Python SeqIO.write方法代码示例

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def flip(args):
    """
    %prog flip fastafile

    Go through each FASTA record, check against Genbank file and determines
    whether or not to flip the sequence. This is useful before updates of the
    sequences to make sure the same orientation is used.
    """
    p = OptionParser(flip.__doc__)
    opts, args = p.parse_args(args)

    if len(args) != 1:
        sys.exit(not p.print_help())

    fastafile, = args
    outfastafile = fastafile.rsplit(".", 1)[0] + ".flipped.fasta"
    fo = open(outfastafile, "w")
    f = Fasta(fastafile, lazy=True)
    for name, rec in f.iteritems_ordered():
        tmpfasta = "a.fasta"
        fw = open(tmpfasta, "w")
        SeqIO.write([rec], fw, "fasta")
        fw.close()

        o = overlap([tmpfasta, name])
        if o.orientation == '-':
            rec.seq = rec.seq.reverse_complement()

        SeqIO.write([rec], fo, "fasta")
        os.remove(tmpfasta)

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def filter(args):
    """
    %prog filter consensus.fasta

    Filter consensus sequence with min cluster size.
    """
    from jcvi.formats.fasta import Fasta, SeqIO

    p = OptionParser(filter.__doc__)
    p.add_option("--minsize", default=10, type="int",
                 help="Minimum cluster size")
    p.set_outfile()
    opts, args = p.parse_args(args)

    if len(args) != 1:
        sys.exit(not p.print_help())

    fastafile, = args
    minsize = opts.minsize
    f = Fasta(fastafile, lazy=True)
    fw = must_open(opts.outfile, "w")
    for desc, rec in f.iterdescriptions_ordered():
        if desc.startswith("singleton"):
            continue
        # consensus_for_cluster_0 with 63 sequences
        name, w, size, seqs = desc.split()
        assert w == "with"
        size = int(size)
        if size < minsize:
            continue
        SeqIO.write(rec, fw, "fasta")

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def extract_ends(rec, sites, flank, fw, maxfragsize=800):
    """
    Extraction of ends of fragments above certain size.
    """
    nsites = len(sites)
    size = len(rec)
    for i, s in enumerate(sites):
        newid = "{0}:{1}".format(rec.name, s)
        recs = []

        if i == 0 or s - sites[i - 1] <= maxfragsize:
            newidL = newid + "L"
            left = max(s - flank, 0)
            right = s
            frag = rec.seq[left:right].strip("Nn")
            recL = SeqRecord(frag, id=newidL, description="")
            if i == 0 and s > maxfragsize:  # Contig L-end
                pass
            else:
                recs.append(recL)

        if i == nsites - 1 or sites[i + 1] - s <= maxfragsize:
            newidR = newid + "R"
            left = s
            right = min(s + flank, size)
            frag = rec.seq[left:right].strip("Nn")
            recR = SeqRecord(frag, id=newidR, description="")
            if i == nsites - 1 and size - s > maxfragsize:  # Contig R-end
                pass
            else:
                recs.append(recR)

        SeqIO.write(recs, fw, "fasta")

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def extract(args):
    """
    %prog extract gffile

    --contigs: Extract particular contig(s) from the gff file. If multiple contigs are
    involved, use "," to separate, e.g. "contig_12,contig_150"
    --names: Provide a file with IDs, one each line
    """
    p = OptionParser(extract.__doc__)
    p.add_option("--contigs",
                help="Extract features from certain contigs [default: %default]")
    p.add_option("--names",
                help="Extract features with certain names [default: %default]")
    p.add_option("--fasta", default=False, action="store_true",
                help="Write FASTA if available [default: %default]")
    set_outfile(p)

    opts, args = p.parse_args(args)

    if len(args) != 1:
        sys.exit(not p.print_help())

    gffile, = args
    contigID = opts.contigs
    namesfile = opts.names

    contigID = set(contigID.split(",")) if contigID else None
    names = set(x.strip() for x in open(namesfile)) if namesfile else None

    outfile = opts.outfile
    fp = open(gffile)
    fw = must_open(outfile, "w")
    for row in fp:
        atoms = row.split()
        if len(atoms) == 0:
            continue
        tag = atoms[0]
        if row[0] == "#":
            if not (tag == RegionTag and contigID and atoms[1] not in contigID):
                print >> fw, row.rstrip()
            if tag == FastaTag:
                break
            continue

        b = GffLine(row)
        is_right_contig = (contigID and tag in contigID) or (not contigID)
        is_right_names = (names and b.attributes["Name"][0] in names) or \
                         (not names)

        if is_right_contig and is_right_names:
            print >> fw, row.rstrip()

    if not opts.fasta:
        return

    f = Fasta(gffile)
    for s in contigID:
        if s in f:
            SeqIO.write([f[s]], fw, "fasta")

