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How to use hierarchy_paths method in Lemoncheesecake

Best Python code snippet using lemoncheesecake

extract_pathway_product_annotations.py

Source:extract_pathway_product_annotations.py

1#!/usr/bin/env python2import os3import argparse4import sys5def get_options():6    parser = argparse.ArgumentParser(description="Script to pull pathway-names, pathway-common-names, rxn-common-name, "7                                                 "num-reactions, num-covered-reactions, orf-count, orf, taxonomy, and "8                                                 "RPKM values for all sequences from various MetaPathways outputs.")9    parser.add_argument("-i", "--hierarchy", required=True,10                        help="The hierarchy text file for mapping components to classes")11    parser.add_argument("-o", "--output", required=True,12                        help="The output file containing mapped values from the hierarchy")13    parser.add_argument("-l", "--comp_list", required=False, default=None,14                        help="An optional list of hierarchy components to return information on")15    parser.add_argument("--pathways", required=False, default=False, action="store_true",16                        help="Flag to indicate the output should be at pathway level [DEFAULT = reaction-level]")17    parser.add_argument("-p", "--pathway_annotations", required=True,18                        help="The output from extract_pathway_table_from_pgdb.pl")19    args = parser.parse_args()20    if not os.path.isfile(args.hierarchy):21        raise IOError("ERROR: " + args.hierarchy + " doesn't exist!")22    return args23def check_inputs(args):24    """25    Checks to make sure the paths and files exist and if the individual files are provided,26    then the metapathways directory is not provided27    :param args: command-line arguments parsed by argparse28    :return: nothing29    """30    # TODO: check input files31    return32def round_up_mp_inputs(args):33    args.sample_id = args.mp_inputs.rstrip(os.sep).split(os.sep)[-1]34    pwy_txt = args.mp_inputs + os.sep + "results" + os.sep + "pgdb" + os.sep + args.sample_id + ".pwy.txt"35    if not os.path.isfile(pwy_txt):36        raise IOError("Unable to find pathway annotations file (pwy.txt) in MetaPathway directory!\n"37                      "Looked for " + pwy_txt + " but file doesn't exist.")38    ptools_input = args.mp_inputs + os.sep + "ptools" + os.sep + "0.pf"39    if not os.path.isfile(ptools_input):40        raise IOError("Unable to find PGDB input file (0.pf) in MetaPathway directory!\n"41                      "Looked for " + ptools_input + " but file doesn't exist.")42    args.pathway_annotations = pwy_txt43    args.pgdb_input = ptools_input44    return args45def get_depth(fields):46    d = 047    while fields[d] == "":48        d += 149    return d50def read_hierarchy(hierarchy):51    prev_depth = -152    path = list()53    paths_dict = dict()54    for line in hierarchy:55        fields = line.rstrip().split('\t')56        curr_depth = get_depth(fields)57        if curr_depth > prev_depth:58            path.append(fields[curr_depth])59        if prev_depth >= curr_depth:60            if path[0] not in paths_dict.keys():61                paths_dict[path[0]] = list()62            paths_dict[path[0]].append(path[1:])63            path = path[0:curr_depth]64            path.append(fields[curr_depth])65            # path.append("--".join(fields[curr_depth:]))66        prev_depth = curr_depth67    paths_dict[path[0]].append(path[1:])68    return paths_dict69def write_long_hierarchy(hierarchy_paths, output):70    for super_class in hierarchy_paths:71        for reaction_path in hierarchy_paths[super_class]:72            output.write(super_class + "\t" + "\t".join(reaction_path) + "\n")73    return74def prune_reactions(hierarchy_paths):75    pathways_dict = dict()76    for super_class in hierarchy_paths:77        if super_class not in pathways_dict.keys():78            pathways_dict[super_class] = list()79        for reaction_path in hierarchy_paths[super_class]:80            pathway_path = reaction_path[0:-1]81            if pathway_path not in pathways_dict[super_class]:82                pathways_dict[super_class].append(pathway_path)83    return pathways_dict84def is_annotated(fields, metacyc=False):85    # orf, contig = fields[0:2]86    annotations = fields[2:]87    for entry in annotations:88        if entry != "" and entry != "\n":89            if metacyc and fields[-1] != "\n":90                return True91            else:92                return False93def get_process_paths(comp_list, hierarchy_paths):94    # Read the list, orf annotations and pathway annotations95    components = list()96    with open(comp_list) as components_list:97        for comp in components_list:98            # print comp99            if "\t" in comp:100                code, common = comp.strip().split("\t")101            else:102                code = comp.strip()103                