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Creating a file for the code shared by all _frequencies functions #690

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Creating a file for the code shared by all _frequencies functions #690

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0e8f12f
Moving a lot of frequency functions to frq_funcs.py
jonbrenas Dec 6, 2024
16fc484
Moved the ploting functions which was more complex than expected
jonbrenas Dec 6, 2024
9837220
Merge branch 'master' into 664-freq-functions
jonbrenas Dec 10, 2024
d021f51
Moved the tests for the plotting functions
jonbrenas Dec 11, 2024
5a57346
Corrected the typing issue
jonbrenas Dec 11, 2024
06be149
Tried to move random_transcript to conftest. WIP.
jonbrenas Dec 11, 2024
fd90c09
Experimenting. I expect a linting isue.
jonbrenas Dec 12, 2024
48d0274
Found a solution. Maybe.
jonbrenas Dec 12, 2024
86e7e02
Extended the tests to CNVs and HAPs
jonbrenas Dec 12, 2024
7b69da9
Test
jonbrenas Dec 12, 2024
c8c4218
Still fighting with haplotype frequencies
jonbrenas Dec 12, 2024
2604b2e
Progress on haplotype frequencies
jonbrenas Dec 12, 2024
677ebcf
Added tests on funestus for hap_frq
jonbrenas Dec 12, 2024
d41ff6d
Trying something
jonbrenas Dec 12, 2024
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13 changes: 7 additions & 6 deletions malariagen_data/anoph/cnv_frq.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,24 +10,25 @@
from numpydoc_decorator import doc # type: ignore

from . import base_params, cnv_params, frq_params
from .frq_funcs import (
prep_samples_for_cohort_grouping,
build_cohorts_from_sample_grouping,
add_frequency_ci,
)
from ..util import (
check_types,
pandas_apply,
Region,
parse_multi_region,
region_str,
simple_xarray_concat,
prep_samples_for_cohort_grouping,
build_cohorts_from_sample_grouping,
add_frequency_ci,
)
from .cnv_data import AnophelesCnvData
from .frq_funcs import AnophelesFrequency
from .sample_metadata import locate_cohorts


class AnophelesCnvFrequencyAnalysis(
AnophelesCnvData,
):
class AnophelesCnvFrequencyAnalysis(AnophelesCnvData, AnophelesFrequency):
def __init__(
self,
**kwargs,
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