comparison data_manager/resource_building.py @ 43:3febf3d1139a draft

planemo upload commit 9b701c1faf8be4835b4e7236780ee9ee26f9a373-dirty

42:5a37a086c9a8

#######################################################################################################
# 2. Peptide Atlas
#######################################################################################################
def peptide_atlas_sources(data_manager_dict, tissue, target_directory):
    # Define organism_id (here Human) - to be upraded when other organism added to the project
    organism_id = "2"
    # Extract sample_category_id and output filename
    tissue=tissue.split(".")
    sample_category_id = tissue[0]
    tissue_name = tissue[1]
    output_file = tissue_name+"_"+time.strftime("%d-%m-%Y") + ".tsv"

    query="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id="+ \
    sample_category_id+"&display_options=ShowAbundances&organism_id="+organism_id+ \
    "&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf\
    &QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY"

        cr = csv.reader(decoded_content.splitlines(), delimiter='\t')

    uni_dict = build_dictionary(cr)

    #columns of data table peptide_atlas
    date = time.strftime("%d-%m-%Y")
    tissue_id = tissue_name+"_"+date
    name = tissue_id.replace("-","/").replace("_"," ")
    path = os.path.join(target_directory,output_file)

    with open(path,"w") as out :

    parser.add_argument("--hpa", metavar = ("HPA_OPTION"))
    parser.add_argument("--peptideatlas", metavar=("SAMPLE_CATEGORY_ID"))
    parser.add_argument("--id_mapping", metavar = ("ID_MAPPING_SPECIES"))
    parser.add_argument("--interactome", metavar = ("PPI"))
    parser.add_argument("--species")
    parser.add_argument("-o", "--output")
    args = parser.parse_args()

    data_manager_dict = {}
    # Extract json file params

            HPA_sources(data_manager_dict, hpa_tissue, target_directory)
    
    ## Download source file from Peptide Atlas query
    try:
        peptide_atlas = args.peptideatlas
    except NameError:
        peptide_atlas = None
    if peptide_atlas is not None:
        #target_directory = "/projet/galaxydev/galaxy/tools/proteore/ProteoRE/tools/resources_building/test-data/"
        peptide_atlas = peptide_atlas.split(",")
        for pa_tissue in peptide_atlas:
            peptide_atlas_sources(data_manager_dict, pa_tissue, target_directory)

    ## Download ID_mapping source file from Uniprot
    try:
        id_mapping=args.id_mapping
    except NameError:

43:3febf3d1139a

#######################################################################################################
# 2. Peptide Atlas
#######################################################################################################
def peptide_atlas_sources(data_manager_dict, tissue, date, target_directory):
    # Define organism_id (here Human) - to be upraded when other organism added to the project
    organism_id = "2"
    # Extract sample_category_id and output filename
    tissue=tissue.split(".")
    sample_category_id = tissue[0]
    tissue_name = tissue[1]
    output_file = tissue_name+"_"+date + ".tsv"

    query="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id="+ \
    sample_category_id+"&display_options=ShowAbundances&organism_id="+organism_id+ \
    "&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf\
    &QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY"

        cr = csv.reader(decoded_content.splitlines(), delimiter='\t')

    uni_dict = build_dictionary(cr)

    #columns of data table peptide_atlas
    tissue_id = tissue_name+"_"+date
    name = tissue_id.replace("-","/").replace("_"," ")
    path = os.path.join(target_directory,output_file)

    with open(path,"w") as out :

    parser.add_argument("--hpa", metavar = ("HPA_OPTION"))
    parser.add_argument("--peptideatlas", metavar=("SAMPLE_CATEGORY_ID"))
    parser.add_argument("--id_mapping", metavar = ("ID_MAPPING_SPECIES"))
    parser.add_argument("--interactome", metavar = ("PPI"))
    parser.add_argument("--species")
    parser.add_argument("--date")
    parser.add_argument("-o", "--output")
    args = parser.parse_args()

    data_manager_dict = {}
    # Extract json file params

            HPA_sources(data_manager_dict, hpa_tissue, target_directory)
    
    ## Download source file from Peptide Atlas query
    try:
        peptide_atlas = args.peptideatlas
        date = args.date
    except NameError:
        peptide_atlas = None
    if peptide_atlas is not None:
        #target_directory = "/projet/galaxydev/galaxy/tools/proteore/ProteoRE/tools/resources_building/test-data/"
        peptide_atlas = peptide_atlas.split(",")
        for pa_tissue in peptide_atlas:
            peptide_atlas_sources(data_manager_dict, pa_tissue, date, target_directory)

    ## Download ID_mapping source file from Uniprot
    try:
        id_mapping=args.id_mapping
    except NameError: