cellmaps-utils 0.5.0__tar.gz → 0.6.0__tar.gz

{cellmaps_utils-0.5.0 → cellmaps_utils-0.6.0}/HISTORY.rst

@@ -2,6 +2,19 @@
 History
 =======
 
+0.6.0 (2025-02-05)
+------------------
+
+* Add ``HierarchyDiff`` class with ``compare_hierarchies`` method to compare two hierarchies in CX2 format, and output
+  a hierarchy with robustness score of each system.
+
+* Add version bounds for required packages.
+
+* Add ``convert_hierarchical_network_to_hcx`` (utility function that aids convertion of a hierarchical network in CX2 to
+  HCX) and ``add_hcx_members_annotation`` (adds 'HCX::members' attribute to nodes) to ``hcx_utils``
+
+* Fixes in IF and APMS tools
+
 0.5.0 (2024-09-05)
 ------------------
 

{cellmaps_utils-0.5.0 → cellmaps_utils-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellmaps_utils
-Version: 0.5.0
+Version: 0.6.0
 Summary: Contains utilities needed by Cell Maps tools
 Home-page: https://github.com/idekerlab/cellmaps_utils
 Author: Cell Maps team
@@ -18,15 +18,15 @@ Classifier: Programming Language :: Python :: 3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS.rst
-Requires-Dist: fairscape-cli==0.2.0
+Requires-Dist: fairscape-cli==1.0.2
 Requires-Dist: ndex2<4.0.0,>=3.8.0
-Requires-Dist: scipy
-Requires-Dist: scikit-learn
-Requires-Dist: pandas
-Requires-Dist: numpy
-Requires-Dist: dill
-Requires-Dist: tqdm
-Requires-Dist: requests
+Requires-Dist: scipy<1.11,>=1.10.1
+Requires-Dist: scikit-learn<1.4.0,>=0.19.0
+Requires-Dist: pandas<3.0.0,>=2.0.0
+Requires-Dist: numpy<2.0.0,>=1.24.4
+Requires-Dist: dill<0.4.0,>=0.3.8
+Requires-Dist: tqdm<5.0.0,>=4.66.6
+Requires-Dist: requests<3.0.0,>=2.31.0
 
 =============================
 Cell Maps Pipeline Utilities
@@ -145,6 +145,19 @@ This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypack
 History
 =======
 
+0.6.0 (2025-02-05)
+------------------
+
+* Add ``HierarchyDiff`` class with ``compare_hierarchies`` method to compare two hierarchies in CX2 format, and output
+  a hierarchy with robustness score of each system.
+
+* Add version bounds for required packages.
+
+* Add ``convert_hierarchical_network_to_hcx`` (utility function that aids convertion of a hierarchical network in CX2 to
+  HCX) and ``add_hcx_members_annotation`` (adds 'HCX::members' attribute to nodes) to ``hcx_utils``
+
+* Fixes in IF and APMS tools
+
 0.5.0 (2024-09-05)
 ------------------
 

{cellmaps_utils-0.5.0 → cellmaps_utils-0.6.0}/cellmaps_utils/__init__.py

@@ -4,6 +4,6 @@
 
 __author__ = 'Cell Maps team'
 __email__ = 'tools@cm4ai.org'
-__version__ = '0.5.0'
+__version__ = '0.6.0'
 __repo_url__ = 'https://github.com/idekerlab/cellmaps_utils'
 __description__ = 'Contains utilities needed by Cell Maps tools'

{cellmaps_utils-0.5.0 → cellmaps_utils-0.6.0}/cellmaps_utils/apmstool.py

@@ -22,6 +22,8 @@ class APMSDataLoader(BaseCommandLineTool):
     """
     COMMAND = 'apmsconverter'
 
+    BAIT_COL_NAME = 'Bait'
+
     def __init__(self, theargs,
                  provenance_utils=ProvenanceUtil()):
         """
@@ -43,6 +45,8 @@ class APMSDataLoader(BaseCommandLineTool):
         self._tissue = theargs.tissue
         self._author = theargs.author
         self._gene_set = theargs.gene_set
+        self._baitcolname = theargs.baitcolname
+        self._set_name = theargs.set_name
         self._provenance_utils = provenance_utils
         self._softwareid = None
         self._input_data_dict = theargs.__dict__
@@ -139,9 +143,11 @@ class APMSDataLoader(BaseCommandLineTool):
         if self._gene_set is not None:
             dir_name += self._gene_set.lower() + '_'
         dir_name += self._cell_line.lower() + '_'
-        dir_name += self._treatment.lower() + '_apms_'
+        dir_name += self._treatment.lower()
+        if self._set_name is not None:
+            dir_name += '_' + self._set_name
+        dir_name += '_apms_'
         dir_name += self._release.lower()
-
         dir_name = dir_name.replace(' ', '_')
         self._outdir = os.path.join(self._outdir, dir_name)
 
