Ankylosing spondylitis

experiments/README.md

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+The experiments directory is for rough experimental code. See [documentation](docs/Getting_Started/e_experiments_directory.md).

experiments/tralfamadorian97/explore_ank_spond.py

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+import polars as pl
+from pathlib import Path
+
+from mecfs_bio.constants.gwaslab_constants import GWASLAB_CHROM_COL, GWASLAB_POS_COL, GWASLAB_EFFECT_ALLELE_COL, \
+    GWASLAB_NON_EFFECT_ALLELE_COL
+
+finn_path = Path(
+    "assets/base_asset_store/gwas/ankylosing_spondylitis/finngne/processed/finngen_ank_spond_harmonized_dump_to_parquet.parquet")
+
+mv_path = Path("assets/base_asset_store/gwas/ankylosing_spondylitis/million_veterans/processed/million_veterans_eur_ank_spond_harmonized_dump_to_parquet.parquet")
+def go():
+    df = pl.read_parquet(finn_path)
+    counts = df.group_by(
+                [
+                    GWASLAB_CHROM_COL,
+                    GWASLAB_POS_COL,
+                    GWASLAB_EFFECT_ALLELE_COL,
+                    GWASLAB_NON_EFFECT_ALLELE_COL
+                ],
+    ).len().sort(by="len",descending=True)
+    import pdb; pdb.set_trace()
+    print("yo")
+
+def go_mv():
+    df = pl.read_parquet(mv_path)
+    counts = df.group_by(
+        [
+            GWASLAB_CHROM_COL,
+            GWASLAB_POS_COL,
+            GWASLAB_EFFECT_ALLELE_COL,
+            GWASLAB_NON_EFFECT_ALLELE_COL
+        ],
+    ).len().sort(by="len",descending=True)
+    import pdb; pdb.set_trace()
+    print("yo")
+
+if __name__ == "__main__":
+    go_mv()
+
+

experiments/tralfamadorian97/get_min_pvalue_ankspond.py

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+import polars as pl
+def go():
+    import duckdb
+
+    # Define the path to your gzipped TSV file
+    file_path = 'assets/base_asset_store/gwas/ankylosing_spondylitis/uk_biobank/raw/GCST90474065.h.tsv.gz'
+
+    # Connect to an in-memory DuckDB database
+    con = duckdb.connect()
+
+    # Query the minimum p-value using read_csv_auto
+    # DuckDB natively handles gzip decompression and detects headers/delimiters
+    query = f"""
+         SELECT MIN(p_value) AS min_p
+         FROM read_csv_auto('{file_path}', delim='\t', header=True)
+     """
+
+    # Execute the query and fetch the single row result
+    result = con.execute(query).fetchone()
+    min_p_value = result[0]
+
+    print(f"The minimum p-value is: {min_p_value}")
+
+if __name__=="__main__":
+    go()

