comparison bigwig_outlier_bed.py @ 3:00b3da7776a0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 06c54e8066ecbc6292167e7c5bdfb8af945a41ba

2:61946b8bd43b

        if isTop:
            bwex = np.r_[False, bw >= self.bwtop, False]  # extend with 0s
        else:
            bwex = np.r_[False, bw <= self.bwbot, False]
        bwexd = np.diff(bwex)
        bwexdnz = bwexd.nonzero()[0]
        bwregions = np.reshape(bwexdnz, (-1, 2))
        return bwregions

    def writeBed(self, bed, bedfname):
        """
        potentially multiple
        """
        bed.sort()
        beds = ["%s\t%d\t%d\t%s\t%d" % x for x in bed]
        with open(bedfname, "w") as bedf:
            bedf.write("\n".join(beds))
            bedf.write("\n")

    def makeTableRow(self, bw, bwlabel, chr):
        """
        called for every contig, but messy inline
        """

        bedhi = []
        bedlo = []
        restab = []
        bwlabels = self.bwlabels
        bwnames = self.bwnames
        bwnames.sort()
        reshead = "bigwig\tcontig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot"
        for i, bwname in enumerate(bwnames):
            bwlabel = bwlabels[i].replace(" ", "")
            fakepath = "in%d.bw" % i
            if os.path.isfile(fakepath):

                            )
                if self.qlo is not None:
                    self.bwbot = np.quantile(bw, self.qlo)
                    bwlo = self.processVals(bw, isTop=False)
                    for j, seg in enumerate(bwlo):
                        if seg[1] - seg[0] >= self.bedwin:
                            score = -1 * np.sum(bw[seg[0]:seg[1]]) / float(seglen)
                            bedlo.append(
                                (
                                    chr,
                                    seg[0],
                                    seg[1],

3:00b3da7776a0

        if isTop:
            bwex = np.r_[False, bw >= self.bwtop, False]  # extend with 0s
        else:
            bwex = np.r_[False, bw <= self.bwbot, False]
        bwexd = np.diff(bwex)
        bwexdnz = bwexd.nonzero()[0]  # start and end transition of each segment - nice!
        bwregions = np.reshape(bwexdnz, (-1, 2))
        return bwregions

    def writeBed(self, bed, bedfname):
        """
        potentially multiple
        """
        bed.sort()
        with open(bedfname, "w") as bedf:
            for b in bed:
                bedf.write("%s\t%d\t%d\t%s\t%d\n" % b)

    def makeTableRow(self, bw, bwlabel, chr):
        """
        called for every contig, but messy inline
        """

        bedhi = []
        bedlo = []
        restab = []
        bwlabels = self.bwlabels
        bwnames = self.bwnames
        reshead = "bigwig\tcontig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot"
        for i, bwname in enumerate(bwnames):
            bwlabel = bwlabels[i].replace(" ", "")
            fakepath = "in%d.bw" % i
            if os.path.isfile(fakepath):

                            )
                if self.qlo is not None:
                    self.bwbot = np.quantile(bw, self.qlo)
                    bwlo = self.processVals(bw, isTop=False)
                    for j, seg in enumerate(bwlo):
                        seglen = seg[1] - seg[0]
                        if seg[1] - seg[0] >= self.bedwin:
                            score = (
                                -1 * np.sum(bw[seg[0]:seg[1]]) / float(seglen)
                            )
                            bedlo.append(
                                (
                                    chr,
                                    seg[0],
                                    seg[1],