def align_contigs_to_genome(self, contig_file):
log.info("Looking for Contig-to-Genome alignment data")
contig_genome_align = self.get_filepath( 'alignments', 'contigs_to_genome.m1' )
if valid_file( contig_genome_align ):
log.info("Using existing Contig->Genome alignment file\n")
else:
log.info("No Contig->Genome alignment found, creating...")
align_best_reference( contig_file, self.human_reference, output=contig_genome_align )
check_output_file( contig_genome_align )
log.info("Finished aligning contigs to the genomic reference\n")
return create_m1_reference( contig_genome_align )
def align_contigs_to_reference(self, contig_file, reference_file):
"""
Align HBAR contigs to an HLA reference Fasta
"""
log.info("Looking for Contig-to-Reference alignment data")
contig_reference_align = self.get_filepath( 'alignments', 'contigs_to_reference.m1' )
if valid_file( contig_reference_align ):
log.info("Using an existing Contig->Reference alignment file\n")
else:
log.info("No Contig->Reference alignment found, creating...")
align_best_reference( contig_file, reference_file, output=contig_reference_align )
check_output_file( contig_reference_align )
log.info("Finished aligning contigs to the HLA reference data\n")
return create_m1_reference( contig_reference_align )
def align_subreads_to_contigs(self, subread_file, contig_file ):
"""
Align the subreads to the contigs assembled by HBAR
"""
log.info("Looking for Subread-to-Contig alignment data")
subread_contig_align = self.get_filepath( 'alignments', 'subreads_to_contigs.m1' )
if valid_file( subread_contig_align ):
log.info("Using existing Subread->Contig alignment file\n")
else:
log.info("No Subread->Contig alignment found, creating...")
align_best_reference( subread_file, contig_file, output=subread_contig_align )
check_output_file( subread_contig_align )
log.info("Finished aligning subreads to the HBAR contigs\n")
return create_m1_reference( subread_contig_align )
def align_contigs_to_genome(self, contig_file):
log.info("Looking for Contig-to-Genome alignment data")
contig_genome_align = self.get_filepath('alignments',
'contigs_to_genome.m1')
if valid_file(contig_genome_align):
log.info("Using existing Contig->Genome alignment file\n")
else:
log.info("No Contig->Genome alignment found, creating...")
align_best_reference(contig_file,
self.human_reference,
output=contig_genome_align)
check_output_file(contig_genome_align)
log.info("Finished aligning contigs to the genomic reference\n")
return create_m1_reference(contig_genome_align)
def align_contigs_to_reference(self, contig_file, reference_file):
"""
Align HBAR contigs to an HLA reference Fasta
"""
log.info("Looking for Contig-to-Reference alignment data")
contig_reference_align = self.get_filepath('alignments',
'contigs_to_reference.m1')
if valid_file(contig_reference_align):
log.info("Using an existing Contig->Reference alignment file\n")
else:
log.info("No Contig->Reference alignment found, creating...")
align_best_reference(contig_file,
reference_file,
output=contig_reference_align)
check_output_file(contig_reference_align)
log.info("Finished aligning contigs to the HLA reference data\n")
return create_m1_reference(contig_reference_align)
def align_subreads_to_contigs(self, subread_file, contig_file):
"""
Align the subreads to the contigs assembled by HBAR
"""
log.info("Looking for Subread-to-Contig alignment data")
subread_contig_align = self.get_filepath('alignments',
'subreads_to_contigs.m1')
if valid_file(subread_contig_align):
log.info("Using existing Subread->Contig alignment file\n")
else:
log.info("No Subread->Contig alignment found, creating...")
align_best_reference(subread_file,
contig_file,
output=subread_contig_align)
check_output_file(subread_contig_align)
log.info("Finished aligning subreads to the HBAR contigs\n")
return create_m1_reference(subread_contig_align)