def read_sequences(filetype, file_list): if filetype == 'fastq': return read_fastq_dict(file_list) elif filetype == 'fasta': return read_fasta_dict(file_list) else: raise ValueError
def read_sequences( filetype, file_list ): if filetype == 'fastq': return read_fastq_dict( file_list ) elif filetype == 'fasta': return read_fasta_dict( file_list ) else: raise ValueError
def from_assembly( contig_file, reference_fofn ): contigs = read_fasta_dict( contig_file ) references = read_reference_fofn( reference_fofn ) all_genes = [] for locus, reference in references.iteritems(): alignment = align_reference_to_contigs( locus, reference, contig_file ) hits = read_blasr_hits( alignment ) hits = pick_blasr_hits( hits ) genes = extract_genes( contigs, hits ) all_genes += genes write_fasta( all_genes, 'output.fasta' )