def annotate(chromos, pos, anno):
"""Annotate genomic locations.
Tests if sites specified by `chromos` and `pos` are annotated by `anno`.
Parameters
----------
chromos: :class:`numpy.ndarray`
:class:`numpy.ndarray` with chromosome of sites.
pos: :class:`numpy.ndarray`
:class:`numpy.ndarray` with position on chromosome of sites.
anno: :class:`pandas.DataFrame`
:class:`pandas.DataFrame` with columns `chromo`, `start`, `end` that
specify annotated regions.
Returns
-------
:class:`numpy.ndarray`
Binary :class:`numpy.ndarray` of same length as `chromos` indicating if
positions are annotated.
"""
idx = []
for chromo in np.unique(chromos):
chromo_pos = pos[chromos == chromo]
chromo_anno = anno.loc[anno.chromo == chromo]
chromo_idx = is_in(chromo_pos,
chromo_anno['start'].values,
chromo_anno['end'].values)
idx.append(chromo_idx)
idx = np.hstack(idx)
return idx
def annotate(chromos, pos, anno):
"""Annotate genomic locations.
Tests if sites specified by `chromos` and `pos` are annotated by `anno`.
Parameters
----------
chromos: :class:`numpy.ndarray`
:class:`numpy.ndarray` with chromosome of sites.
pos: :class:`numpy.ndarray`
:class:`numpy.ndarray` with position on chromosome of sites.
anno: :class:`pandas.DataFrame`
:class:`pandas.DataFrame` with columns `chromo`, `start`, `end` that
specify annotated regions.
Returns
-------
:class:`numpy.ndarray`
Binary :class:`numpy.ndarray` of same length as `chromos` indicating if
positions are annotated.
"""
idx = []
for chromo in np.unique(chromos):
chromo_pos = pos[chromos == chromo]
chromo_anno = anno.loc[anno.chromo == chromo]
chromo_idx = is_in(chromo_pos, chromo_anno['start'].values,
chromo_anno['end'].values)
idx.append(chromo_idx)
idx = np.hstack(idx)
return idx
def test_is_in():
ys = [2, 4, 12, 17]
ye = [2, 8, 15, 18]
x = [-1, 2, 2, 3, 4, 8, 15, 16]
expect = [False, True, True, False, True, True, True, False]
result = annos.is_in(x, ys, ye)
npt.assert_array_equal(result, expect)
def test_is_in():
ys = [2, 4, 12, 17]
ye = [2, 8, 15, 18]
x = [-1, 2, 2, 3, 4, 8, 15, 16]
expect = [False, True, True, False, True, True, True, False]
result = annos.is_in(x, ys, ye)
npt.assert_array_equal(result, expect)
def annotate(anno_file, chromo, pos):
anno_file = dat.GzipFile(anno_file, 'r')
anno = pd.read_table(anno_file, header=None, usecols=[0, 1, 2],
dtype={0: 'str', 1: 'int32', 2: 'int32'})
anno_file.close()
anno.columns = ['chromo', 'start', 'end']
anno.chromo = anno.chromo.str.upper().str.replace('CHR', '')
anno = anno.loc[anno.chromo == chromo]
anno.sort_values('start', inplace=True)
start, end = an.join_overlapping(anno.start.values, anno.end.values)
anno = np.array(an.is_in(pos, start, end), dtype='int8')
return anno
def annotate(anno_file, chromo, pos):
anno_file = dat.GzipFile(anno_file, 'r')
anno = pd.read_table(anno_file, header=None, usecols=[0, 1, 2],
dtype={0: 'str', 1: 'int32', 2: 'int32'})
anno_file.close()
anno.columns = ['chromo', 'start', 'end']
anno.chromo = anno.chromo.str.upper().str.replace('CHR', '')
anno = anno.loc[anno.chromo == chromo]
anno.sort_values('start', inplace=True)
start, end = an.join_overlapping(anno.start.values, anno.end.values)
anno = np.array(an.is_in(pos, start, end), dtype='int8')
return anno
