def __init__(self, metassembledir, refphylfile, refstatsfile, contigs_to_refs_file, sep="\t"):
self.metassembledir = metassembledir.rstrip('/')
self.refphylfile = refphylfile
self.refstatsfile = refstatsfile
self.contigs_to_refs_file = contigs_to_refs_file
self.contigs_to_refs_dict = read_2col_table(contigs_to_refs_file, sep=sep)
self.refs = ReferenceSet(refphylfile, refstatsfile, self.contigs_to_refs_dict)
def __init__(self, *args, **kwargs):
self.bamref = kwargs.pop("bamref", None)
self.bamasm = kwargs.pop("bamasm", None)
self.refs = kwargs.pop("referenceset", None)
refstatsfile = kwargs.pop("refstatsfile", None)
refphylfile = kwargs.pop("refphylfile", None)
self.covbedasm = kwargs.pop("covbedasm", None)
self.cut_off = kwargs.pop("cut_off", 100)
self.missing_value = kwargs.pop("missing_value", "N/A")
contigs_to_refs_table = kwargs.pop("contigs_to_refs_table", None)
self.jellyfish_output = kwargs.pop("jellyfish_output", None)
self.jellyfish_reffa = kwargs.pop("jellyfish_reffa", None)
if contigs_to_refs_table:
self.contigs_to_refs_dict = read_2col_table(contigs_to_refs_table, sep="\t")
else:
self.contigs_to_refs_table = None
if len(kwargs) > 0:
raise(Exception("Unexpected keyword argument found %s" % kwargs))
self.asmfa = args[0]
self.coordsfile = args[1]
# Determine reference metagenome
if not self.refs:
if refphylfile and refstatsfile:
self.refs = ReferenceSet(refphylfile, refstatsfile, contigs_to_refs_dict=self.contigs_to_refs_dict)
else:
raise(Exception("Either supply refphylfile and refstatsfile or an existing reference set"))
# Determine read-contig and read-reference mappings from bam files if
# available
if self.bamref and self.bamasm and self.covbedasm:
self.reads, self.contigs = assembly.get_read_contig_mappings(self.bamref,
self.bamasm,
self.refs,
self.asmfa,
self.cut_off)
self.contigs.parse_cov_bed(self.covbedasm)
else:
self.contigs = assembly.ContigDict()
self.contigs.parse_fasta_lengths(self.asmfa)
# Calculate stats from nucmer alignments
self.coords = nucmer.Coords(self.coordsfile)
self.coords.calc_max_aln_purity_per_contig(self.contigs, self.cut_off)
if self.jellyfish_output and self.jellyfish_reffa:
self.jfr = jellyfish.JellyfishRef(args.jellyfish_reffa, args.jellyfish_output)