@@ -154,7 +160,13 @@ class APMSDataLoader(BaseCommandLineTool):
         """
         df_list = []
         for input in self._inputs:
-            cur_df = pd.read_csv(input, sep='\t')
+            thesep = '\t'
+            if input.endswith('.csv'):
+                thesep = ','
+            cur_df = pd.read_csv(input, sep=thesep, na_filter=False)
+            if self._baitcolname != 'Bait':
+                if self._baitcolname in cur_df.columns:
+                    cur_df.rename({self._baitcolname: 'Bait'}, axis=1, inplace=True)
             # Handles case where HDAC2 in initial cm4ai dataset
             # had several columns lacking .x suffix
             # we are fixing this by checking for those columns and if
@@ -173,6 +185,7 @@ class APMSDataLoader(BaseCommandLineTool):
         df = pd.concat(df_list)
 
         apms_path = os.path.join(self._outdir, constants.APMS_TSV_FILE)
+
         df.to_csv(apms_path, sep='\t', index=False)
         return apms_path
 
@@ -263,11 +276,17 @@ class APMSDataLoader(BaseCommandLineTool):
         parser.add_argument('--gene_set', choices=['chromatin', 'metabolic'],
                             default='chromatin',
                             help='Gene set for dataset')
+        parser.add_argument('--set_name',
+                            help='If set, adds value to RO-Crate folder name before _apms_<version>. '
+                                 'Example values set1')
         parser.add_argument('--tissue', choices=['undifferentiated', 'neuron',
                                                  'cardiomyocytes', ''],
                             default='breast; mammary gland',
                             help='Tissue for dataset. Since the default --cell_line '
                                  'is MDA-MB-468, this value is set to the tissue '
                                  'for that cell line')
+        parser.add_argument('--baitcolname', default='Bait',
+                            help='Name of bait column in input file(s)')
+
         return parser
 

{cellmaps_utils-0.5.0 → cellmaps_utils-0.6.0}/cellmaps_utils/crisprtool.py

@@ -246,7 +246,7 @@ class CRISPRDataLoader(BaseCommandLineTool):
         if self._gene_set is not None:
             dir_name += self._gene_set.lower() + '_'
         dir_name += self._cell_line.lower() + '_'
-        dir_name += re.sub('[^a-zA-Z0-9\w\n\.]', '_', self._tissue.lower()) + '_'
+        dir_name += re.sub(r'[^a-zA-Z0-9\w\n\.]', '_', self._tissue.lower()) + '_'
         dir_name += self._treatment.lower() + '_crispr_'
         if self._dataset.lower() != '':
             dir_name += self._dataset.lower() + '_'
@@ -308,8 +308,8 @@ class CRISPRDataLoader(BaseCommandLineTool):
 
         Version {version}
 
-        {cmd} Loads CRISPR data into a RO-Crate by creating a 
-        directory, copying over relevant and using FAIRSCAPE CLI to 
+        {cmd} Loads CRISPR data into a RO-Crate by creating a
+        directory, copying over relevant and using FAIRSCAPE CLI to
         register the data files in the directory known as an RO-Crate
 
