Python filter示例

示例#1

文件： mummerplot.py 项目： rrane/jcvi

def main(args):
    """
    %prog deltafile refidsfile query.fasta ref.fasta

    Plot one query. Extract the references that have major matches to this
    query. Control "major" by option --refcov.
    """
    p = OptionParser(main.__doc__)
    p.add_option("--refcov", default=.01, type="float",
                 help="Minimum reference coverage [default: %default]")
    p.add_option("--all", default=False, action="store_true",
                 help="Plot one pdf file per ref in refidsfile [default: %default]")
    p.set_align(pctid=96, hitlen=500)
    opts, args = p.parse_args(args)

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

    deltafile, refidsfile, queryfasta, reffasta = args
    qsizes = Sizes(queryfasta).mapping
    rsizes = Sizes(reffasta).mapping
    refs = SetFile(refidsfile)
    refcov = opts.refcov
    pctid = opts.pctid
    hitlen = opts.hitlen
    deltafile = filter([deltafile, "--pctid={0}".format(pctid),
                        "--hitlen={0}".format(hitlen)])

    if opts.all:
        for r in refs:
            pdffile = plot_some_queries([r], qsizes, rsizes, deltafile, refcov)
            if pdffile:
                sh("mv {0} {1}.pdf".format(pdffile, r))
    else:
        plot_some_queries(refs, qsizes, rsizes, deltafile, refcov)

示例#2

文件： mummerplot.py 项目： Hensonmw/jcvi

def main(args):
    """
    %prog deltafile

    Plot one query. Extract the references that have major matches to this
    query. Control "major" by option --refcov.
    """
    p = OptionParser(main.__doc__)
    p.add_option("--refids", help="Use subset of contigs in the ref")
    p.add_option("--refcov", default=.01, type="float",
                 help="Minimum reference coverage [default: %default]")
    p.add_option("--all", default=False, action="store_true",
                 help="Plot one pdf file per ref in refidsfile [default: %default]")
    p.add_option("--color", default="similarity",
                 choices=("similarity", "direction", "none"),
                 help="Color the dots based on")
    p.add_option("--nolayout", default=False, action="store_true",
                 help="Do not rearrange contigs")
    p.set_align(pctid=0, hitlen=0)
    opts, args = p.parse_args(args)

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

    deltafile, = args
    reffasta, queryfasta = open(deltafile).readline().split()
    color = opts.color
    layout = not opts.nolayout
    prefix = op.basename(deltafile).split(".")[0]
    qsizes = Sizes(queryfasta).mapping
    rsizes = Sizes(reffasta).mapping

    refs = SetFile(opts.refids) if opts.refids else set(rsizes.keys())
    refcov = opts.refcov
    pctid = opts.pctid
    hitlen = opts.hitlen
    deltafile = filter([deltafile, "--pctid={0}".format(pctid),
                        "--hitlen={0}".format(hitlen)])

    if opts.all:
        for r in refs:
            pdffile = plot_some_queries([r], qsizes, rsizes, deltafile, refcov,
                                        prefix=prefix, color=color,
                                        layout=layout)
            if pdffile:
                sh("mv {0} {1}.pdf".format(pdffile, r))
    else:
        plot_some_queries(refs, qsizes, rsizes,
                          deltafile, refcov,
                          prefix=prefix, color=color, layout=layout)

示例#3

文件： mummerplot.py 项目： zjwang6/jcvi

def main(args):
    """
    %prog deltafile

    Plot one query. Extract the references that have major matches to this
    query. Control "major" by option --refcov.
    """
    p = OptionParser(main.__doc__)
    p.add_option("--refids", help="Use subset of contigs in the ref")
    p.add_option("--refcov", default=.01, type="float",
                 help="Minimum reference coverage [default: %default]")
    p.add_option("--all", default=False, action="store_true",
                 help="Plot one pdf file per ref in refidsfile [default: %default]")
    p.add_option("--color", default="similarity",
                 choices=("similarity", "direction", "none"),
                 help="Color the dots based on")
    p.add_option("--nolayout", default=False, action="store_true",
                 help="Do not rearrange contigs")
    p.set_align(pctid=0, hitlen=0)
    opts, args = p.parse_args(args)

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

    deltafile, = args
    reffasta, queryfasta = open(deltafile).readline().split()
    color = opts.color
    layout = not opts.nolayout
    prefix = op.basename(deltafile).split(".")[0]
    qsizes = Sizes(queryfasta).mapping
    rsizes = Sizes(reffasta).mapping

    refs = SetFile(opts.refids) if opts.refids else set(rsizes.keys())
    refcov = opts.refcov
    pctid = opts.pctid
    hitlen = opts.hitlen
    deltafile = filter([deltafile, "--pctid={0}".format(pctid),
                        "--hitlen={0}".format(hitlen)])

    if opts.all:
        for r in refs:
            pdffile = plot_some_queries([r], qsizes, rsizes, deltafile, refcov,
                                        prefix=prefix, color=color,
                                        layout=layout)
            if pdffile:
                sh("mv {0} {1}.pdf".format(pdffile, r))
    else:
        plot_some_queries(refs, qsizes, rsizes,
                          deltafile, refcov,
                          prefix=prefix, color=color, layout=layout)

示例#4

文件： mummerplot.py 项目： radaniba/jcvi

def main(args):
    """
    %prog deltafile refidsfile query.fasta ref.fasta

    Plot one query. Extract the references that have major matches to this
    query. Control "major" by option --refcov.
    """
    p = OptionParser(main.__doc__)
    p.add_option("--refcov",
                 default=.01,
                 type="float",
                 help="Minimum reference coverage [default: %default]")
    p.add_option(
        "--all",
        default=False,
        action="store_true",
        help="Plot one pdf file per ref in refidsfile [default: %default]")
    p.set_align(pctid=96, hitlen=500)
    opts, args = p.parse_args(args)

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

    deltafile, refidsfile, queryfasta, reffasta = args
    qsizes = Sizes(queryfasta).mapping
    rsizes = Sizes(reffasta).mapping
    refs = SetFile(refidsfile)
    refcov = opts.refcov
    pctid = opts.pctid
    hitlen = opts.hitlen
    deltafile = filter([
        deltafile, "--pctid={0}".format(pctid), "--hitlen={0}".format(hitlen)
    ])

    if opts.all:
        for r in refs:
            pdffile = plot_some_queries([r], qsizes, rsizes, deltafile, refcov)
            if pdffile:
                sh("mv {0} {1}.pdf".format(pdffile, r))
    else:
        plot_some_queries(refs, qsizes, rsizes, deltafile, refcov)