experiments/tralfamadorian97/runs/as_runs.py

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+from mecfs_bio.analysis.runner.default_runner import DEFAULT_RUNNER
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.finngen.analysis.finngen_ank_spond_manhattan import \
+    FINGEN_ANK_SPOND_MANHATTAN
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.finngen.processed.finngen_ank_spond_sumstats import \
+    FINGNEN_ANK_SPOND_SUMSTATS
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.finngen.processed.finngen_ank_spond_sumstats_harmonized import \
+    FINGNEN_ANK_SPOND_SUMSTATS_HARMONIZED
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.finngen.raw.raw_finngen_ank_spond_data import \
+    FINNGEN_ANKYLOSING_SPONDYLITIS_DATA_RAW
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.fixed_effects_meta_analysis.processed.ank_spond_meta_analysis import \
+    ANK_SPOND_FIXED_EFFECTS_META_ANALYSIS
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.million_veterans.analysis.mv_ankspond_manhattan import \
+    MV_ANK_SPOND_MANHATTAN
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.million_veterans.processed.mv_eur_ank_spond_sumstats import \
+    MILLION_VETERAN_ANKYLOSING_SPONDYLITIS_SUMSTATS
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.million_veterans.processed.mv_eur_ank_spond_sumstats_dump_to_parquet import \
+    MILLION_VETERANS_ANK_SPOND_SUMSTATS_37_DUMP_TO_PARQUET
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.million_veterans.processed.mv_eur_ank_spond_sumstats_harmonized import \
+    MILLION_VETERANS_ANK_SPOND_SUMSTATS_HARMONIZED
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.million_veterans.raw.raw_mv_eur_ank_spond_data import \
+    MILLION_VETERAN_ANKYLOSING_SPONDYLITIS_EUR_DATA_RAW
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.ukbb.processed.ukbb_ank_spond_sumstats import \
+    UK_BIOBANK_ANKYLOSING_SPONDYLITIS_SUMSTATS
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.ukbb.processed.ukbb_ank_spond_sumstats_harmonized import \
+    UKBB_ANK_SPOND_SUMSTATS_HARMONIZED
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.ukbb.processed.ukbb_eur_ank_spond_filtered import \
+    FILTERED_UKBB_ANK_SPOND
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.ukbb.processed.ukbb_eur_ank_spond_parquet import \
+    UKBB_ANK_SPOND_PARQUET
+from mecfs_bio.assets.gwas.ankylosing_spondylitis.ukbb.raw.raw_ukbb_eur_ank_spond_data import \
+    UK_BIOBANK_ANKYLOSING_SPONDYLITIS_EUR_DATA_RAW
+
+
+
+def go():
+    DEFAULT_RUNNER.run(
+        (
+            [
+                # MILLION_VETERAN_ANKYLOSING_SPONDYLITIS_SUMSTATS,
+                # FINGNEN_ANK_SPOND_SUMSTATS
+                # MILLION_VETERAN_ANKYLOSING_SPONDYLITIS_EUR_DATA_RAW,
+                # FINNGEN_ANKYLOSING_SPONDYLITIS_DATA_RAW
+             # UK_BIOBANK_ANKYLOSING_SPONDYLITIS_EUR_DATA_RAW
+             #    FILTERED_UKBB_ANK_SPOND
+             #    UKBB_ANK_SPOND_PARQUET
+             #    MILLION_VETERANS_ANK_SPOND_SUMSTATS_37_DUMP_TO_PARQUET
+             #    FILTERED_UKBB_ANK_SPOND
+             #    UK_BIOBANK_ANKYLOSING_SPONDYLITIS_SUMSTATS
+
+                # FINGNEN_ANK_SPOND_SUMSTATS_HARMONIZED,
+                # MILLION_VETERANS_ANK_SPOND_SUMSTATS_HARMONIZED,
+                #
+                # UKBB_ANK_SPOND_SUMSTATS_HARMONIZED
+                ANK_SPOND_FIXED_EFFECTS_META_ANALYSIS
+                # FINGEN_ANK_SPOND_MANHATTAN
+                # MV_ANK_SPOND_MANHATTAN
+            ]
+        ),
+
+        incremental_save=True,
+        must_rebuild_transitive=[
+        ]
+
+    )
+
+if __name__ == '__main__':
+    go()

experiments/tralfamadorian97/runs/lupus_runs.py

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+from mecfs_bio.analysis.runner.default_runner import DEFAULT_RUNNER
+from mecfs_bio.assets.gwas.systemic_lupus_erythematosus.bentham_et_al_2015.analysis_results.bentham_2015_standard_analysis import (
+    BENTHAM_LUPUS_STANDARD_ANALYSIS,
+)
+
+
+def lupus_analysis():
+    """
+    Script to analyze the lupus GWAS of Bentham et al
+    """
+    DEFAULT_RUNNER.run(
+        BENTHAM_LUPUS_STANDARD_ANALYSIS.magma_tasks.inner.terminal_tasks(),
+        incremental_save=True,
+        must_rebuild_transitive=[],
+    )
+
+
+if __name__ == "__main__":
+    lupus_analysis()