         """.format(version=cellmaps_utils.__version__,

cellmaps_utils-0.6.0/cellmaps_utils/hcx_utils.py

@@ -0,0 +1,198 @@
+import json
+import os
+
+import ndex2
+from ndex2.cx2 import CX2Network, RawCX2NetworkFactory
+
+from cellmaps_utils.exceptions import CellMapsError
+
+
+def get_host_and_uuid_from_network_url(network_url):
+    """
+    Extracts the host and UUID from a given NDEx network URL.
+
+    :param network_url: The URL of the NDEx network.
+    :type network_url: str
+    :return: A tuple containing the host and the UUID of the network.
+    :rtype: tuple
+    """
+    if network_url is None:
+        return None, None
+    parts = network_url.replace('https://', '').replace('http:/', '').split('/')
+    host, uuid = parts[0], parts[-1]
+    return host, uuid
+
+
+def get_interactome(host, uuid, username, password, parent_edgelist):
+    """
+    Retrieves the interactome either from NDEx or from a local edge list.
+
+    :param host: The NDEx server host.
+    :type host: str
+    :param uuid: The UUID of the interactome network in NDEx.
+    :type uuid: str
+    :param username: The NDEx username for authentication.
+    :type username: str
+    :param password: The NDEx password for authentication.
+    :type password: str
+    :param parent_edgelist: Path to a file containing the interactome edge list.
+    :type parent_edgelist: str
+    :return: A CX2Network object representing the interactome.
+    :rtype: CX2Network
+    """
+    interactome = CX2Network()
+    if parent_edgelist is not None:
+        with open(parent_edgelist, 'r') as f:
+            for line in f:
+                parts = line.split()
+                id_source_node = interactome.lookup_node_id_by_name(parts[0])
+                source_node = id_source_node if id_source_node is not None else interactome.add_node(
+                    attributes={'name': parts[0]})
+                id_target_node = interactome.lookup_node_id_by_name(parts[1])
+                target_node = id_target_node if id_target_node is not None else interactome.add_node(
+                    attributes={'name': parts[1]})
+                interactome.add_edge(source=source_node, target=target_node)
+    elif host is not None and uuid is not None:
+        client = ndex2.client.Ndex2(host=host, username=username, password=password)
+        factory = RawCX2NetworkFactory()
+        client_resp = client.get_network_as_cx2_stream(uuid)
+        interactome = factory.get_cx2network(json.loads(client_resp.content))
+    return interactome
+
+
+def get_root_nodes(hierarchy):
+    """
+    Identifies the root nodes in a hierarchical network.
+
+    In CDAPS the root node has only source edges to children
+    so this function counts up number of target edges for each node
+    and the one with 0 is the root
+
+    :return: root node ids
+    :rtype: set
+    """
+    all_nodes = set()
+    for node_id, node_obj in hierarchy.get_nodes().items():
+        all_nodes.add(node_id)
+
+    nodes_with_targets = set()
+    for edge_id, edge_obj in hierarchy.get_edges().items():
+        nodes_with_targets.add(edge_obj['t'])
+    return all_nodes.difference(nodes_with_targets)
+
+
+def add_isroot_node_attribute(hierarchy, root_nodes):
+    """
+    Using the **root_nodes** set or list, add
+    ``HCX::isRoot`` to
+    every node setting value to ``True``
+    if node id is in **root_nodes**
+    otherwise set the value to ``False``
+    """
+    attr_name = 'HCX::isRoot'
+    for node_id, node_obj in hierarchy.get_nodes().items():
+        if node_id in root_nodes:
+            hierarchy.add_node_attribute(node_id, attr_name, True)
+        else:
+            hierarchy.add_node_attribute(node_id, attr_name, False)
+
+
+def add_hcx_network_annotations(hierarchy, interactome=None, output_dir='.',
+                                interactome_name='hierarchy_parent.cx2', host='www.ndexbio.org', uuid=None):
+    """
+    Adds HCX network annotations to the hierarchy.
+
+    :param hierarchy: The hierarchical network in CX2 format.
+    :type hierarchy: CX2Network
+    :param interactome: The interactome network.
+    :type interactome: CX2Network, optional
+    :param output_dir: Directory where the interactome file will be saved.
