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from genomicranges import GenomicRanges, SeqInfo | ||
from iranges import IRanges | ||
from biocframe import BiocFrame | ||
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from .parser import get_class | ||
from .pdf import as_pandas_from_dframe | ||
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__author__ = "jkanche" | ||
__copyright__ = "jkanche" | ||
__license__ = "MIT" | ||
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def as_granges(robj): | ||
"""Parse an R object as a :py:class:`~genomicranges.GenomicRanges.GenomicRanges`. | ||
Args: | ||
robj: | ||
Object parsed from the `RDS` file. | ||
Usually the result of :py:func:`~rds2py.parser.read_rds`. | ||
Returns: | ||
A ``GenomicRanges`` object. | ||
""" | ||
_cls = get_class(robj) | ||
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if _cls not in ["GenomicRanges", "GRanges"]: | ||
raise TypeError(f"obj is not genomic ranges, but is `{_cls}`.") | ||
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_range_start = robj["attributes"]["ranges"]["attributes"]["start"]["data"] | ||
_range_width = robj["attributes"]["ranges"]["attributes"]["width"]["data"] | ||
_range_names = None | ||
if "NAMES" in robj["attributes"]["ranges"]["attributes"]: | ||
_range_names = robj["attributes"]["ranges"]["attributes"]["NAMES"]["data"] | ||
_ranges = IRanges(_range_start, _range_width, names=_range_names) | ||
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_seqnames = _as_list(robj["attributes"]["seqnames"]) | ||
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_strand_obj = robj["attributes"]["strand"]["attributes"]["values"] | ||
_strands = _strand_obj["data"] | ||
if "attributes" in _strands: | ||
if "levels" in _strands["attributes"]: | ||
_levels_data = _strands["attributes"]["levels"]["data"] | ||
_strands = [_levels_data[x] for x in _strands] | ||
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_seqinfo_seqnames = robj["attributes"]["seqinfo"]["attributes"]["seqnames"]["data"] | ||
_seqinfo_seqlengths = robj["attributes"]["seqinfo"]["attributes"]["seqlengths"][ | ||
"data" | ||
] | ||
_seqinfo_is_circular = robj["attributes"]["seqinfo"]["attributes"]["is_circular"][ | ||
"data" | ||
] | ||
_seqinfo_genome = robj["attributes"]["seqinfo"]["attributes"]["genome"]["data"] | ||
_seqinfo = SeqInfo( | ||
seqnames=_seqinfo_seqnames, | ||
seqlengths=[None if x == -2147483648 else x for x in _seqinfo_seqlengths], | ||
is_circular=[None if x == -2147483648 else x for x in _seqinfo_is_circular], | ||
genome=_seqinfo_genome, | ||
) | ||
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_mcols = BiocFrame.from_pandas( | ||
as_pandas_from_dframe(robj["attributes"]["elementMetadata"]) | ||
) | ||
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_gr_names = None | ||
if "NAMES" in robj["attributes"]: | ||
_gr_names = robj["attributes"]["NAMES"]["data"] | ||
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return GenomicRanges( | ||
seqnames=_seqnames, | ||
ranges=_ranges, | ||
names=_gr_names, | ||
mcols=_mcols, | ||
seqinfo=_seqinfo, | ||
) | ||
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def _as_list(robj): | ||
"""Parse an R object as a :py:class:`~list`. | ||
Args: | ||
robj: | ||
Object parsed from the `RDS` file. | ||
Usually the result of :py:func:`~rds2py.parser.read_rds`. | ||
Returns: | ||
A ``list`` of the Rle class. | ||
""" | ||
_cls = get_class(robj) | ||
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if _cls not in ["Rle"]: | ||
raise TypeError(f"obj is not Rle, but is `{_cls}`.") | ||
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_attr_vals = robj["attributes"] | ||
_data = _attr_vals["values"]["data"].tolist() | ||
if "attributes" in _attr_vals["values"]: | ||
if "levels" in _attr_vals["values"]["attributes"]: | ||
_levels_data = _attr_vals["values"]["attributes"]["levels"]["data"] | ||
_data = [_levels_data[x - 1] for x in _data] | ||
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if "lengths" in _attr_vals: | ||
_final = [] | ||
_lengths = _attr_vals["lengths"]["data"] | ||
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for idx, lg in enumerate(_lengths.tolist()): | ||
_final.extend([_data[idx]] * lg) | ||
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_data = _final | ||
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return _data |
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import pytest | ||
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from rds2py.granges import as_granges | ||
from rds2py.parser import read_rds | ||
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from genomicranges import GenomicRanges | ||
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__author__ = "jkanche" | ||
__copyright__ = "jkanche" | ||
__license__ = "MIT" | ||
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def test_granges(): | ||
robj = read_rds("tests/data/granges.rds") | ||
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gr = as_granges(robj=robj) | ||
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assert isinstance(gr, GenomicRanges) |