
return typing
def __init__( self ):
# Parse the options
parse_args()
self._config = ConfigParser.SafeConfigParser()
self._config.read( args.config_file )
# Initialize output folder and sub-folders
self.subfolders = _initialize_folders( args.output )
# Initialize logging
log_file = os.path.join( args.output, "HLA_Pipeline.log" )
initialize_logger( log, log_file=log_file )
def __init__(self):
# Parse the options
parse_args()
self._config = ConfigParser.SafeConfigParser()
self._config.read(args.config_file)
# Initialize output folder and sub-folders
self.subfolders = _initialize_folders(args.output)
# Initialize logging
log_file = os.path.join(args.output, "HLA_Pipeline.log")
initialize_logger(log, log_file=log_file)
def _align_multiple_sequences(sequences, output=None):
"""
Align
"""
temp_in = _write_temp_fasta( sequences )
temp_out = NamedTemporaryFile(suffix=".afa", delete=False)
multi_sequence_alignment( temp_in, temp_out.name )
os.unlink( temp_in )
return temp_out.name
def sorted_sequences( sequence_file ):
"""
Yield successive reads in descending order of NumReads
"""
seqs = list(AmpliconAnalysisReader( sequence_file ))
for seq in sorted(seqs, key=lambda s: s.num_reads, reverse=True):
yield seq
if __name__ == "__main__":
import sys
from pbhla.log import initialize_logger
query_file = sys.argv[1]
debug_flag = bool(sys.argv[2]) if len(sys.argv) > 2 else None
initialize_logger( log_level='INFO' )
cd = ChimeraDetector(debug=debug_flag)
cd.run( query_file )