common = ""104            components.append(code)105    # Map the processes in components to the hierarchy106    process_hierarchy_map = dict()107    for process in components:108        process_hierarchy_map[process] = list()109        for sub_class in hierarchy_paths.values():110            for path in sub_class:111                if process in path:112                    start = path.index(process)113                    process_hierarchy_map[process].append(path[start+1:])114    # Remove processes with no entry in the hierarchy115    no_hierarchy = list()116    for process in process_hierarchy_map:117        if len(process_hierarchy_map[process]) == 0:118            print "No entries found for", process, "in hierarchy"119            no_hierarchy.append(process)120    for process in no_hierarchy:121        process_hierarchy_map.pop(process)122    return process_hierarchy_map123def write_process_annotations(orf_annotations, output, num_processes):124    output.write("Process\tSample\tPathway\tPathway Common Name\tNumber of reactions"125                 "\tNumber covered\tReaction\tORF name\n")126    annotations_found = 0127    for process in orf_annotations.keys():128        if len(orf_annotations[process]) == 0:129            print "No entries found for", process, "in annotations"130        elif len(orf_annotations[process]) > 0:131            annotations_found += 1132            previous_annotation = ""133            process_annotations = sorted(orf_annotations[process])134            for annotation in process_annotations:135                if annotation != previous_annotation:136                    output.write(process + "\t" + "\t".join(annotation) + "\n")137                previous_annotation = annotation138    print annotations_found, "/", num_processes, "processes mapped to annotations"139    return140def search_dict(query_one, query_two, dictionary):141    """142    Matches a word with a key in the dictionary143    :param word: A pathway name144    :param dictionary: A collection of process names (which are anything in the metacyc hierarchy) and all145    processes associated with it from the hierarchy146    :return: a list packing the process and path associated with word or nothing147    """148    process_annotations = list()149    for process, path in dictionary.items():150        for pairs in path:151            if query_two in pairs:152                process_annotations.append([process, pairs[0]])153            if query_one in pairs:154                process_annotations.append([process, path[0]])155    if len(process_annotations) == 0:156        return False157    else:158        return process_annotations159def read_pwy_txt(pathway_annotations, process_hierarchy_map):160    orf_annotations = dict()161    with open(pathway_annotations) as pwy_txt:162        line = pwy_txt.readline()163        while line:164            fields = line.split("\t")165            if not fields[0] == "SAMPLE":166                # Match the pathway name with the process of interest, if possible167                process_annotations = search_dict(fields[1], fields[3], process_hierarchy_map)168                if process_annotations:169                    for path in process_annotations:170                        process = path[0]171                        if process not in orf_annotations.keys():172                            orf_annotations[process] = list()173                        orf = fields[-1].strip()174                        sample = fields[0]175                        n_reactions = fields[5]176                        n_covered = fields[6]177                        pwy_name = fields[1]178                        pwy_common = fields[2]179                        rxn_name = fields[3]180                        orf_annotations[process].append([sample, pwy_name, pwy_common,181                                                         n_reactions, n_covered, rxn_name, orf])182            line = pwy_txt.readline()183    # Add the missing processes to the orf_annotations with empty lists184    for process in process_hierarchy_map:185        if process not in orf_annotations.keys():186            orf_annotations[process] = list()187    return orf_annotations188def main():189    args = get_options()190    check_inputs(args)191    hierarchy = open(args.hierarchy, 'r')192    hierarchy_paths = read_hierarchy(hierarchy)193    hierarchy.close()194    if args.pathways:195        hierarchy_paths = prune_reactions(hierarchy_paths)196    try:197        output = open(args.output, 'w')198    except:199        raise IOError("ERROR: cannot make " + args.output + "!")200    if args.comp_list is None:201        write_long_hierarchy(hierarchy_paths, output)202    else:203        process_hierarchy_map = get_process_paths(args.comp_list, hierarchy_paths)204        orf_annotations = read_pwy_txt(args.pathway_annotations, process_hierarchy_map)205        write_process_annotations(orf_annotations, output, len(process_hierarchy_map.keys()))206    output.close()...