+    :type output_dir: str, optional
+    :param interactome_name: Name of the interactome file.
+    :type interactome_name: str, optional
+    :param host: NDEx host for interactome retrieval.
+    :type host: str, optional
+    :param uuid: UUID of the interactome in NDEx.
+    :type uuid: str, optional
+    :return: The updated hierarchy network with annotations.
+    :rtype: CX2Network
+    """
+    if not isinstance(hierarchy, CX2Network):
+        raise CellMapsError("Hierarchy must be an instance of CX2Network.")
+    if uuid is None and interactome is None:
+        raise CellMapsError("UUID of interactome or interactome (instance of CX2Network) must be specified!")
+
+    hierarchy.add_network_attribute('ndexSchema', 'hierarchy_v0.1',
+                                    datatype='string')
+    hierarchy.add_network_attribute('HCX::modelFileCount', '2',
+                                    datatype='integer')
+
+    if host and uuid:
+        hierarchy.add_network_attribute('HCX::interactionNetworkHost', host)
+        hierarchy.add_network_attribute('HCX::interactionNetworkUUID', uuid)
+    else:
+        interactome_path = os.path.join(output_dir, interactome_name)
+        interactome.write_as_raw_cx2(interactome_path)
+        hierarchy.add_network_attribute('HCX::interactionNetworkName', interactome_name,
+                                        datatype='string')
+    return hierarchy
+
+
+def add_hcx_members_annotation(hierarchy, interactome, gene_column='CD_MemberList'):
+    """
+    Adds the 'HCX::members' attribute to nodes in the hierarchy based on the interactome.
+
+    :param hierarchy: The hierarchical network in CX2 format.
+    :type hierarchy: CX2Network
+    :param interactome: The interactome network.
+    :type interactome: CX2Network
+    :param gene_column: Column name containing gene members.
+    :type gene_column: str, optional
+    """
+    for node_id, node_obj in hierarchy.get_nodes().items():
+        memberlist = hierarchy.get_node(node_id).get('v', {}).get(gene_column, '').split(' ')
+        membersids = []
+        for member in memberlist:
+            id_interactome = interactome.lookup_node_id_by_name(member)
+            if id_interactome is not None:
+                membersids.append(id_interactome)
+        hierarchy.add_node_attribute(node_id, 'HCX::members', membersids, datatype='list_of_integer')
+
+
+def convert_hierarchical_network_to_hcx(hierarchy, interactome_url, ndex_username=None, ndex_password=None,
+                                        gene_column='CD_MemberList'):
+    """
+    Converts a hierarchical network into HCX format by adding necessary annotations and interactome details.
+
+    :param hierarchy: The hierarchical network in CX2 format or a path to the CX2 file.
+    :type hierarchy: CX2Network or str
+    :param interactome_url: URL of the interactome network in NDEx.
+    :type interactome_url: str
+    :param ndex_username: NDEx username for authentication.
+    :type ndex_username: str, optional
+    :param ndex_password: NDEx password for authentication.
+    :type ndex_password: str, optional
+    :param gene_column: Column name containing gene members.
+    :type gene_column: str, optional
+    :return: The updated hierarchy network in CX2 format with HCX annotations.
+    :rtype: CX2Network
+    """
+    factory = RawCX2NetworkFactory()
+    if isinstance(hierarchy, str):
+        hierarchy = factory.get_cx2network(hierarchy)
+
+    # Get the host and uuid of the interactome
+    host, uuid = get_host_and_uuid_from_network_url(interactome_url)
+    hierarchy = add_hcx_network_annotations(hierarchy, host=host, uuid=uuid)
+
+    # Create CX2Network object from interactome from NDEx
+    client = ndex2.client.Ndex2(host=host, username=ndex_username, password=ndex_password)
+    client_resp = client.get_network_as_cx2_stream(uuid)
+    interactome = factory.get_cx2network(json.loads(client_resp.content))
+
+    # Add HCX::members attribute to node attributes
+    add_hcx_members_annotation(hierarchy, interactome, gene_column)
+
+    # Add isRoot attribute to node attributes
+    add_isroot_node_attribute(hierarchy, get_root_nodes(hierarchy))
+    return hierarchy