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def extract_full(rec, sites, flank, fw):
    """
    Full extraction of seq flanking the sites.
    """
    for s in sites:
        newid = "{0}:{1}".format(rec.name, s)
        left = max(s - flank, 0)
        right = min(s + flank, len(rec))
        frag = rec.seq[left:right].strip("Nn")
        newrec = SeqRecord(frag, id=newid, description="")
        SeqIO.write([newrec], fw, "fasta")

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def filter(args):
    """
    %prog filter *.consensus.fasta

    Filter consensus sequence with min cluster size.
    """
    from jcvi.formats.fasta import Fasta, SeqIO

    p = OptionParser(filter.__doc__)
    p.add_option("--minsize", default=2, type="int",
                 help="Minimum cluster size")
    p.set_outfile()
    opts, args = p.parse_args(args)

    if len(args) < 1:
        sys.exit(not p.print_help())

    fastafiles = args
    minsize = opts.minsize
    totalreads = totalassembled = 0
    fw = must_open(opts.outfile, "w")
    for i, fastafile in enumerate(fastafiles):
        f = Fasta(fastafile, lazy=True)
        pf = "s{0:03d}".format(i)
        nreads = nsingletons = nclusters = 0
        for desc, rec in f.iterdescriptions_ordered():
            nclusters += 1
            if desc.startswith("singleton"):
                nsingletons += 1
                nreads += 1
                continue
            # consensus_for_cluster_0 with 63 sequences
            name, w, size, seqs = desc.split()
            assert w == "with"
            size = int(size)
            nreads += size
            if size < minsize:
                continue
            rec.description = rec.description.split(None, 1)[-1]
            rec.id = pf + "_" + rec.id
            SeqIO.write(rec, fw, "fasta")
        logging.debug("Scanned {0} clusters with {1} reads ..".\
                       format(nclusters, nreads))
        cclusters, creads = nclusters - nsingletons, nreads - nsingletons
        logging.debug("Saved {0} clusters (min={1}) with {2} reads (avg:{3}) [{4}]".\
                       format(cclusters, minsize, creads, creads / cclusters, pf))
        totalreads += nreads
        totalassembled += nreads - nsingletons
    logging.debug("Total assembled: {0}".\
                  format(percentage(totalassembled, totalreads)))

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def merge(args):
    """
    %prog merge gffiles

    Merge several gff files into one. When only one file is given, it is assumed
    to be a file with a list of gff files.
    """
    p = OptionParser(merge.__doc__)
    set_outfile(p)

    opts, args = p.parse_args(args)

    nargs = len(args)
    if nargs < 1:
        sys.exit(not p.print_help())

    if nargs == 1:
        listfile, = args
        fp = open(listfile)
        gffiles = [x.strip() for x in fp]
    else:
        gffiles = args

    outfile = opts.outfile

    deflines = set()
    fw = must_open(outfile, "w")
    fastarecs = {}
    for gffile in gffiles:
        fp = open(gffile)
        for row in fp:
            row = row.rstrip()
            if row[0] == '#':
                if row == FastaTag:
                    break
                if row in deflines:
                    continue
                else:
                    deflines.add(row)

            print >> fw, row

        f = Fasta(gffile, lazy=True)
        for key, rec in f.iteritems_ordered():
            if key in fastarecs.keys():
                continue
            fastarecs[key] = rec

    print >> fw, FastaTag
    SeqIO.write(fastarecs.values(), fw, "fasta")

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def needle(args):
    """
    %prog needle nw.pairs a.pep.fasta b.pep.fasta

