comparison pairend_distro.py @ 3:aa9409835045 draft default tip

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit e1bfc70a74f12ef8182d9afa0b3ab69d620fb3a8"

2:1a4662c69bee

# warn if very few elements in distribution
min_elements = 1000
if len(L) < min_elements:
    sys.stderr.write("Warning: only %s elements in distribution (min: %s)\n" %
                     (len(L), min_elements))
    mean = "NA"
    stdev = "NA"

else:
    # Remove outliers

    med, umad = unscaled_upper_mad(L)
    upper_cutoff = med + options.mads * umad
    L = L[L < upper_cutoff]
    new_len = len(L)
    removed = c - new_len
    sys.stderr.write("Removed %d outliers with isize >= %d\n" %
                     (removed, upper_cutoff))
    c = new_len

    mean = np.mean(L)
    stdev = np.std(L)

3:aa9409835045

# warn if very few elements in distribution
min_elements = 1000
if len(L) < min_elements:
    sys.stderr.write("Warning: only %s elements in distribution (min: %s)\n" %
                     (str(len(L)), str(min_elements)))
    mean = "NA"
    stdev = "NA"

else:
    # Remove outliers

    med, umad = unscaled_upper_mad(L)
    upper_cutoff = med + options.mads * umad
    L = L[L < upper_cutoff]
    new_len = len(L)
    removed = c - new_len
    sys.stderr.write("Removed %s outliers with isize >= %s\n" %
                     (str(removed), str(upper_cutoff)))
    c = new_len

    mean = np.mean(L)
    stdev = np.std(L)