cellmaps_utils-0.6.0/cellmaps_utils/hierdiff.py

@@ -0,0 +1,81 @@
+import logging
+from ndex2.cx2 import RawCX2NetworkFactory, CX2Network
+
+logger = logging.getLogger(__name__)
+
+
+class HierarchyDiff:
+    """
+    A class to compare two hierarchies in CX2 (HCX)
+    """
+
+    def __init__(self):
+        """
+        Constructor
+        """
+        pass
+
+    def compare_hierarchies_from_files(self, hierarchy_a_path=None, hierarchy_b_path=None):
+        """
+        Compare two hierarchies from file paths.
+
+        :param hierarchy_a_path: Path to hierarchy to compare
+        :type hierarchy_a_path: str
+        :param hierarchy_b_path: Path to hierarchy to compare
+        :type hierarchy_b_path: str
+        """
+        factory = RawCX2NetworkFactory()
+        hierarchy_a = factory.get_cx2network(hierarchy_a_path)
+        hierarchy_b = factory.get_cx2network(hierarchy_b_path)
+        return self.compare_hierarchies(hierarchy_a, hierarchy_b)
+
+    @staticmethod
+    def compare_hierarchies(hierarchy_a=None, hierarchy_b=None):
+        """
+        Compare two hierarchies in CX2 format. It looks at each system and outputs a robustness score
+        which correlates to how stable the system is in the hierarchies generated. It outputs a hierarchy with
+        the robustness score added to the systems.
+
+        :param hierarchy_a: Hierarchy to compare
+        :type hierarchy_a: ndex2.cx2.CX2Network
+        :param hierarchy_b: Hierarchy to compare
+        :type hierarchy_b: ndex2.cx2.CX2Network
+        """
+        nodes_a = hierarchy_a.get_nodes()
+        nodes_b = hierarchy_b.get_nodes()
+
+        # Compute overlap scores for nodes based on CD_MemberList
+        all_node_ids = set(nodes_a.keys()).union(nodes_b.keys())
+        node_overlap_scores = {}
+
+        for node_id in all_node_ids:
+            members_a = set(nodes_a.get(node_id, {}).get('v', {}).get('CD_MemberList', '').split())
+            members_b = set(nodes_b.get(node_id, {}).get('v', {}).get('CD_MemberList', '').split())
+
+            if members_a and members_b:
+                # Calculate overlap score based on intersection and union
+                overlap = len(members_a.intersection(members_b))
+                union = len(members_a.union(members_b))
+                score = overlap / union if union > 0 else 0
+            else:
+                score = 0
+
+            node_overlap_scores[node_id] = score
+
+        # Create a new hierarchy to store results
+        result_hierarchy = CX2Network()
+
+        # Add nodes from hierarchy_a with robustness scores
+        for node_id, data in nodes_a.items():
+            score = node_overlap_scores.get(node_id, 0)
+            data['v']['robustness_score'] = score
+            result_hierarchy.add_node(node_id=node_id, attributes=data['v'])
+
+        # Add nodes from hierarchy_b if they don't already exist in the result hierarchy
+        for node_id, data in nodes_b.items():
+            if node_id not in nodes_a:
+                score = node_overlap_scores.get(node_id, 0)
+                data['v']['robustness_score'] = score
+                result_hierarchy.add_node(node_id=node_id, attributes=data['v'])
+
+        return result_hierarchy

{cellmaps_utils-0.5.0 → cellmaps_utils-0.6.0}/cellmaps_utils/ifimage_readme.txt

@@ -1,8 +1,8 @@
 This data set has been generated in the Emma Lundberg lab (https://ell-core.stanford.edu/)
-in July-August 2023 as part of the CM4AI Research Program (https://cm4ai.org/).
+as part of the CM4AI Research Program (https://cm4ai.org/).
 
-This data set displays the spatial localization of 95 proteins in the breast cancer
-cell line MDA-MB-468. MDA-MB-468 cells were seeded into 96-well glass bottom plates
+This data set displays the spatial localization of proteins in the cell line MDA-MB-468.
+MDA-MB-468 cells were seeded into 96-well glass bottom plates
 and treated either with the chemotherapeutic drug Paclitaxel or with the chemotherapeutic
 drug Vorinostat (SAHA) or not treated. For drug treatment, higher cell numbers were
 seeded than for the cells that were not treated to reach a sufficient amount of
@@ -14,7 +14,7 @@ DAPI (to label nuclei, "blue" channel),
 a Calreticulin antibody (to label the endoplasmic reticulum, "yellow" channel),
 a Tubulin antibody (to label Microtubuli, "red" channel), and an antibody against a
 protein of interest (a different antibody / protein for each well, "green" channel).
-In the green channel, for each well, one of 95 proteins was stained with an antibody
+In the green channel, for each well, each one of the proteins was stained with an antibody
 from the proteinatlas.org project.
 
 The .tsv file describes each image in the data set. Each row represents one image.