    Take protein pairs and needle them
    Automatically writes output file `nw.scores`
    """
    from jcvi.formats.fasta import Fasta, SeqIO

    p = OptionParser(needle.__doc__)

    opts, args = p.parse_args(args)

    if len(args) != 3:
        sys.exit(not p.print_help())

    manager = mp.Manager()
    results = manager.list()
    needle_pool = mp.Pool(processes=mp.cpu_count())

    pairsfile, apep, bpep = args
    afasta, bfasta = Fasta(apep), Fasta(bpep)
    fp = must_open(pairsfile)
    for i, row in enumerate(fp):
        a, b = row.split()
        a, b = afasta[a], bfasta[b]
        fa, fb = must_open("{0}_{1}_a.fasta".format(pairsfile, i), "w"), \
            must_open("{0}_{1}_b.fasta".format(pairsfile, i), "w")
        SeqIO.write([a], fa, "fasta")
        SeqIO.write([b], fb, "fasta")
        fa.close()
        fb.close()

        needlefile = "{0}_{1}_ab.needle".format(pairsfile, i)
        needle_pool.apply_async(_needle, \
            (fa.name, fb.name, needlefile, a.id, b.id, results))

    needle_pool.close()
    needle_pool.join()

    fp.close()

    scoresfile = "{0}.scores".format(pairsfile.rsplit(".")[0])
    fw = must_open(scoresfile, "w")
    for result in results:
        print(result, file=fw)
    fw.close()

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def circular(args):
    """
    %prog circular fastafile startpos

    Make circular genome, startpos is the place to start the sequence. This can
    be determined by mapping to a reference. Self overlaps are then resolved.
    Startpos is 1-based.
    """
    from jcvi.assembly.goldenpath import overlap

    p = OptionParser(circular.__doc__)
    p.add_option("--flip", default=False, action="store_true",
                 help="Reverse complement the sequence")
    p.set_outfile()
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    fastafile, startpos = args
    startpos = int(startpos)
    key, seq = parse_fasta(fastafile).next()
    aseq = seq[startpos:]
    bseq = seq[:startpos]
    aseqfile, bseqfile = "a.seq", "b.seq"

    for f, s in zip((aseqfile, bseqfile), (aseq, bseq)):
        fw = must_open(f, "w")
        print >> fw, ">{0}\n{1}".format(f, s)
        fw.close()

    o = overlap([aseqfile, bseqfile])
    seq = aseq[:o.qstop] + bseq[o.sstop:]
    seq = Seq(seq)

    if opts.flip:
        seq = seq.reverse_complement()

    for f in (aseqfile, bseqfile):
        os.remove(f)

    fw = must_open(opts.outfile, "w")
    rec = SeqRecord(seq, id=key, description="")
    SeqIO.write([rec], fw, "fasta")
    fw.close()

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def needle(args):
    """
    %prog needle pairs a.pep.fasta b.pep.fasta

    Take protein pairs and needle them.
    """
    from Bio.Emboss.Applications import NeedleCommandline

    from jcvi.formats.fasta import Fasta, SeqIO
    from jcvi.formats.base import FileShredder

    p = OptionParser(needle.__doc__)
    opts, args = p.parse_args(args)

    if len(args) != 3:
        sys.exit(not p.print_help())

    pairsfile, apep, bpep = args
    afasta = Fasta(apep)
    bfasta = Fasta(bpep)
    fp = open(pairsfile)
    for row in fp:
        fa = open(pairsfile + "_a.fasta", "w")
        fb = open(pairsfile + "_b.fasta", "w")
        a, b = row.split()
        a = afasta[a]
        b = bfasta[b]
        SeqIO.write([a], fa, "fasta")
        SeqIO.write([b], fb, "fasta")
        fa.close()
        fb.close()
        needlefile = pairsfile + "_ab.needle"
        needle_cline = NeedleCommandline(asequence=fa.name,
                            bsequence=fb.name,
                            gapopen=10, gapextend=0.5,
                            outfile=needlefile)
        stdout, stderr = needle_cline()
        print >> sys.stderr, stdout + stderr
        #align = AlignIO.read(needlefile, "emboss")
        nh = NeedleHeader(needlefile)
        print "\t".join((a.id, b.id, nh.identity, nh.score))
        FileShredder([fa.name, fb.name, needlefile])

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def overlapbatch(args):
    """
    %prog overlapbatch ctgfasta poolfasta

    Fish out the sequences in `poolfasta` that overlap with `ctgfasta`.
    Mix and combine using `minimus2`.
    """
    p = OptionParser(overlap.__doc__)
    opts, args = p.parse_args(args)
    if len(args) != 2:
        sys.exit(not p.print_help())

    ctgfasta, poolfasta = args
    f = Fasta(ctgfasta)
    for k, rec in f.iteritems_ordered():
        fastafile = k + ".fasta"
        fw = open(fastafile, "w")
        SeqIO.write([rec], fw, "fasta")
        fw.close()

        overlap([fastafile, poolfasta])

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def expand(args):
    """
    %prog expand bes.fasta reads.fastq

    Expand sequences using short reads. Useful, for example for getting BAC-end
    sequences. The template to use, in `bes.fasta` may just contain the junction
    sequences, then align the reads to get the 'flanks' for such sequences.
    """
    import math

    from jcvi.formats.fasta import Fasta, SeqIO
    from jcvi.formats.fastq import readlen, first, fasta
    from jcvi.formats.blast import Blast
    from jcvi.formats.base import FileShredder
    from jcvi.apps.bowtie import align, get_samfile
    from jcvi.apps.align import blast

    p = OptionParser(expand.__doc__)
    p.set_depth(depth=200)
    p.set_firstN()
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    bes, reads = args
    size = Fasta(bes).totalsize
    rl = readlen([reads])
    expected_size = size + 2 * rl
    nreads = expected_size * opts.depth / rl
    nreads = int(math.ceil(nreads / 1000.)) * 1000

    # Attract reads
    samfile, logfile = align([bes, reads, "--reorder", "--mapped",
           "--firstN={0}".format(opts.firstN)])

    samfile, mapped, _ = get_samfile(reads, bes, bowtie=True, mapped=True)
    logging.debug("Extract first {0} reads from `{1}`.".format(nreads, mapped))

    pf = mapped.split(".")[0]
    pf = pf.split("-")[0]
    bespf = bes.split(".")[0]
    reads = pf + ".expand.fastq"
    first([str(nreads), mapped, "-o", reads])

    # Perform mini-assembly
    fastafile = reads.rsplit(".", 1)[0] + ".fasta"
    qualfile = ""
    if need_update(reads, fastafile):
        fastafile, qualfile = fasta([reads])

    contigs = op.join(pf, "454LargeContigs.fna")
    if need_update(fastafile, contigs):
        cmd = "runAssembly -o {0} -cpu 8 {1}".format(pf, fastafile)
        sh(cmd)
    assert op.exists(contigs)

    # Annotate contigs
    blastfile = blast([bes, contigs])
    mapping = {}
    for query, b in Blast(blastfile).iter_best_hit():
        mapping[query] = b

    f = Fasta(contigs, lazy=True)
    annotatedfasta = ".".join((pf, bespf, "fasta"))
    fw = open(annotatedfasta, "w")
    keys = list(Fasta(bes).iterkeys_ordered())  # keep an ordered list
    recs = []
    for key, v in f.iteritems_ordered():
        vid = v.id
        if vid not in mapping:
            continue
        b = mapping[vid]
        subject = b.subject
        rec = v.reverse_complement() if b.orientation == '-' else v
        rec.id = rid = "_".join((pf, vid, subject))
        rec.description = ""
        recs.append((keys.index(subject), rid, rec))

    recs = [x[-1] for x in sorted(recs)]
    SeqIO.write(recs, fw, "fasta")
    fw.close()

    FileShredder([samfile, logfile, mapped, reads, fastafile, qualfile, blastfile, pf])
    logging.debug("Annotated seqs (n={0}) written to `{1}`.".\
                    format(len(recs), annotatedfasta))

    return annotatedfasta

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def prepare(args):
    """
    %prog prepare --rearray_lib=<rearraylibrary> --orig_lib_file=<origlibfile>

    Inferred file names
    ---------------------------------------------
    `lookuptblfile` : rearraylibrary.lookup
    `rearraylibfile`: rearraylibrary.fasta

    Pick sequences from the original library file and the rearrayed library file
    based on the mapping information provided in the `lookuptblfile`.

