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