pheval 0.3.4__py3-none-any.whl → 0.3.5__py3-none-any.whl
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- pheval/prepare/prepare_corpus.py +10 -4
- {pheval-0.3.4.dist-info → pheval-0.3.5.dist-info}/METADATA +1 -1
- {pheval-0.3.4.dist-info → pheval-0.3.5.dist-info}/RECORD +6 -6
- {pheval-0.3.4.dist-info → pheval-0.3.5.dist-info}/LICENSE +0 -0
- {pheval-0.3.4.dist-info → pheval-0.3.5.dist-info}/WHEEL +0 -0
- {pheval-0.3.4.dist-info → pheval-0.3.5.dist-info}/entry_points.txt +0 -0
pheval/prepare/prepare_corpus.py
CHANGED
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@@ -1,4 +1,5 @@
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import logging
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+
import shutil
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from pathlib import Path
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from pheval.prepare.create_spiked_vcf import create_spiked_vcf
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@@ -56,12 +57,17 @@ def prepare_corpus(
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f"Removed {phenopacket_path.name} from the corpus due to missing disease fields."
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)
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continue
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if gene_identifier:
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create_updated_phenopacket(
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gene_identifier, phenopacket_path, output_dir.joinpath("phenopackets")
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)
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if hg19_template_vcf or hg38_template_vcf:
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output_dir.joinpath("vcf").mkdir(exist_ok=True)
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create_spiked_vcf(
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output_dir.joinpath("vcf"), phenopacket_path, hg19_template_vcf, hg38_template_vcf
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)
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if gene_identifier:
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create_updated_phenopacket(
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gene_identifier, phenopacket_path, output_dir.joinpath("phenopackets")
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)
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else:
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# if not updating phenopacket gene identifiers then copy phenopacket as is to output directory
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shutil.copy(
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phenopacket_path, output_dir.joinpath(f"phenopackets/{phenopacket_path.name}")
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)
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@@ -29,7 +29,7 @@ pheval/prepare/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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pheval/prepare/create_noisy_phenopackets.py,sha256=UbBRWDD95BFHPv03VYx04v35AGwJ9ynLltYKqQJHbZ0,11236
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pheval/prepare/create_spiked_vcf.py,sha256=KZIyjtDDTqJj3hxL3u4YP6P0toA4RN1oPeDrzLMB2z4,20235
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pheval/prepare/custom_exceptions.py,sha256=_G3_95dPtHIs1SviYBV1j7cYc-hxlhuw8hhnYdzByYY,1719
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-
pheval/prepare/prepare_corpus.py,sha256=
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pheval/prepare/prepare_corpus.py,sha256=BzRra3VyPWHeT7zwH78vYEabo_hddBanJxVwPzw0YEU,3456
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pheval/prepare/update_phenopacket.py,sha256=21fzUPbwKN6Ey5TSh9PFzjT2x86U19RAE6WmkjG8u28,4770
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pheval/resources/alternate_ouputs/CADA_results.txt,sha256=Rinn2TtfwFNsx0aEWegKJOkjKnBm-Mf54gdaT3bWP0k,547
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pheval/resources/alternate_ouputs/DeepPVP_results.txt,sha256=MF9MZJYa4r4PEvFzALpi-lNGLxjENOnq_YgrgFMn-oQ,1508
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@@ -50,8 +50,8 @@ pheval/utils/file_utils.py,sha256=9HoCmtF73D3wY6bBhFLefMBI5uhvCe_meZeHXQzF_ts,46
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pheval/utils/phenopacket_utils.py,sha256=4inrnhZ4UjYgO0Y85ls_Nxq6voAIIXQV57_fMeIX-24,26792
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pheval/utils/semsim_utils.py,sha256=s7ZCR2VfPYnOh7ApX6rv66eGoVSm9QJaVYOWBEhlXpo,6151
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pheval/utils/utils.py,sha256=9V6vCT8l1g4O2-ZATYqsVyd7AYZdWGd-Ksy7_oIC3eE,2343
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-
pheval-0.3.
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pheval-0.3.
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pheval-0.3.
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pheval-0.3.
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pheval-0.3.
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pheval-0.3.5.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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pheval-0.3.5.dist-info/METADATA,sha256=LB8Oe6wFj-iebn32q3kH5Yqk23ElXvF6My1w_cytWds,1810
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pheval-0.3.5.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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56
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pheval-0.3.5.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
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pheval-0.3.5.dist-info/RECORD,,
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File without changes
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File without changes
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File without changes
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