def type_hla_sequences(self, sequence_file):
print self.loci
log.info('Typing the selected HLA consensus sequences')
typing = type_sequences(sequence_file,
grouping='locus',
exon_fofn=self.exon_reference,
genomic_reference=self.locus_reference,
cDNA_reference=self.cDNA_reference,
loci=self.loci)
check_output_file(typing)
log.info('Finished typing the selected HLA sequences\n')
return typing
def type_hla_sequences(self, sequence_file ):
print self.loci
log.info('Typing the selected HLA consensus sequences')
typing = type_sequences( sequence_file,
grouping='locus',
exon_fofn=self.exon_reference,
genomic_reference=self.locus_reference,
cDNA_reference=self.cDNA_reference,
loci=self.loci)
check_output_file( typing )
log.info('Finished typing the selected HLA sequences\n')
return typing
#! /usr/bin/env python
from pbhla.typing.sequences import type_sequences
if __name__ == '__main__':
import argparse
parser = argparse.ArgumentParser()
add = parser.add_argument
add('amplicon_analysis', metavar='INPUT',
help="Fasta/Fastq/Folder of Amplicon Analysis output")
add('-g', '--grouping', metavar='METHOD', default='both',
help="Method of selecting output sequences {locus, barcode, both, all} default=both")
add('-e', '--exon_reference', metavar='REFERENCE', default=None,
help='Dictionary file of Locus-specific exon references')
add('-n', '--nucleotide_reference', metavar='FASTA', default=None,
help='File of FASTA sequences from nucleotide references')
add('-c', '--cDNA_reference', metavar='FASTA', default=None,
help='File of FASTA sequences from cDNA references')
add('--debug', action='store_true',
help="Flag to enable Debug mode")
args = parser.parse_args()
type_sequences( args.amplicon_analysis, args.grouping,
args.exon_reference,
args.nucleotide_reference,
args.cDNA_reference )
metavar='REFERENCE',
default=None,
help='Dictionary file of Locus-specific exon references')
add('-n',
'--nucleotide_reference',
metavar='FASTA',
default=None,
help='File of FASTA sequences from nucleotide references')
add('-c',
'--cDNA_reference',
metavar='FASTA',
default=None,
help='File of FASTA sequences from cDNA references')
add('-t',
'--trim',
metavar='INT',
default=0,
type=int,
help='Number of bases to trim from the ends of sequences before typing'
)
add('--debug', action='store_true', help="Flag to enable Debug mode")
args = parser.parse_args()
type_sequences(args.amplicon_analysis,
grouping=args.grouping,
exon_fofn=args.exon_reference,
genomic_reference=args.nucleotide_reference,
cDNA_reference=args.cDNA_reference,
trim=args.trim,
debug=args.debug)