110 lines
2.6 KiB
Plaintext
110 lines
2.6 KiB
Plaintext
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from pathlib import Path
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from os.path import dirname
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from snakemake.utils import min_version
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min_version("7.20")
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configfile: "config/config.yml"
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ucmr_data = {
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1: (
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"https://www.epa.gov/sites/default/files/2015-09/ucmr1_list1and2chem.zip",
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"ucmr1_list1and2chem_final.xls",
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),
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2: (
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"https://www.epa.gov/sites/default/files/2015-09/ucmr2_occurrencedata_jan12.zip",
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"UCMR2_All_OccurrenceData_Jan12.txt",
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),
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3: (
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"https://www.epa.gov/sites/default/files/2017-02/ucmr-3-occurrence-data.zip",
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"UCMR3_All.txt",
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),
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4: (
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"https://www.epa.gov/sites/default/files/2020-04/ucmr_4_occurrence_data.zip",
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"UCMR4_All.txt",
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),
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}
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rule download_ucmr:
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output:
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"resources/ucmr/{ucmr}.zip",
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params:
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url=lambda w: ucmr_data[int(w.ucmr)][0],
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shell:
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"curl -sS -L -o {output} {params.url}"
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rule unzip_ucmr_1:
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input:
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expand(rules.download_ucmr.output, ucmr=1),
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output:
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"results/ucmr/ucmr_unzipped_1/ucmr1_list1and2chem_final.xls",
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params:
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zipdest=lambda _, output: dirname(output[0]),
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shell:
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"""
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rm -rf {params.zipdest} && \
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mkdir {params.zipdest} && \
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unzip {input} -d {params.zipdest}
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"""
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use rule unzip_ucmr_1 as unzip_ucmr_2 with:
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input:
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expand(rules.download_ucmr.output, ucmr=2),
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output:
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"results/ucmr/ucmr_unzipped_2/UCMR2_All_OccurrenceData_Jan12.txt",
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use rule unzip_ucmr_1 as unzip_ucmr_3 with:
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input:
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expand(rules.download_ucmr.output, ucmr=3),
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output:
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"results/ucmr/ucmr_unzipped_3/UCMR3_All.txt",
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use rule unzip_ucmr_1 as unzip_ucmr_4 with:
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input:
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expand(rules.download_ucmr.output, ucmr=4),
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output:
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"results/ucmr/ucmr_unzipped_4/UCMR4_All.txt",
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rule fix_ucmr4_data_tbl:
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input:
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rules.unzip_ucmr_4.output,
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output:
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"results/ucmr/ucmr_unzipped_4/UCMR4_All_fixed.txt",
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shell:
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"""
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cat {input} | sed 's/(\\xB5g\\/L)//' > {output}
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"""
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rule standardize_ucmr_3:
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input:
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rules.unzip_ucmr_3.output,
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output:
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"results/ucmr_data/all_std_3.txv.gz",
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conda:
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"envs/tidyverse.yml"
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script:
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"scripts/standardize_ucmr_34.R"
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use rule standardize_ucmr_3 as standardize_ucmr_4 with:
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input:
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rules.fix_ucmr4_data_tbl.output,
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output:
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"results/ucmr_data/all_std_4.txv.gz",
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rule all:
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input:
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rules.standardize_ucmr_3.output,
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rules.standardize_ucmr_4.output,
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# expand(rules.unzip_ucmr.output, ucmr=[1, 2, 3]),
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# rules.fix_ucmr4_data_tbl.output,
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