How to use Create_assets method in locust

Best Python code snippet using locust

create_assets.smk

Source:create_assets.smk

1###-----------------------------------------------------------------------------------------------------------------###2# Notes on where variables are defined, if not defined in obs_exp.smk3#4# output_directory        - workflow/Snakefile5# config                  - workflow/Snakefile6# get_biscuit_refererence - workflow/rules/biscuit.smk7#8###-----------------------------------------------------------------------------------------------------------------###9# Verify the provided genome is one of the available genomes10def check_genome(wildcards):11    if config['create_assets']['run'] and config['create_assets']['genome'] not in ['hg38', 'hg19', 'mm10', 'mm9']:12        print('hg38, hg19, mm10, and mm9 are the only available genomes for creating asset files')13        exit(1)14    elif config['create_assets']['run'] and config['create_assets']['genome'] in ['hg38', 'hg19', 'mm10', 'mm9']:15        return config['create_assets']['genome']16# Determine which GENCODE annotation file to download17def get_annotation_file(wildcards):18    base = 'http://ftp.ebi.ac.uk/pub/databases/gencode'19    gen = check_genome(wildcards)20    if gen == 'hg38':21        return f'{base}/Gencode_human/release_38/gencode.v38.annotation.gtf.gz'22    elif gen == 'hg19':23        return f'{base}/Gencode_human/release_19/gencode.v19.annotation.gtf.gz'24    elif gen == 'mm9':25        return f'{base}/Gencode_mouse/release_M1/gencode.vM1.annotation.gtf.gz'26    else:27        return f'{base}/Gencode_mouse/release_M27/gencode.vM27.annotation.gtf.gz'28rule general_assets:29    input:30        ref = get_biscuit_reference,31    output:32        cpg = f'assets/{config["create_assets"]["genome"]}/cpg.bed.gz',33        bot = f'assets/{config["create_assets"]["genome"]}/windows100bp.gc_content.bot10p.bed.gz',34        top = f'assets/{config["create_assets"]["genome"]}/windows100bp.gc_content.top10p.bed.gz',35        cgi = f'assets/{config["create_assets"]["genome"]}/cpg_islands.bed.gz',36        opn = f'assets/{config["create_assets"]["genome"]}/cpg_open_seas.bed.gz',37        shl = f'assets/{config["create_assets"]["genome"]}/cpg_shelves.bed.gz',38        sho = f'assets/{config["create_assets"]["genome"]}/cpg_shores.bed.gz',39        exn = f'assets/{config["create_assets"]["genome"]}/exon.bed.gz',40        gen = f'assets/{config["create_assets"]["genome"]}/genic.bed.gz',41        inr = f'assets/{config["create_assets"]["genome"]}/intergenic.bed.gz',42        msk = f'assets/{config["create_assets"]["genome"]}/rmsk.bed.gz',43    params:44        annt = get_annotation_file,45        gen = check_genome,46        dir = f'assets/{config["create_assets"]["genome"]}',47        tmp_sho = f'assets/{config["create_assets"]["genome"]}/shores.tmp.bed',48        tmp_shl = f'assets/{config["create_assets"]["genome"]}/shelves.tmp.bed',49        tmp_gen = f'assets/{config["create_assets"]["genome"]}/gene.tmp.bed',50        tmp_exn = f'assets/{config["create_assets"]["genome"]}/exon.tmp.bed',51    log:52        f'{output_directory}/logs/general_assets.log',53    benchmark:54        f'{output_directory}/benchmarks/general_assets.txt',55    threads: 156    resources:57        mem_gb = config['hpcParameters']['intermediateMemoryGb'],58        walltime = config['walltime']['medium']59    conda:60        '../envs/biscuit.yaml'61    envmodules:62        config['envmodules']['bedtools'],63        config['envmodules']['biscuit'],64    shell:65        """66        set +o pipefail;67        echo "Create output directory" 1> {log}68        mkdir -p {params.dir}69        70        echo "Set reference location" 1> {log}71        # Reference location72        