import argparse
LOG_FORMAT = "%(asctime)-15s %(levelname)s %(relativeCreated)dms " \
"%(filename)s::%(funcName)s():%(lineno)d %(message)s"
"""
Sets format of logging messages
"""
RO_CRATE_METADATA_FILE = 'ro-crate-metadata.json'
"""
`rocrate <https://www.researchobject.org/ro-crate>`__ metadata JSON file name
"""
PROVENANCE_ERRORS_FILE = 'provenance_errors.json'
"""
Contains log of any failed fairscape-cli calls
"""
TASK_FILE_PREFIX = 'task_'
"""
Prefix for task file
"""
TASK_START_FILE_SUFFIX = '_start.json'
"""
Suffix for task start file
"""
TASK_FINISH_FILE_SUFFIX = '_finish.json'
"""
Suffix for task finish file
"""
OUTPUT_LOG_FILE = 'output.log'
"""
Output log file name
"""
ERROR_LOG_FILE = 'error.log'
"""
Error log file name
"""
IMAGE_EMBEDDING_FILE = 'image_emd.tsv'
"""
Name of image embedding file
"""
IMAGE_LABELS_PROBABILITY_FILE = 'labels_prob.tsv'
"""
Name of image labels probability file
"""
PPI_EMBEDDING_FILE = 'ppi_emd.tsv'
"""
Name of Protein to Protein embedding file
"""
CO_EMBEDDING_FILE = 'coembedding_emd.tsv'
"""
Name of file containing coembedding
"""
IMAGE_GENE_NODE_ATTR_FILE = 'image_gene_node_attributes.tsv'
"""
Image gene node attributes filename
"""
IMAGE_GENE_NODE_ERRORS_FILE = 'image_gene_node_attributes.errors'
"""
Image gene node attributes errors filename
"""
PERTURBATION_FILE = 'perturbation.h5ad'
"""
Perturbation/CRISPRi h5ad file
"""
ANTIBODY_GENE_TABLE_FILE = 'antibody_gene_table.tsv'
"""
Antibody Gene Table file
"""
IMAGE_GENE_NODE_NAME_COL = 'name'
"""
Gene Symbol name column
"""
IMAGE_GENE_NODE_REPRESENTS_COL = 'represents'
"""
Ensembl ids column
"""
IMAGE_GENE_NODE_AMBIGUOUS_COL = 'ambiguous'
"""
Ambiguous column
"""
IMAGE_GENE_NODE_ANTIBODY_COL = 'antibody'
"""
Antibody name column
"""
IMAGE_GENE_NODE_FILENAME_COL = 'filename'
"""
File name column
"""
IMAGE_GENE_NODE_IMAGEURL_COL = 'imageurl'
"""
Image URL column
"""
IMAGE_GENE_NODE_COLS = [IMAGE_GENE_NODE_NAME_COL,
IMAGE_GENE_NODE_REPRESENTS_COL,
IMAGE_GENE_NODE_AMBIGUOUS_COL,
IMAGE_GENE_NODE_ANTIBODY_COL,
IMAGE_GENE_NODE_FILENAME_COL,
IMAGE_GENE_NODE_IMAGEURL_COL]
"""
Columns in :py:const:`IMAGE_GENE_NODE_ATTR_FILE` file
"""
APMS_TSV_FILE = 'apms.tsv'
"""
AP-MS tsv file
"""
PPI_EDGELIST_FILE = 'ppi_edgelist.tsv'
"""
Protein to Protein interaction edgelist file name
"""
PPI_EDGELIST_GENEA_COL = 'geneA'
"""
First column name
"""
PPI_EDGELIST_GENEB_COL = 'geneB'
"""
Second column name
"""
PPI_EDGELIST_COLS = [PPI_EDGELIST_GENEA_COL,
PPI_EDGELIST_GENEB_COL]
"""
Columns in :py:const:`PPI_EDGELIST_FILE`
"""
WEIGHTED_PPI_EDGELIST_WEIGHT_COL = 'Weight'
"""
weight column
"""
WEIGHTED_PPI_EDGELIST_COLS = [PPI_EDGELIST_GENEA_COL,
PPI_EDGELIST_GENEB_COL,
WEIGHTED_PPI_EDGELIST_WEIGHT_COL]
PPI_GENE_NODE_ATTR_FILE = 'ppi_gene_node_attributes.tsv'
"""
Protein to Protein gene node attributes file
"""
PPI_GENE_NODE_COLS = ['name', 'represents', 'ambiguous', 'bait']
"""
Columns in :py:const:`PPI_GENE_NODE_ATTR_FILE`
"""
PPI_GENE_NODE_ERRORS_FILE = 'ppi_gene_node_attributes.errors'
