Snakefile-post-etl

rule Merge:
    input:
        code = config['MERGE_SCRIPT'],
        umls_nodes = config['UMLS_OUTPUT_NODES_FILE'],
        umls_edges = config['UMLS_OUTPUT_EDGES_FILE'],
        ont_nodes = config['ONT_OUTPUT_NODES_FILE'],
        ont_edges = config['ONT_OUTPUT_EDGES_FILE'],
        uniprot_nodes = config['UNIPROTKB_OUTPUT_NODES_FILE'],
        uniprot_edges = config['UNIPROTKB_OUTPUT_EDGES_FILE'],
        semmeddb_nodes = config['SEMMEDDB_OUTPUT_NODES_FILE'],
        semmeddb_edges = config['SEMMEDDB_OUTPUT_EDGES_FILE'],
        chembl_nodes = config['CHEMBL_OUTPUT_NODES_FILE'],
        chembl_edges = config['CHEMBL_OUTPUT_EDGES_FILE'],
        ensembl_nodes = config['ENSEMBL_OUTPUT_NODES_FILE'],
        ensembl_edges = config['ENSEMBL_OUTPUT_EDGES_FILE'],
        unichem_nodes = config['UNICHEM_OUTPUT_NODES_FILE'],
        unichem_edges = config['UNICHEM_OUTPUT_EDGES_FILE'],
        ncbigene_nodes = config['NCBIGENE_OUTPUT_NODES_FILE'],
        ncbigene_edges = config['NCBIGENE_OUTPUT_EDGES_FILE'],
        dgidb_nodes = config['DGIDB_OUTPUT_NODES_FILE'],
        dgidb_edges = config['DGIDB_OUTPUT_EDGES_FILE'],
        repodb_nodes = config['REPODB_OUTPUT_NODES_FILE'],
        repodb_edges = config['REPODB_OUTPUT_EDGES_FILE'],
        drugbank_nodes = config['DRUGBANK_OUTPUT_NODES_FILE'],
        drugbank_edges = config['DRUGBANK_OUTPUT_EDGES_FILE'],
        smpdb_nodes = config['SMPDB_OUTPUT_NODES_FILE'],
        smpdb_edges = config['SMPDB_OUTPUT_EDGES_FILE'],
        hmdb_nodes = config['HMDB_OUTPUT_NODES_FILE'],
        hmdb_edges = config['HMDB_OUTPUT_EDGES_FILE'],
        go_annotations_nodes = config['GO_ANNOTATIONS_OUTPUT_NODES_FILE'],
        go_annotations_edges = config['GO_ANNOTATIONS_OUTPUT_EDGES_FILE'],
        reactome_nodes = config['REACTOME_OUTPUT_NODES_FILE'],
        reactome_edges = config['REACTOME_OUTPUT_EDGES_FILE'],
        mirbase_nodes = config['MIRBASE_OUTPUT_NODES_FILE'],
        mirbase_edges = config['MIRBASE_OUTPUT_EDGES_FILE'],
        jensenlab_nodes = config['JENSENLAB_OUTPUT_NODES_FILE'],
        jensenlab_edges = config['JENSENLAB_OUTPUT_EDGES_FILE'],
        drugcentral_nodes = config['DRUGCENTRAL_OUTPUT_NODES_FILE'],
        drugcentral_edges = config['DRUGCENTRAL_OUTPUT_EDGES_FILE'],
        intact_nodes = config['INTACT_OUTPUT_NODES_FILE'],
        intact_edges = config['INTACT_OUTPUT_EDGES_FILE'],
        disgenet_nodes = config['DISGENET_OUTPUT_NODES_FILE'],
        disgenet_edges = config['DISGENET_OUTPUT_EDGES_FILE'],
        kegg_nodes = config['KEGG_OUTPUT_NODES_FILE'],
        kegg_edges = config['KEGG_OUTPUT_EDGES_FILE']
    output:
        nodes = config['MERGED_OUTPUT_NODES_FILE'],
        edges = config['MERGED_OUTPUT_EDGES_FILE'],
        orph = config['OUTPUT_FILE_ORPHAN_EDGES']
    log:
        config['MERGE_LOG']
    shell:
        config['PYTHON_COMMAND'] + " {input.code} " + config['TEST_ARG'] + \
            " --kgFileOrphanEdges {output.orph}" + \
            " --outputNodesFile {output.nodes} " + \
            " --outputEdgesFile {output.edges} " + \
            " --kgNodesFiles " + \
            "{input.umls_nodes} " + \
            "{input.ont_nodes} " + \
            "{input.semmeddb_nodes} " + \
            "{input.uniprot_nodes} " + \
            "{input.ensembl_nodes} " + \
            "{input.unichem_nodes} " + \
            "{input.chembl_nodes} " + \
            "{input.ncbigene_nodes} " + \
            "{input.dgidb_nodes} " + \
            "{input.repodb_nodes} " + \
            "{input.smpdb_nodes} " + \
            "{input.drugbank_nodes} " + \
            "{input.hmdb_nodes} " + \
            "{input.go_annotations_nodes} " + \
            "{input.reactome_nodes} " + \
            "{input.mirbase_nodes} " + \
            "{input.jensenlab_nodes} " + \
            "{input.drugcentral_nodes} " + \
            "{input.intact_nodes} " + \
            "{input.disgenet_nodes} " + \
            "{input.kegg_nodes} " + \
            " --kgEdgesFiles " + \
            "{input.umls_edges} " + \
            "{input.ont_edges} " + \
            "{input.semmeddb_edges} " + \
            "{input.uniprot_edges} " + \
            "{input.ensembl_edges} " + \
            "{input.unichem_edges} " + \
            "{input.chembl_edges} " + \
            "{input.ncbigene_edges} " + \
            "{input.dgidb_edges} " + \
            "{input.repodb_edges} " + \
            "{input.smpdb_edges} " + \
            "{input.drugbank_edges} " + \
            "{input.hmdb_edges} " + \
            "{input.go_annotations_edges} " + \
            "{input.reactome_edges} " + \
            "{input.mirbase_edges} " + \
            "{input.jensenlab_edges} " + \
            "{input.drugcentral_edges} " + \
            "{input.intact_edges} " + \
            "{input.disgenet_edges} " + \
            "{input.kegg_edges} > {log} 2>&1"