REFLOC={input.ref}.fai73        echo "Retrieve CpG island file" 1> {log}74        # CpG Islands from UCSC on only the canonical chromosomes75        wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/{params.gen}/database/cpgIslandExt.txt.gz | \76        gunzip -c | \77        awk 'BEGIN{{ OFS="\\t"; }}{{ print $2, $3, $4; }}' | \78        awk '{{ if ($1 ~ /^chr[1234567890XYM]{{1,2}}$/) {{ print }} }}' | \79        bedtools sort -i - | \80        gzip -c > {output.cgi}81        echo "CpG island file retrieved" 1> {log}82        # Create middles for finding locations83        bedtools slop \84            -i {output.cgi} \85            -g ${{REFLOC}} \86            -b 2000 | \87        bedtools merge -i - \88        > {params.tmp_sho}89        bedtools slop \90            -i {output.cgi} \91            -g ${{REFLOC}} \92            -b 4000 | \93        bedtools merge -i - \94        > {params.tmp_shl}95        # CpG Open Seas (intervening locations)96        sort -k1,1 -k2,2n ${{REFLOC}} | \97        bedtools complement -L -i {params.tmp_shl} -g - | \98        gzip -c > {output.opn}99        # CpG Shelves (shores +/- 2kb)100        bedtools subtract \101            -a {params.tmp_shl} \102            -b {params.tmp_sho} | \103        gzip -c > {output.shl}104        # CpG Shores (island +/- 2kb)105        bedtools subtract \106            -a {params.tmp_sho} \107            -b {output.cgi} | \108        gzip -c > {output.sho}109        # Clean up CpG temporary files110        rm -f {params.tmp_shl} {params.tmp_sho}111        echo "CpG seascape created and cleaned up" 1> {log}112        # BISCUIT assets (includes CpG and top/bottom 10% GC-content files)113        build_biscuit_QC_assets.pl --outdir {params.dir} --ref {input.ref} 1> {log}114        # Repeat-masked file115        if [[ {params.gen} != "mm9" ]]; then116            wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/{params.gen}/database/rmsk.txt.gz | \117            gunzip -c | \118            awk 'BEGIN{{ OFS="\\t"; }}{{ print $6, $7, $8; }}' | \119            awk '{{ if ($1 ~ /^chr[1234567890XYM]{{1,2}}$/) {{ print }} }}' | \120            bedtools sort -i - | \121            bedtools merge -i - | \122            gzip -c > {output.msk}123        else124            wget -q -nd -r -nH -np --accept-regex 'chr[1234567890XYM]*_rmsk.txt.gz$' \125                --regex-type=posix http://hgdownload.cse.ucsc.edu/goldenpath/mm9/database/126            cat chr*_rmsk.txt.gz | \127            gunzip -c | \128            awk 'BEGIN{{ OFS="\\t"; }}{{ print $6, $7, $8; }}' | \129            bedtools sort -i - | \130            bedtools merge -i - | \131            gzip -c > {output.msk}132            if [[ -f index.html ]]; then rm index.html; fi133            if [[ -f robots.txt ]]; then rm robots.txt; fi134            rm chr*_rmsk.txt.gz135        fi136        # Genic, intergenic, and exon files137        wget -qO- {params.annt} | \138        gunzip -c | \139        awk 'BEGIN{{ OFS="\\t"; }}{{ if ($3 == "gene") {{ print $1, $4, $5 > "{params.tmp_gen}"; }} else if ($3 == "exon") {{ print $1, $4, $5 > "{params.tmp_exn}"; }} }}'140        bedtools sort -i {params.tmp_gen} | \141        bedtools merge -i - | \142        gzip -c > {output.gen}143        bedtools sort -i {params.tmp_exn} | \144        bedtools merge -i - | \145        gzip -c > {output.exn}146        sort -k1,1 -k2,2n {input.ref}.fai | \147        bedtools complement -L -i {output.gen} -g - | \148        gzip -c > {output.inr}149        # Clean up150        rm -f {params.tmp_gen} {params.tmp_exn}151        """       152rule bismap_assets:153    input:154        cpg = f'assets/{config["create_assets"]["genome"]}/cpg.bed.gz',155        cgi = f'assets/{config["create_assets"]["genome"]}/cpg_islands.bed.gz',156        exn = f'assets/{config["create_assets"]["genome"]}/exon.bed.gz',157        gen = f'assets/{config["create_assets"]["genome"]}/genic.bed.gz',158        inr = f'assets/{config["create_assets"]["genome"]}/intergenic.bed.gz',159        msk = f'assets/{config["create_assets"]["genome"]}/rmsk.bed.gz',160        ref = get_biscuit_reference,161    output:162        bis = f'assets/{config["create_assets"]["genome"]}/k100.bismap.bedgraph.gz',163        sor = f'assets/{config["create_assets"]["genome"]}/k100.bismap.sorted.bed.gz',164        wgt = f'assets/{config["create_assets"]["genome"]}/k100.bismap.10kb_avg.bed.gz',165        cpg = f'assets/{config["create_assets"]["genome"]}/cpg_bismap.bed.gz',166        cgi = f'assets/{config["create_assets"]["genome"]}/cgi_bismap.bed.gz',167        exn = f'assets/{config["create_assets"]["genome"]}/exon_bismap.bed.gz',168        gen = f'assets/{config["create_assets"]["genome"]}/genic_bismap.bed.gz',169        inr = f'assets/{config["create_assets"]["genome"]}/intergenic_bismap.bed.gz',170        msk = f'assets/{config["create_assets"]["genome"]}/rmsk_bismap.bed.gz',171        byn = f'assets/{config["create_assets"]["genome"]}/genome_window_10kb.bed.gz',172    params:173        gen = check_genome,174        dir = f'assets/{config["create_assets"]["genome"]}',175    log:176        f'{output_directory}/logs/bismap_assets.log',177    benchmark:178        f'{output_directory}/benchmarks/bismap_assets.txt',179    threads: 1180    resources:181        mem_gb = config['hpcParameters']['intermediateMemoryGb'],182        walltime = config['walltime']['medium']183    conda:184        '../envs/biscuit.yaml'185    envmodules:186        config['envmodules']['bedtools'],187    shell:188        """189        set +o pipefail;190        #cd {params.dir}191        wget -P {params.dir} --no-check-certificate -q https://bismap.hoffmanlab.org/raw/{params.gen}/k100.bismap.bedgraph.gz192        # Create average mappability scores in 10kb windows193        zcat {output.bis} | sort -k1,1 -k2,2n | gzip > {output.sor}194        bedtools makewindows -w 10000 -g {input.ref}.fai | gzip 1> {output.byn} 2> {log}195        bedtools map -a {output.byn} -b {output.sor} -c 4 -o mean | gzip 1> {output.wgt} 2> {log}196        bedtools intersect -a {output.bis} -b {input.cpg} | gzip -c 1> {output.cpg} 2> {log}197        bedtools intersect -a {output.bis} -b {input.cgi} | gzip -c 1> {output.cgi} 2> {log}198        bedtools intersect -a {output.bis} -b {input.exn} | gzip -c 1> {output.exn} 2> {log}199        bedtools intersect -a {output.bis} -b {input.gen} | gzip -c 1> {output.gen} 2> {log}200        bedtools intersect -a {output.bis} -b {input.inr} | gzip -c 1> {output.inr} 2> {log}201        bedtools intersect -a {output.bis} -b {input.msk} | gzip -c 1> {output.msk} 2> {log}...

generate_static_assets.py

Source:generate_static_assets.py

1from pathlib import Path2from types import ModuleType3import erdantic as erd4import erdantic.erd5import erdantic.examples.dataclasses6import erdantic.examples.pydantic7import erdantic.version8ASSETS_DIR = Path(__file__).resolve().parents[1] / "assets"9# monkeypatch __version__10erd.__version__ = erdantic.erd.__version__ = erdantic.version.__version__ = "TEST"11def create_assets(examples: ModuleType):12    stem = examples.__name__.rsplit(".", 1)[1]13    (ASSETS_DIR / stem).mkdir(exist_ok=True)14    diagram = erd.create(examples.Party)15    diagram.draw(out=ASSETS_DIR / stem / "diagram.png")16    diagram.draw(out=ASSETS_DIR / stem / "diagram.svg")17    with (ASSETS_DIR / stem / "diagram.dot").open("w") as fp:18        fp.write(diagram.to_dot())19if __name__ == "__main__":20    for module in [erdantic.examples.dataclasses, erdantic.examples.pydantic]:...

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