"""
Protein to Protein gene node attributes error filename
"""
PPI_NETWORK_PREFIX = 'ppi'
HIERARCHY_NETWORK_PREFIX = 'hierarchy'
"""
CX2 format hierarchy filename
"""
HIERARCHY_PARENT_NETWORK_PREFIX = 'hierarchy_parent'
"""
CX2 format hierarchy parent (interactome) filename
"""
HIERARCHY_NODES_FILE = 'hierarchy_node_attributes.tsv'
"""
Hierarchy node attributes file
"""
CX_SUFFIX = '.cx'
"""
Suffix for files in `CX <https://cytoscape.org/cx/specification/2022/01/11/cytoscape-exchange-format-specification-(version-1).html>`__ format
"""
CX2_SUFFIX = '.cx2'
"""
Suffix for files in `CX 2.0<https://cytoscape.org/cx/cx2/specification/2022/12/01/cytoscape-exchange-format-specification-(version-2).html>`__ format
"""
HCX_SUFFIX = '.hcx'
"""
Suffix for files in `HCX <https://cytoscape.org/cx>`__ format
"""
RED = 'red'
"""
Red color directory name and color name
in red color files
"""
BLUE = 'blue'
"""
Blue color directory name and color name
in blue color files
"""
GREEN = 'green'
"""
Green color directory name and color name
in green color files
"""
YELLOW = 'yellow'
"""
Yellow color directory name and color name
in yellow color files
"""
COLORS = [RED, BLUE, GREEN, YELLOW]
"""
List of colors
"""
COLOR_INDEXS = {
'red': 0,
'green': 1,
'blue': 2,
'yellow': 0,
}
"""
Indexes for colors in .jpeg image
"""
COLOR_LABELS_MAP = {
GREEN: 'protein of interest',
RED: 'Microtubules (Tubulin antibody)',
BLUE: 'Nucleus (DAPI)',
YELLOW: 'ER (Calreticulin antibody)',
}
"""
Map of what each color refers to
"""
IMAGE_DOWNLOAD_STEP_DIR = '1.image_download'
"""
Name of directory where downloaded images are stored
"""
PPI_DOWNLOAD_STEP_DIR = '1.ppi_download'
"""
Name of directory where downloaded PPI edge and
baitlist are stored
"""
PPI_EMBEDDING_STEP_DIR = '2.ppi_embedding'
"""
Name of directory where PPI embeddings are stored
"""
IMAGE_EMBEDDING_STEP_DIR = '2.image_embedding_fold'
"""
Name of directory where image embeddings are stored
"""
COEMBEDDING_STEP_DIR = '3.coembedding_fold'
"""
Name of directory where co-embeddings are stored
"""
HIERARCHY_STEP_DIR = '4.hierarchy'
"""
Name of directory where hierarchies are stored
"""
HIERARCHYEVAL_STEP_DIR = '5.hierarchyeval'
"""
Name of directory where hierarchy evaluations are stored
"""
DATASET_INFO_FILE = 'dataset_info.json'
"""
Name of file where information about a dataset is stored
"""
DATASET_NAME = 'name'
"""
Name of the dataset
"""
DATASET_ORGANIZATION_NAME = 'organization_name'
"""
Name of the organization
"""
DATASET_PROJECT_NAME = 'project_name'
"""
Name of the project
"""
DATASET_RELEASE = 'release'
"""
Release of the dataset
"""
DATASET_CELL_LINE = 'cell_line'
"""
Cell line
"""
DATASET_TREATMENT = 'treatment'
"""
Treatment
"""
DATASET_TISSUE = 'tissue'
"""
Tissue
"""
DATASET_AUTHOR = 'author'
"""
Author of the dataset
"""
DATASET_SLICE = 'slice'
"""
Slice
"""
DATASET_GENE_SET = 'gene_set'
"""
Gene set
"""
DATASET_COLLECTION_SET = 'collection_set'
"""
Collection set
"""