Python DictFile.keys方法代码示例

# 需要导入模块: from jcvi.formats.base import DictFile [as 别名]
# 或者: from jcvi.formats.base.DictFile import keys [as 别名]
def htg(args):
    """
    %prog htg fastafile template.sbt

    Prepare sqnfiles for Genbank HTG submission to update existing records.

    `fastafile` contains the records to update, multiple records are allowed
    (with each one generating separate sqn file in the sqn/ folder). The record
    defline has the accession ID. For example,
    >AC148290.3

    Internally, this generates two additional files (phasefile and namesfile)
    and download records from Genbank. Below is implementation details:

    `phasefile` contains, for each accession, phase information. For example:
    AC148290.3      3       HTG     2       mth2-45h12

    which means this is a Phase-3 BAC. Record with only a single contig will be
    labeled as Phase-3 regardless of the info in the `phasefile`. Template file
    is the Genbank sbt template. See jcvi.formats.sbt for generation of such
    files.

    Another problem is that Genbank requires the name of the sequence to stay
    the same when updating and will kick back with a table of name conflicts.
    For example:

    We are unable to process the updates for these entries
    for the following reason:

    Seqname has changed

    Accession Old seq_name New seq_name
    --------- ------------ ------------
    AC239792 mtg2_29457 AC239792.1

    To prepare a submission, this script downloads genbank and asn.1 format,
    and generate the phase file and the names file (use formats.agp.phase() and
    apps.gbsubmit.asn(), respectively). These get automatically run.

    However, use --phases if the genbank files contain outdated information.
    For example, the clone name changes or phase upgrades. In this case, run
    formats.agp.phase() manually, modify the phasefile and use --phases to override.
    """
    from jcvi.formats.fasta import sequin, ids
    from jcvi.formats.agp import phase
    from jcvi.apps.fetch import entrez

    p = OptionParser(htg.__doc__)
    p.add_option("--phases", default=None,
            help="Use another phasefile to override [default: %default]")
    p.add_option("--comment", default="",
            help="Comments for this update [default: %default]")
    opts, args = p.parse_args(args)

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

    fastafile, sbtfile = args
    pf = fastafile.rsplit(".", 1)[0]

    idsfile = pf + ".ids"
    phasefile = pf + ".phases"
    namesfile = pf + ".names"

    ids([fastafile, "--outfile={0}".format(idsfile)])

    asndir = "asn.1"
    mkdir(asndir)
    entrez([idsfile, "--format=asn.1", "--outdir={0}".format(asndir)])
    asn(glob("{0}/*".format(asndir)) + \
            ["--outfile={0}".format(namesfile)])

    if opts.phases is None:
        gbdir = "gb"
        mkdir(gbdir)
        entrez([idsfile, "--format=gb", "--outdir={0}".format(gbdir)])
        phase(glob("{0}/*".format(gbdir)) + \
                ["--outfile={0}".format(phasefile)])
    else:
        phasefile = opts.phases

    assert op.exists(namesfile) and op.exists(phasefile)

    newphasefile = phasefile + ".new"
    newphasefw = open(newphasefile, "w")
    comment = opts.comment

    fastadir = "fasta"
    sqndir = "sqn"
    mkdir(fastadir)
    mkdir(sqndir)

    from jcvi.graphics.histogram import stem_leaf_plot

    names = DictFile(namesfile)
    assert len(set(names.keys())) == len(set(names.values()))

    phases = DictFile(phasefile)
    ph = [int(x) for x in phases.values()]
    # vmin 1, vmax 4, bins 3
#.........这里部分代码省略.........