array2scaffolds.py 文件源码

def array2scaffolds(outbase, infile, infile2, fasta, threads, minWindows, scaffolds=[]):
    """Return scaffolds computed for given matrix"""
    logger("Loading FastA...")
    faidx = FastaIndex(fasta)
    logger(" %s bp in %s contigs"%(faidx.genomeSize, len(faidx)))

    logger("Loading matrix from %s ..."%infile)
    d, bin_chr, bin_position, contig2size = load_matrix(infile, scaffolds=scaffolds, verbose=1)
    logger(" matrix of %s windows for %s contigs summing %s bp"%(d.shape[0], len(contig2size), sum(contig2size.values())))

    # make sure all contigs from matrix are present in FastA
    diff = set(contig2size.keys()).difference(faidx)
    if diff:
        sys.stderr.write("[ERROR] %s / %s contigs are missing from provided FastA!\n"%(len(diff), len(contig2size)))
        sys.exit(1)

    logger("Calculating linkage matrix & tree...")
    names = ["%s %7sk"%(get_name(c), s/1000) for c, (s, e) in zip(bin_chr, bin_position)]
    d = transform(d)
    t = array2tree(d, names, outbase)
    del d

    logger("Assigning contigs to clusters/scaffolds...") 
    clusters = get_clusters(outbase, t, contig2size, bin_chr)

    logger("Constructing scaffolds...")
    if threads > 1: 
        scaffolds = clusters2scaffolds_multi(clusters, infile2, minWindows, scaffolds, threads)
    else:
        scaffolds = clusters2scaffolds(clusters, infile2, minWindows, scaffolds)

    logger("Reporting %s scaffolds..."%len(scaffolds))
    fastafn = report_scaffolds(outbase, infile, scaffolds, faidx)

    return scaffolds, fastafn