experiments/tralfamadorian97/try_ieugwas.py

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+import ieugwaspy
+def go():
+    # result = ieugwaspy.gwasinfo_files("finn-b-M13_ANKYLOSPON")
+    result = ieugwaspy.gwasinfo_files("ukb-b-18194")
+    print(result)
+    import pdb; pdb.set_trace()
+    print("testing")
+
+if __name__ == '__main__':
+    go()

mecfs_bio/assets/gwas/ankylosing_spondylitis/finngen/analysis/finngen_ank_spond_manhattan.py

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+from mecfs_bio.assets.gwas.ankylosing_spondylitis.finngen.processed.finngen_ank_spond_sumstats_harmonized import \
+    FINGNEN_ANK_SPOND_SUMSTATS_HARMONIZED
+from mecfs_bio.build_system.task.gwaslab.gwaslab_manhattan_and_qq_plot_task import GWASLabManhattanAndQQPlotTask
+
+FINGEN_ANK_SPOND_MANHATTAN=GWASLabManhattanAndQQPlotTask.create(
+FINGNEN_ANK_SPOND_SUMSTATS_HARMONIZED,
+    asset_id="fingen_ank_spond_manhattan",
+    plot_setting="m"
+)

mecfs_bio/assets/gwas/ankylosing_spondylitis/finngen/processed/finngen_ank_spond_harmonized_dump_to_parquet.py

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+from mecfs_bio.assets.gwas.ankylosing_spondylitis.finngen.processed.finngen_ank_spond_sumstats_harmonized import (
+    FINGNEN_ANK_SPOND_SUMSTATS_HARMONIZED,
+)
+from mecfs_bio.build_system.task.gwaslab.gwaslab_sumstats_to_table_task import (
+    GwasLabSumstatsToTableTask,
+)
+
+FINNGEN_ANK_SPOND_HARMONIZED_DUMP_TO_PARQUET = (
+    GwasLabSumstatsToTableTask.create_from_source_task(
+        source_tsk=FINGNEN_ANK_SPOND_SUMSTATS_HARMONIZED,
+        asset_id="finngen_ank_spond_harmonized_dump_to_parquet",
+        sub_dir="processed",
+    )
+)

mecfs_bio/assets/gwas/ankylosing_spondylitis/finngen/processed/finngen_ank_spond_sumstats.py

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+from mecfs_bio.assets.gwas.ankylosing_spondylitis.finngen.raw.raw_finngen_ank_spond_data import (
+    FINNGEN_ANKYLOSING_SPONDYLITIS_DATA_RAW,
+)
+from mecfs_bio.build_system.meta.asset_id import AssetId
+from mecfs_bio.build_system.task.gwaslab.gwaslab_create_sumstats_task import (
+    GWASLabColumnSpecifiers,
+    GWASLabCreateSumstatsTask,
+)
+from mecfs_bio.build_system.task.pipes.composite_pipe import CompositePipe
+from mecfs_bio.build_system.task.pipes.str_split_exact_col import SplitExactColPipe
+
+FINGNEN_ANK_SPOND_SUMSTATS = GWASLabCreateSumstatsTask(
+    df_source_task=FINNGEN_ANKYLOSING_SPONDYLITIS_DATA_RAW,
+    asset_id=AssetId("finngen_ank_spond_sumstats"),
+    basic_check=True,
+    genome_build="infer",
+    liftover_to="19",
+    fmt=GWASLabColumnSpecifiers(
+        rsid="ID",
+        chrom="CHROM",
+        pos="POS",
+        nea="REF",
+        ea="ALT",
+        beta="ES",
+        se="SE",
+        mlog10p="LP",
+        eaf="AF",
+    ),
+    pre_pipe=CompositePipe(
+        [
+            SplitExactColPipe(
+                col_to_split="finn-b-M13_ANKYLOSPON",
+                split_by=":",
+                new_col_names=tuple(["ES", "SE", "LP", "AF"]),
+            )
+        ]
+    ),
+    # pre_pipe=pre_pipe,
+)

mecfs_bio/assets/gwas/ankylosing_spondylitis/finngen/processed/finngen_ank_spond_sumstats_harmonized.py