rule Stats:
    input:
        code = config['REPORT_SCRIPT'],
        nodes = config['MERGED_OUTPUT_NODES_FILE'],
        edges = config['MERGED_OUTPUT_EDGES_FILE']
    output:
        config['REPORT_FILE']
    log: 
        config['REPORT_LOG']
    shell:
        config['PYTHON_COMMAND'] + " {input.code} {input.nodes} {input.edges} {output}  > {log} 2>&1"

rule Simplify:
    input:
        code = config['SIMPLIFY_SCRIPT'],
        nodes = config['MERGED_OUTPUT_NODES_FILE'],
        edges = config['MERGED_OUTPUT_EDGES_FILE']
    output:
        nodes = config['SIMPLIFIED_OUTPUT_NODES_FILE'],
        edges = config['SIMPLIFIED_OUTPUT_EDGES_FILE']
    log:
        config['SIMPLIFY_LOG']
    shell:
        "bash -x {input.code} {input.nodes} {input.edges} {output.nodes} {output.edges} " + config['VERSION_FILE'] + " " + config['TEST_FLAG'] + " > {log} 2>&1" 

rule Slim:
    input:
        code = config['SLIM_SCRIPT'],
        nodes = config['SIMPLIFIED_OUTPUT_NODES_FILE'],
        edges = config['SIMPLIFIED_OUTPUT_EDGES_FILE']
    output:
        nodes = config['SLIM_OUTPUT_NODES_FILE'],
        edges = config['SLIM_OUTPUT_EDGES_FILE']
    log:
        config['SLIM_LOG']
    shell:
        config['PYTHON_COMMAND'] + " {input.code} " + config['TEST_ARG'] + " {input.nodes} {input.edges} {output.nodes} {output.edges} > {log} 2>&1"

rule Simplify_Stats:
    input:
        code = config['REPORT_SCRIPT'],
        nodes = config['SIMPLIFIED_OUTPUT_NODES_FILE'],
        edges = config['SIMPLIFIED_OUTPUT_EDGES_FILE']
    output:
        config['SIMPLIFIED_REPORT_FILE']
    log:
        config['SIMPLIFIED_REPORT_LOG']
    shell:
        config['PYTHON_COMMAND'] + " {input.code} --useSimplifiedPredicates {input.nodes} {input.edges} {output} > {log} 2>&1"

rule TSV:
    input:
        code = config['TSV_SCRIPT'],
        nodes = config['SIMPLIFIED_OUTPUT_NODES_FILE'],
        edges = config['SIMPLIFIED_OUTPUT_EDGES_FILE'],
        mapping_file = config['INFORES_MAPPING_FILE']
    output:
        placeholder = config['TSV_PLACEHOLDER']
    log:
        config['TSV_LOG']
    run:
        shell("rm -rf " + config['KG2_TSV_DIR'])
        shell("mkdir -p " + config['KG2_TSV_DIR'])
        shell(config['PYTHON_COMMAND'] + " {input.code} {input.nodes} {input.edges} {input.mapping_file} " + config['KG2_TSV_DIR'] + " > {log} 2>&1")
        shell("touch {output.placeholder}")