get_user_hierarchy_group.py

Source:get_user_hierarchy_group.py

...56    def hierarchy_group_id(self) -> str:57        return pulumi.get(self, "hierarchy_group_id")58    @property59    @pulumi.getter(name="hierarchyPaths")60    def hierarchy_paths(self) -> Sequence['outputs.GetUserHierarchyGroupHierarchyPathResult']:61        """62        A block that contains information about the levels in the hierarchy group. The `hierarchy_path` block is documented below.63        """64        return pulumi.get(self, "hierarchy_paths")65    @property66    @pulumi.getter67    def id(self) -> str:68        """69        The provider-assigned unique ID for this managed resource.70        """71        return pulumi.get(self, "id")72    @property73    @pulumi.getter(name="instanceId")74    def instance_id(self) -> str:...

script_create_excel_TT.py

Source:script_create_excel_TT.py

1import json2import xlsxwriter3BASE_URL = 'https://datasets.freesound.org'4workbook = xlsxwriter.Workbook('name.xlsx')5worksheet = workbook.add_worksheet('Hyperlinks')6url_format = workbook.add_format({7    'font_color': 'blue',8    'underline':  19})10id_url = json.load(open('id_url.json'))11ontology = json.load(open('ontology/ontology.json', 'rb'))12ontology_by_id = {o['id']:o for o in ontology}13hierarchy_paths = json.load(open('json/hierarchy_paths.json', 'rb'))14categories = ['/m/02jz0l',15 '/m/0l14qv',16 '/m/07rv9rh',17 '/m/0xzly',18 '/m/03qc9zr',19 '/m/0l14_3',20 '/m/0jb2l',21 '/m/0130jx',22 '/m/06rvn',23 '/m/0261r1',24 '/m/0dwsp',25 '/m/02dgv',26 '/t/dd00037',27 '/m/03dnzn',28 '/m/07st88b',29 '/m/081rb',30 '/m/0bm0k',31 '/m/03v3yw',32 '/m/0l15bq',33 '/m/04s8yn',34 '/m/0mkg',35 '/m/01yrx',36 '/m/01p970',37 '/m/07pn_8q',38 '/m/04zjc',39 '/m/02g901',40 '/m/02zsn',41 '/m/01jnbd',42 '/m/02_nn',43 '/t/dd00031',44 '/m/0242l',45 '/t/dd00129',46 '/m/07pggtn',47 '/m/0dwtp',48 '/m/07pjwq1',49 '/m/0ytgt',50 '/t/dd00005',51 '/m/04brg2',52 '/m/06_fw',53 '/m/0fx9l',54 '/m/05jcn',55 '/m/04_sv',56 '/m/02yds9',57 '/m/03k3r',58 '/m/04cvmfc',59 '/m/07qn4z3',60 '/m/03w41f',61 '/t/dd00033',62 '/m/028ght',63 '/m/07plz5l',64 '/m/012xff',65 '/m/03vt0',66 '/m/03wvsk',67 '/t/dd00013',68 '/m/025_jnm',69 '/m/0lyf6',70 '/m/05_wcq',71 '/m/07ppn3j',72 '/m/0fqfqc',73 '/m/015lz1',74 '/m/02hnl',75 '/m/07pbtc8',76 '/m/020bb7',77 '/m/0bm02',78 '/m/01j423',79 '/m/01gp74',80 '/m/0838f',81 '/m/01lsmm',82 '/m/09xqv',83 '/t/dd00003',84 '/m/0zmy2j9',85 '/m/07s0dtb',86 '/m/01g90h',87 '/m/0642b4',88 '/m/09x0r',89 '/t/dd00128',90 '/m/0ltv',91 '/t/dd00018',92 '/m/02rtxlg',93 '/t/dd00134',94 '/m/016622',95 '/t/dd00126',96 '/m/04szw',97 '/m/03qtq',98 '/m/02pjr4',99 '/t/dd00032',100 '/m/01b_21',101 '/m/09l8g',102 '/m/01j3sz',103 '/m/02_41',104 '/m/068zj',105 '/m/05r5c',106 '/m/09b5t',107 '/m/0463cq4',108 '/m/026t6',109 '/m/06h7j',110 '/m/0btp2',111 '/m/0239kh',112 '/m/0l14md',113 '/m/0dv5r',114 '/m/07rn7sz',115 '/m/07qn5dc',116 '/m/011k_j',117 '/m/01h8n0',118 '/m/0g6b5',119 '/m/07brj',120 '/m/023pjk',121 '/m/01dwxx',122 '/m/0ghcn6',123 '/m/0k65p',124 '/t/dd00135',125 '/m/07rpkh9',126 '/m/053hz1',127 '/m/01jwx6',128 '/m/07r_80w',129 '/m/03qtwd',130 '/m/0939n_',131 '/m/0dwt5',132 '/m/01d3sd',133 '/m/09d5_',134 '/m/07pp_mv',135 '/m/0dl9sf8',136 '/m/0brhx',137 '/m/0c2wf',138 '/m/05rj2',139 '/m/07rkbfh',140 '/m/01jg02',141 '/m/0l14jd',142 '/m/015p6',143 '/m/0d31p',144 '/m/0mbct',145 '/m/06bxc',146 '/m/018w8',147 '/t/dd00001',148 '/m/01jt3m',149 '/m/021wwz',150 '/m/0d8_n',151 '/m/0llzx',152 '/m/0316dw',153 '/t/dd00130',154 '/m/0l14gg',155 '/m/03cczk',156 '/m/07sr1lc',157 '/m/03q5_w',158 '/t/dd00002',159 '/m/01xq0k1',160 '/m/05zppz',161 '/m/03qjg',162 '/m/09ld4',163 '/m/01j4z9',164 '/m/07rjwbb',165 '/m/02k_mr',166 '/m/02bk07',167 '/t/dd00112',168 '/t/dd00127',169 '/m/07qrkrw',170 '/m/0jbk',171 '/m/042v_gx',172 '/t/dd00004',173 '/m/0dxrf',174 '/m/05mxj0q',175 '/m/01hsr_',176 '/m/01b9nn',177 '/m/07p6fty',178 '/m/05r5wn',179 '/m/01z5f',180 '/m/01m2v',181 '/m/02bm9n',182 '/m/0ngt1',183 '/m/05tny_',184 '/m/0j45pbj',185 '/m/07qf0zm',186 '/m/07s0s5r',187 '/m/0bt9lr',188 '/t/dd00071',189 '/m/01s0vc',190 '/m/0cfdd']191categories_with_paths = [(node_id, ' > '.join([ontology_by_id[n]['name'] for n in hierarchy_paths[node_id][0]])) for node_id in categories]192coordinates = ['A'+str(1+x) for x in range(len(categories))]193for idx, category in enumerate(categories_with_paths):194    worksheet.write_url(coordinates[idx], BASE_URL+id_url[category[0]].replace('contribute', 'annotate'), url_format, category[1])...

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