    # lookuptblfile format: column number (index)
    # 1 (0)          2 (1)          3 (2)         4 (3)        5 (4)        6 (5)
    # source_clone   source_plate   source_well   dest_clone   dest_plate   dest_well

    The 1st and 4th column in the `lookuptblfile` form the pair of clones which
    constitute the elements used for the per-clone assembly.
    """
    from operator import itemgetter
    from jcvi.formats.fasta import Fasta, SeqIO

    p = OptionParser(prepare.__doc__)
    p.add_option("--rearray_lib", default=None,
            help="name of the rearrayed library [default: %default]")
    p.add_option("--orig_lib_file",
            help="fasta file containing reads from the original libraries [default: %default]")

    g = OptionGroup(p, "Optional parameters")
    g.add_option("--output_folder", default="to_assemble",
            help="output folder to write the FASTA files to [default: %default]")
    p.add_option_group(g)

    opts, args = p.parse_args(args)

    if not opts.rearray_lib or not opts.orig_lib_file:
        logging.error("Please specify the required parameters")
        sys.exit(not p.print_help())

    rearraylib, origlibfile = opts.rearray_lib, opts.orig_lib_file

    if not op.isfile(origlibfile):
        logging.error("Original library reads file `{0}` does not exist!".format(origlibfile))
        sys.exit()

    lookuptblfile  = rearraylib + '.lookup'
    logging.debug(lookuptblfile)
    if not op.isfile(lookuptblfile):
        logging.error("Lookup table file `{0}` does not exist!".format(lookuptblfile))
        sys.exit()

    rearraylibfile = rearraylib + '.fasta'
    logging.debug(rearraylibfile)
    if not op.isfile(rearraylibfile):
        logging.error("Rearrayed library reads file `{0}` does not exist!".format(rearraylibfile))
        sys.exit()

    origlibFasta = Fasta(origlibfile)
    rearraylibFasta = Fasta(rearraylibfile)

    origlibids = [o for o in origlibFasta.iterkeys_ordered()]
    rearraylibids = [r for r in rearraylibFasta.iterkeys_ordered()]

    if not op.isdir(opts.output_folder):
        logging.warning("Output directory `{0}` missing. Creating it now...".format(opts.output_folder))
        os.makedirs(opts.output_folder)

    logfile = rearraylib + '.log'
    log = open(logfile, 'w')

    fp = open(lookuptblfile, 'r')
    for row in fp:
        origprefix, rearrayprefix = itemgetter(0,3)(row.split('\t'))
        libpair = origprefix + '_' + rearrayprefix
        outfile = opts.output_folder + '/' + libpair + '.fasta'
        ofp = open(outfile, 'w')

        for o in origlibids:
            if re.match(origprefix, o):
                SeqIO.write(origlibFasta[o], ofp, 'fasta')

        for r in rearraylibids:
            if re.match(rearrayprefix, r):
                SeqIO.write(rearraylibFasta[r], ofp, 'fasta')

        ofp.close()
        print >>log, outfile

    log.close()
    logging.debug('Wrote log file `{0}`'.format(logfile))

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def longest(args):
    """
    %prog longest pasa.fasta output.subclusters.out

    Find the longest PASA assembly and label it as full-length. Also removes
    transcripts shorter than half the length of the longest, or shorter than
    200bp. The assemblies for the same locus is found in
    `output.subclusters.out`. In particular the lines that look like:

    sub-cluster: asmbl_25 asmbl_26 asmbl_27
    """
    from jcvi.formats.fasta import Fasta, SeqIO
    from jcvi.formats.sizes import Sizes

    p = OptionParser(longest.__doc__)
    p.add_option("--prefix", default="pasa",
                 help="Replace asmbl_ with prefix [default: %default]")
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    fastafile, subclusters = args
    prefix = fastafile.rsplit(".", 1)[0]

    idsfile = prefix + ".fl.ids"
    fw = open(idsfile, "w")
    sizes = Sizes(fastafile).mapping

    name_convert = lambda x: x.replace("asmbl", opts.prefix)

    keep = set()  # List of IDs to write
    fp = open(subclusters)
    nrecs = 0
    for row in fp:
        if not row.startswith("sub-cluster:"):
            continue
        asmbls = row.split()[1:]
        longest_asmbl = max(asmbls, key=lambda x: sizes[x])
        longest_size = sizes[longest_asmbl]
        print(name_convert(longest_asmbl), file=fw)
        nrecs += 1
        cutoff = max(longest_size / 2, 200)
        keep.update(set(x for x in asmbls if sizes[x] >= cutoff))

    fw.close()
    logging.debug("{0} fl-cDNA records written to `{1}`.".format(nrecs, idsfile))

    f = Fasta(fastafile, lazy=True)
    newfastafile = prefix + ".clean.fasta"
    fw = open(newfastafile, "w")
    nrecs = 0
    for name, rec in f.iteritems_ordered():
        if name not in keep:
            continue

        rec.id = name_convert(name)
        rec.description = ""
        SeqIO.write([rec], fw, "fasta")
        nrecs += 1

    fw.close()
    logging.debug("{0} valid records written to `{1}`.".format(nrecs, newfastafile))