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+from mecfs_bio.assets.gwas.ankylosing_spondylitis.finngen.processed.finngen_ank_spond_sumstats import (
+    FINGNEN_ANK_SPOND_SUMSTATS,
+)
+from mecfs_bio.build_system.task.gwaslab.gwaslab_create_sumstats_task import (
+    GwasLabTransformSpec,
+    GWASLabVCFRef,
+    HarmonizationOptions,
+)
+from mecfs_bio.build_system.task.gwaslab.gwaslab_transform_sumstats import (
+    GWASLabTransformSumstatsTask,
+)
+
+FINGNEN_ANK_SPOND_SUMSTATS_HARMONIZED = (
+    GWASLabTransformSumstatsTask.create_from_source_task(
+        source_tsk=FINGNEN_ANK_SPOND_SUMSTATS,
+        asset_id="finngen_ank_spond_sumstats_37_harmonized",
+        spec=GwasLabTransformSpec(
+            harmonize_options=HarmonizationOptions(
+                ref_infer=GWASLabVCFRef(name="1kg_eur_hg19", ref_alt_freq="AF"),
+                ref_seq="ucsc_genome_hg19",
+                check_ref_files=True,
+                drop_missing_from_ref_seq=True,
+                drop_missing_from_ref_infer_or_ambiguous=True,
+                cores=1,
+            )
+        ),
+    )
+)

mecfs_bio/assets/gwas/ankylosing_spondylitis/finngen/raw/raw_finngen_ank_spond_data.py

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+"""
+Summary statistics from Ankylosing spondylitis in Finngen
+
+
+See: https://opengwas.io/datasets/finn-b-M13_ANKYLOSPON#
+
+opengwas only provides a temporary link, so I mirrored on dropbox.
+
+
+Note: This dataset appears to contain some anomalies, probably due to the conversion of multi-allelic to bi-allelic genetic variants
+- e.g. There are duplicated genetic variants with different effect sizes
+"""
+
+from pathlib import PurePath
+
+import polars as pl
+
+from mecfs_bio.build_system.meta.asset_id import AssetId
+from mecfs_bio.build_system.meta.gwas_summary_file_meta import GWASSummaryDataFileMeta
+from mecfs_bio.build_system.meta.read_spec.dataframe_read_spec import (
+    DataFrameReadSpec,
+    DataFrameTextFormat,
+)
+from mecfs_bio.build_system.task.download_file_task import DownloadFileTask
+
+FINNGEN_ANKYLOSING_SPONDYLITIS_DATA_RAW = DownloadFileTask(
+    meta=GWASSummaryDataFileMeta(
+        id=AssetId("finngen_spond_eur_raw"),
+        trait="ankylosing_spondylitis",
+        project="finngne",
+        sub_dir="raw",
+        project_path=PurePath("finn-b-M13_ANKYLOSPON.vcf.gz"),
+        read_spec=DataFrameReadSpec(
+            format=DataFrameTextFormat(
+                separator="\t",
+                has_header=False,
+                column_names=[
+                    "CHROM",
+                    "POS",
+                    "ID",
+                    "REF",
+                    "ALT",
+                    "QUAL",
+                    "FILTER",
+                    "INFO",
+                    "FORMAT",
+                    "finn-b-M13_ANKYLOSPON",
+                ],
+                comment_char="#",
+                schema_overrides={"CHROM": pl.String()},
+            )
+        ),
+    ),
+    url="https://www.dropbox.com/scl/fi/keanskgpwrf26ngdly3dm/finn-b-M13_ANKYLOSPON.vcf.gz?rlkey=gwzualqvpiyktd965yhpdpztn&dl=1",
+    md5_hash=None,
+)