{cellmaps_utils-0.5.0 → cellmaps_utils-0.6.0}/cellmaps_utils/iftool.py

@@ -138,13 +138,13 @@ class FakeImageDownloader(ImageDownloader):
                 raise CellMapsError('Unable to download ' +
                                     str(entry))
             fname = os.path.basename(entry[1])
-            color = re.sub('\..*$', '', re.sub('^.*_', '', fname))
+            color = re.sub(r'\..*$', '', re.sub('^.*_', '', fname))
             src_image_dict[color] = entry[1]
 
         for entry in download_list[5:]:
             t.update()
             fname = os.path.basename(entry[1])
-            color = re.sub('\..*$', '', re.sub('^.*_', '', fname))
+            color = re.sub(r'\..*$', '', re.sub('^.*_', '', fname))
             shutil.copy(src_image_dict[color], entry[1])
         return []
 
@@ -316,14 +316,20 @@ class IFImageDataConverter(BaseCommandLineTool):
                     os.path.join(self._outdir, 'readme.txt'))
 
         # download the images
-        self._download_data(filtered_df['Baselink'].values.tolist())
+        if 'Baselink' in filtered_df:
+            baselink_name = 'Baselink'
+        else:
+            baselink_name = 'base_web_link'
+
+        self._download_data(filtered_df[baselink_name].values.tolist())
 
         # remove Baselink column
-        filtered_df.drop('Baselink', axis=1, inplace=True)
+        filtered_df.drop(baselink_name, axis=1, inplace=True)
 
         # remove Slice column if set
         if self._slice is not None:
-            filtered_df.drop('Slice', axis=1, inplace=True)
+            if 'Slice' in filtered_df:
+                filtered_df.drop('Slice', axis=1, inplace=True)
 
         file_path = os.path.join(self._outdir, constants.ANTIBODY_GENE_TABLE_FILE)
 
@@ -346,7 +352,8 @@ class IFImageDataConverter(BaseCommandLineTool):
         gen_dsets.extend(self._register_downloaded_images(description=description,
                                                           keywords=keywords))
         self._register_software(keywords=keywords, description=description)
-        self._register_computation(generated_dataset_ids=gen_dsets,
+        logger.info('Registering only 1st 1000 datasets into computation due to limitations of fairscape-cli')
+        self._register_computation(generated_dataset_ids=gen_dsets[:1000],
                                    description=description,
                                    keywords=keywords)
         return 0
@@ -491,15 +498,26 @@ class IFImageDataConverter(BaseCommandLineTool):
 
         # keep only slice specified
         if self._slice is not None:
-            logger.info('Keeping only slice: ' + str(self._slice))
-            df = df[df['Slice'] == self._slice]
-            logger.debug(str(len(df)) + ' rows remain after slice filter')
+            if 'Slice' in df:
+                logger.info('Keeping only slice: ' + str(self._slice))
+                df = df[df['Slice'] == self._slice]
+                logger.debug(str(len(df)) + ' rows remain after slice filter')
+            else:
+                # attempt to find slice from base_web_link
+                if 'base_web_link' in df:
+                    logger.info('Keeping only slice: ' + str(self._slice) + ' by parsing base_web_link')
+                    df = df[df['base_web_link'].str.contains('_' + self._slice + '_', case=False)]
+                    logger.debug(str(len(df)) + ' rows remain after slice filter')
 
         # keep only treatment specified
         logger.info('Keeping only treatment: ' + str(self._treatment))
         df = df[df['Treatment'].str.contains(self._treatment, case=False)]
         logger.debug(str(len(df)) + ' rows remain after treatment filter')
 
+        # remove negative-ctrl rows
+        logger.debug('Removing NEGATIVE rows')
+        df = df[df["Antibody ID"].str.contains('NEGATIVE') == False]
+
         return df
 
