Python fasta.SeqIO类代码示例

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")

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")

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)

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")

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")

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")

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)))

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()

def phase(accession):
    gbdir = "gb"
    gbfile = op.join(gbdir, accession + ".gb")
    if not op.exists(gbfile):
        entrez([accession, "--skipcheck", "--outdir=" + gbdir, "--format=gb"])
    rec = SeqIO.parse(gbfile, "gb").next()
    ph, keywords = get_phase(rec)
    return ph, len(rec)

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()

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])

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])

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))

def load(args):
    '''
    %prog load gff_file fasta_file [--options]

    Parses the selected features out of GFF, with subfeatures concatenated.
    For example, to get the CDS sequences, do this::

    $ %prog load athaliana.gff athaliana.fa --parents mRNA --children CDS
    '''
    from jcvi.formats.fasta import Seq, SeqRecord

    p = OptionParser(load.__doc__)
    p.add_option("--parents", dest="parents", default="mRNA",
            help="list of features to extract, use comma to separate (e.g."
            "'gene,mRNA') [default: %default]")
    p.add_option("--children", dest="children", default="CDS",
            help="list of features to extract, use comma to separate (e.g."
            "'five_prime_UTR,CDS,three_prime_UTR') [default: %default]")
    p.add_option("--attribute",
            help="The attribute field to extract [default: %default]")
    set_outfile(p)

    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(p.print_help())

    gff_file, fasta_file = args

    g = make_index(gff_file)
    f = Fasta(fasta_file, index=False)
    fw = must_open(opts.outfile, "w")

    parents = set(opts.parents.split(','))
    children_list = set(opts.children.split(','))
    attr = opts.attribute

    for feat in get_parents(gff_file, parents):

        children = []
        for c in g.children(feat.id, 1):

            if c.featuretype not in children_list:
                continue
            child = f.sequence(dict(chr=c.chrom, start=c.start, stop=c.stop,
                strand=c.strand))
            children.append((child, c))

        if not children:
            print >>sys.stderr, "[warning] %s has no children with type %s" \
                                    % (feat.id, ','.join(children_list))
            continue
        # sort children in incremental position
        children.sort(key=lambda x: x[1].start)
        # reverse children if negative strand
        if feat.strand == '-':
            children.reverse()
        feat_seq = ''.join(x[0] for x in children)

        description = ",".join(feat.attributes[attr]) \
                if attr and attr in feat.attributes else ""
        description = description.replace("\"", "")

        rec = SeqRecord(Seq(feat_seq), id=feat.id, description=description)
        SeqIO.write([rec], fw, "fasta")
        fw.flush()

def install(args):
    """
    %prog install patchers.bed patchers.fasta backbone.fasta alt.fasta

    Install patches into backbone, using sequences from alternative assembly.
    The patches sequences are generated via jcvi.assembly.patch.fill().

    The output is a bedfile that can be converted to AGP using
    jcvi.formats.agp.frombed().
    """
    from jcvi.apps.align import blast
    from jcvi.formats.fasta import SeqIO

    p = OptionParser(install.__doc__)
    p.set_rclip(rclip=1)
    p.add_option("--maxsize", default=300000, type="int",
            help="Maximum size of patchers to be replaced [default: %default]")
    p.add_option("--prefix", help="Prefix of the new object [default: %default]")
    p.add_option("--strict", default=False, action="store_true",
            help="Only update if replacement has no gaps [default: %default]")
    opts, args = p.parse_args(args)

    if len(args) != 4:
        sys.exit(not p.print_help())

    pbed, pfasta, bbfasta, altfasta = args
    maxsize = opts.maxsize  # Max DNA size to replace gap
    rclip = opts.rclip

    blastfile = blast([altfasta, pfasta,"--wordsize=100", "--pctid=99"])
    order = Bed(pbed).order
    beforebed, afterbed = blast_to_twobeds(blastfile, order, rclip=rclip,
                                           maxsize=maxsize)

    beforefasta = fastaFromBed(beforebed, bbfasta, name=True, stranded=True)
    afterfasta = fastaFromBed(afterbed, altfasta, name=True, stranded=True)

    # Exclude the replacements that contain more Ns than before
    ah = SeqIO.parse(beforefasta, "fasta")
    bh = SeqIO.parse(afterfasta, "fasta")
    count_Ns = lambda x: x.seq.count('n') + x.seq.count('N')
    exclude = set()
    for arec, brec in zip(ah, bh):
        an = count_Ns(arec)
        bn = count_Ns(brec)
        if opts.strict:
            if bn == 0:
                continue

        elif bn < an:
            continue

        id = arec.id
        exclude.add(id)

    logging.debug("Ignore {0} updates because of decreasing quality."\
                    .format(len(exclude)))


    abed = Bed(beforebed, sorted=False)
    bbed = Bed(afterbed, sorted=False)
    abed = [x for x in abed if x.accn not in exclude]
    bbed = [x for x in bbed if x.accn not in exclude]

    abedfile = "before.filtered.bed"
    bbedfile = "after.filtered.bed"
    afbed = Bed()
    afbed.extend(abed)
    bfbed = Bed()
    bfbed.extend(bbed)

    afbed.print_to_file(abedfile)
    bfbed.print_to_file(bbedfile)

    shuffle_twobeds(afbed, bfbed, bbfasta, prefix=opts.prefix)