def separate_contigs_by_locus( self, hla_contigs, contig_loci ):
"""
Separate the on-target contigs by the locus to which they align
"""
log.info("Looking for locus-specific contig files")
locus_contig_fofn = self.get_filepath( "references", "Locus_Contig_Files.fofn" )
if valid_file( locus_contig_fofn ):
log.info("Using existing locus contig files and FOFN\n")
return locus_contig_fofn
log.info("No locus subread files found, creating...")
file_prefix = self.get_filepath( "references", "Locus" )
locus_files = separate_sequences( hla_contigs, contig_loci, file_prefix )
write_sequence_fofn( locus_files, locus_contig_fofn )
log.info('Finished separating subreads by locus\n')
return locus_contig_fofn
def separate_subreads_by_locus( self, hla_subreads, subread_loci ):
"""
Separate the on-target subreads by the locus to which their HBAR contig aligns
"""
log.info("Looking for locus-specific subread files")
locus_subread_fofn = self.get_filepath( "subreads", "Locus_Subread_Files.fofn" )
if valid_file( locus_subread_fofn ):
log.info("Using existing locus subread files and FOFN\n")
return locus_subread_fofn
log.info("No locus subread files found, creating...")
subread_prefix = self.get_filepath( "subreads", "Locus" )
locus_files = separate_sequences( hla_subreads, subread_loci, subread_prefix )
write_sequence_fofn( locus_files, locus_subread_fofn )
log.info('Finished separating subreads by locus\n')
return locus_subread_fofn
def separate_subreads_by_contig( self, hla_subreads, subread_contigs ):
"""
Separate the on-target subreads by the HBAR contig to which they align
"""
log.info("Looking for contig-specific subread files")
contig_subread_fofn = self.get_filepath( "subreads", "Contig_Subread_Files.fofn" )
if valid_file( contig_subread_fofn ):
log.info("Using existing contig subread files and FOFN\n")
return contig_subread_fofn
log.info("No contig subread files found, creating...")
subread_prefix = self.get_filepath( "subreads", "Contig" )
contig_files = separate_sequences( hla_subreads, subread_contigs, subread_prefix )
write_sequence_fofn( contig_files, contig_subread_fofn )
log.info('Finished separating subreads by contig\n')
return contig_subread_fofn
def separate_contigs_by_locus(self, hla_contigs, contig_loci):
"""
Separate the on-target contigs by the locus to which they align
"""
log.info("Looking for locus-specific contig files")
locus_contig_fofn = self.get_filepath("references",
"Locus_Contig_Files.fofn")
if valid_file(locus_contig_fofn):
log.info("Using existing locus contig files and FOFN\n")
return locus_contig_fofn
log.info("No locus subread files found, creating...")
file_prefix = self.get_filepath("references", "Locus")
locus_files = separate_sequences(hla_contigs, contig_loci, file_prefix)
write_sequence_fofn(locus_files, locus_contig_fofn)
log.info('Finished separating subreads by locus\n')
return locus_contig_fofn
def separate_subreads_by_locus(self, hla_subreads, subread_loci):
"""
Separate the on-target subreads by the locus to which their HBAR contig aligns
"""
log.info("Looking for locus-specific subread files")
locus_subread_fofn = self.get_filepath("subreads",
"Locus_Subread_Files.fofn")
if valid_file(locus_subread_fofn):
log.info("Using existing locus subread files and FOFN\n")
return locus_subread_fofn
log.info("No locus subread files found, creating...")
subread_prefix = self.get_filepath("subreads", "Locus")
locus_files = separate_sequences(hla_subreads, subread_loci,
subread_prefix)
write_sequence_fofn(locus_files, locus_subread_fofn)
log.info('Finished separating subreads by locus\n')
return locus_subread_fofn
def separate_subreads_by_contig(self, hla_subreads, subread_contigs):
"""
Separate the on-target subreads by the HBAR contig to which they align
"""
log.info("Looking for contig-specific subread files")
contig_subread_fofn = self.get_filepath("subreads",
"Contig_Subread_Files.fofn")
if valid_file(contig_subread_fofn):
log.info("Using existing contig subread files and FOFN\n")
return contig_subread_fofn
log.info("No contig subread files found, creating...")
subread_prefix = self.get_filepath("subreads", "Contig")
contig_files = separate_sequences(hla_subreads, subread_contigs,
subread_prefix)
write_sequence_fofn(contig_files, contig_subread_fofn)
log.info('Finished separating subreads by contig\n')
return contig_subread_fofn