     def _register_downloaded_images(self,
@@ -601,11 +619,10 @@ class IFImageDataConverter(BaseCommandLineTool):
                                        description=desc,
                                        formatter_class=constants.ArgParseFormatter)
         parser.add_argument('outdir',
-                            help='Directory where RO-Crate will be created '
-                                 'store results in')
+                            help='Directory where RO-Crate will be created')
         parser.add_argument('--input', required=True,
                             help='Table file with the following '
-                                 'fields: [Antibody ID, ENSEMBL ID, Treatment, Well, Region, Slice, Baselink] ')
+                                 'fields: [Antibody ID, ENSEMBL ID|ENSG, Treatment, Well, Region, Slice, Baselink|base_web_link] ')
         parser.add_argument('--author', default='Lundberg Lab',
                             help='Author that created this data')
         parser.add_argument('--name', default='IF images',
@@ -624,15 +641,17 @@ class IFImageDataConverter(BaseCommandLineTool):
         parser.add_argument('--cell_line', default='MDA-MB-468',
                             help='Name of cell line. For example MDA-MB-468')
         parser.add_argument('--gene_set', choices=['chromatin', 'metabolic'],
-                            default='chromatin',
-                            help='Gene set for dataset')
+                            help='Gene set for dataset, standard names are '
+                                 + 'chromatin, metabolic, or leave it unset')
         parser.add_argument('--tissue', choices=['undifferentiated', 'neuron',
                                                  'cardiomyocytes', ''],
                             default='breast; mammary gland',
                             help='Tissue for dataset. Since the default --cell_line '
                                  'is MDA-MB-468, this value is set to the tissue '
                                  'for that cell line')
-        parser.add_argument('--slice', default='z01',
-                            help='Slice to keep')
+        parser.add_argument('--slice',
+                            help='Slice to keep. Example names are z01, z02. If unset '
+                                 + 'all slices are kept')
+
         return parser
 

{cellmaps_utils-0.5.0 → cellmaps_utils-0.6.0}/cellmaps_utils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellmaps_utils
-Version: 0.5.0
+Version: 0.6.0
 Summary: Contains utilities needed by Cell Maps tools
 Home-page: https://github.com/idekerlab/cellmaps_utils
 Author: Cell Maps team
@@ -18,15 +18,15 @@ Classifier: Programming Language :: Python :: 3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS.rst
-Requires-Dist: fairscape-cli==0.2.0
+Requires-Dist: fairscape-cli==1.0.2
 Requires-Dist: ndex2<4.0.0,>=3.8.0
-Requires-Dist: scipy
-Requires-Dist: scikit-learn
-Requires-Dist: pandas
-Requires-Dist: numpy
-Requires-Dist: dill
-Requires-Dist: tqdm
-Requires-Dist: requests
+Requires-Dist: scipy<1.11,>=1.10.1
+Requires-Dist: scikit-learn<1.4.0,>=0.19.0
+Requires-Dist: pandas<3.0.0,>=2.0.0
+Requires-Dist: numpy<2.0.0,>=1.24.4
+Requires-Dist: dill<0.4.0,>=0.3.8
+Requires-Dist: tqdm<5.0.0,>=4.66.6
+Requires-Dist: requests<3.0.0,>=2.31.0
 
 =============================
 Cell Maps Pipeline Utilities
@@ -145,6 +145,19 @@ This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypack
 History
 =======
 
+0.6.0 (2025-02-05)
+------------------
+
+* Add ``HierarchyDiff`` class with ``compare_hierarchies`` method to compare two hierarchies in CX2 format, and output
+  a hierarchy with robustness score of each system.
+
+* Add version bounds for required packages.
+
+* Add ``convert_hierarchical_network_to_hcx`` (utility function that aids convertion of a hierarchical network in CX2 to
+  HCX) and ``add_hcx_members_annotation`` (adds 'HCX::members' attribute to nodes) to ``hcx_utils``
+
+* Fixes in IF and APMS tools
+
 0.5.0 (2024-09-05)
 ------------------
 

{cellmaps_utils-0.5.0 → cellmaps_utils-0.6.0}/cellmaps_utils.egg-info/SOURCES.txt

@@ -18,6 +18,7 @@ cellmaps_utils/ddotconverter.py
 cellmaps_utils/exceptions.py
 cellmaps_utils/hcx_utils.py
 cellmaps_utils/hidefconverter.py
+cellmaps_utils/hierdiff.py
 cellmaps_utils/ifimage_readme.txt
 cellmaps_utils/iftool.py
 cellmaps_utils/logutils.py

cellmaps_utils-0.6.0/cellmaps_utils.egg-info/requires.txt

@@ -0,0 +1,9 @@
+fairscape-cli==1.0.2
+ndex2<4.0.0,>=3.8.0
+scipy<1.11,>=1.10.1
+scikit-learn<1.4.0,>=0.19.0
+pandas<3.0.0,>=2.0.0
+numpy<2.0.0,>=1.24.4
+dill<0.4.0,>=0.3.8
+tqdm<5.0.0,>=4.66.6
+requests<3.0.0,>=2.31.0