# 需要导入模块: from jcvi.formats.fasta import SeqIO [as 别名]
# 或者: from jcvi.formats.fasta.SeqIO import write [as 别名]
def overlap(args):
    """
    %prog overlap ctgfasta poolfasta

    Fish out the sequences in `poolfasta` that overlap with `ctgfasta`.
    Mix and combine using `minimus2`.
    """
    p = OptionParser(overlap.__doc__)
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    ctgfasta, poolfasta = args
    prefix = ctgfasta.split(".")[0]
    rid = list(Fasta(ctgfasta).iterkeys())
    assert len(rid) == 1, "Use overlapbatch() to improve multi-FASTA file"

    rid = rid[0]
    splitctgfasta = ctgfasta.rsplit(".", 1)[0] + ".split.fasta"
    ctgfasta = run_gapsplit(infile=ctgfasta, outfile=splitctgfasta)

    # Run BLAST
    blastfile = ctgfasta + ".blast"
    run_megablast(infile=ctgfasta, outfile=blastfile, db=poolfasta)

    # Extract contigs and merge using minimus2
    closuredir = prefix + ".closure"
    closure = False
    if need_update(blastfile, closuredir):
        mkdir(closuredir, overwrite=True)
        closure = True

    if closure:
        idsfile = op.join(closuredir, prefix + ".ids")
        cmd = "cut -f2 {0} | sort -u".format(blastfile)
        sh(cmd, outfile=idsfile)

        idsfastafile = op.join(closuredir, prefix + ".ids.fasta")
        cmd = "faSomeRecords {0} {1} {2}".format(poolfasta, idsfile, idsfastafile)
        sh(cmd)

        # This step is a hack to weight the bases from original sequences more
        # than the pulled sequences, by literally adding another copy to be used
        # in consensus calls.
        redundantfastafile = op.join(closuredir, prefix + ".redundant.fasta")
        format([ctgfasta, redundantfastafile, "--prefix=RED."])

        mergedfastafile = op.join(closuredir, prefix + ".merged.fasta")
        cmd = "cat {0} {1} {2}".format(ctgfasta, redundantfastafile, idsfastafile)
        sh(cmd, outfile=mergedfastafile)

        afgfile = op.join(closuredir, prefix + ".afg")
        cmd = "toAmos -s {0} -o {1}".format(mergedfastafile, afgfile)
        sh(cmd)

        cwd = os.getcwd()
        os.chdir(closuredir)
        cmd = "minimus2 {0} -D REFCOUNT=0".format(prefix)
        cmd += " -D OVERLAP=100 -D MINID=98"
        sh(cmd)
        os.chdir(cwd)

    # Analyze output, make sure that:
    # + Get the singletons of the original set back
    # + Drop any contig that is comprised entirely of pulled set
    originalIDs = set(Fasta(ctgfasta).iterkeys())
    minimuscontig = op.join(closuredir, prefix + ".contig")
    c = ContigFile(minimuscontig)
    excludecontigs = set()
    for rec in c.iter_records():
        reads = set(x.id for x in rec.reads)
        if reads.isdisjoint(originalIDs):
            excludecontigs.add(rec.id)

    logging.debug("Exclude contigs: {0}".\
            format(", ".join(sorted(excludecontigs))))

    finalfasta = prefix + ".improved.fasta_"
    fw = open(finalfasta, "w")
    minimusfasta = op.join(closuredir, prefix + ".fasta")
    f = Fasta(minimusfasta)
    for id, rec in f.iteritems_ordered():
        if id in excludecontigs:
            continue
        SeqIO.write([rec], fw, "fasta")

    singletonfile = op.join(closuredir, prefix + ".singletons")
    singletons = set(x.strip() for x in open(singletonfile))
    leftovers = singletons & originalIDs

    logging.debug("Pull leftover singletons: {0}".\
            format(", ".join(sorted(leftovers))))

    f = Fasta(ctgfasta)
    for id, rec in f.iteritems_ordered():
        if id not in leftovers:
            continue
        SeqIO.write([rec], fw, "fasta")

#.........这里部分代码省略.........