def __init__(self, gene_source, tf_source=None, alias_source=None,
filter_havana=False, protein_coding=False, known_only=False):
# Class Objects
self.gene_list = [] # Represents gene annotation.
self.tf_list = [] # Represents TF PWM annotation.
self.alias_dict = dict() # Gene Symbol or other IDs -> ENSEMBL ID
self.symbol_dict = dict() # ENSEMBL ID -> Official gene symbol
# Initializing Required Field - Gene List
if isinstance(gene_source, list): # It can be a matrix - Used by internal methods.
self.gene_list = gene_source
if isinstance(gene_source, str): # It can be a string.
if os.path.isfile(gene_source): # The string may represent a path to a gtf file.
# FTT for TDF True
# filter_havana = False
protein_coding = False
known_only = False
self.load_gene_list(gene_source,
filter_havana=filter_havana,
protein_coding=protein_coding,
known_only=known_only)
else: # The string may represent an organism which points to a gtf file within data.config.
genome_data = GenomeData(gene_source)
self.load_gene_list(genome_data.get_annotation(),
filter_havana=filter_havana,
protein_coding=protein_coding,
known_only=known_only)
# Initializing Optional Field - TF List
if tf_source:
if isinstance(tf_source, list):
if isinstance(tf_source[0], list): # It can be a matrix
self.tf_list = tf_source
else:
mtf_file_list = []
motif_data = MotifData()
for e in tf_source:
if os.path.isfile(e): # It can be a path to a mtf file.
mtf_file_list.append(e)
else: # It can represent an organism which points to an mtf file within data.config.
mtf_file = motif_data.get_mtf_path(e)
mtf_file_list.append(mtf_file)
self.load_tf_list(mtf_file_list)
else:
pass # TODO Throw error.
# Initializing Optional Field - Alias Dictionary
if alias_source:
if isinstance(alias_source, dict): # It can be a dictionary - Used by internal methods.
self.alias_dict = alias_source
if isinstance(alias_source, str): # It can be a string.
if os.path.isfile(alias_source): # The string may represent a path to a txt alias file.
self.load_alias_dict(alias_source)
else: # The string may represent an organism which points to a txt alias file within data.config.
genome_data = GenomeData(alias_source)
self.load_alias_dict(genome_data.get_gene_alias())
else:
pass # TODO Throw error
def __init__(self, gene_source, tf_source=None, alias_source=None,
filter_havana=False, protein_coding=False, known_only=False):
# Class Objects
self.gene_list = [] # Represents gene annotation.
self.tf_list = [] # Represents TF PWM annotation.
self.alias_dict = dict() # Gene Symbol or other IDs -> ENSEMBL ID
self.symbol_dict = dict() # ENSEMBL ID -> Official gene symbol
# Initializing Required Field - Gene List
if isinstance(gene_source,list): # It can be a matrix - Used by internal methods.
self.gene_list = gene_source
if isinstance(gene_source,str): # It can be a string.
if os.path.isfile(gene_source): # The string may represent a path to a gtf file.
# FTT for TDF True
#filter_havana = False
protein_coding = False
known_only = False
self.load_gene_list(gene_source,
filter_havana=filter_havana,
protein_coding=protein_coding,
known_only=known_only)
else: # The string may represent an organism which points to a gtf file within data.config.
genome_data = GenomeData(gene_source)
self.load_gene_list(genome_data.get_annotation(),
filter_havana=filter_havana,
protein_coding=protein_coding,
known_only=known_only)
# Initializing Optional Field - TF List
if tf_source:
if isinstance(tf_source, list):
if isinstance(tf_source[0], list): # It can be a matrix
self.tf_list = tf_source
else:
mtf_file_list = []
motif_data = MotifData()
for e in tf_source:
if os.path.isfile(e): # It can be a path to a mtf file.
mtf_file_list.append(e)
else: # It can represent an organism which points to an mtf file within data.config.
mtf_file = motif_data.get_mtf_path(e)
mtf_file_list.append(mtf_file)
self.tf_list = self.load_tf_list(mtf_file_list)
else: pass # TODO Throw error.
# Initializing Optional Field - Alias Dictionary
if alias_source:
if isinstance(alias_source,dict): # It can be a dictionary - Used by internal methods.
self.alias_dict = alias_source
if isinstance(alias_source,str): # It can be a string.
if os.path.isfile(alias_source): # The string may represent a path to a txt alias file.
self.load_alias_dict(alias_source)
else: # The string may represent an organism which points to a txt alias file within data.config.
genome_data = GenomeData(alias_source)
self.load_alias_dict(genome_data.get_gene_alias())
else: pass # TODO Throw error
def __init__(self, gene_source, tf_source=None, alias_source=None):
"""
Initializes AnnotationSet.
Keyword arguments:
gene_source -- Gene source annotation. It will be used to create the gene_list
element. It can be:
* A matrix (list of lists): An AnnotationSet will be created based on such
matrix.
* A string representing a gtf file: An AnnotationSet will be created based
on such gtf file.
* A string representing an organism: An AnnotationSet will be created based
on the gtf file for that organism in data.config file.
tf_source -- TF source annotation. After initialization, this object is mapped with
gene_list. It can be:
* A matrix (list of lists): Represents a final tf_list element.
* A list of mtf files: The tf_list will be created based on all mtf files.
* A list of repositories: The tf_list will be created based on the mtf files
associated with such repositories in data.config.
alias_source -- Alias dictionary source annotation. It can be:
* A dictionary: An alias dictionary will be created based on such dictionary.
* A string representing a alias (txt) file: An alias dictionary will be created
based on such txt file.
* A string representing an organism: An alias dictionary will be created based
on the txt file for that organism in data.config file.
"""
# Class Objects
self.gene_list = [] # Represents gene annotation.
self.tf_list = [] # Represents TF PWM annotation.
self.alias_dict = dict() # Gene Symbol or other IDs -> ENSEMBL ID
self.symbol_dict = dict() # ENSEMBL ID -> Official gene symbol
# Initializing Required Field - Gene List
if (isinstance(
gene_source,
list)): # It can be a matrix - Used by internal methods.
self.gene_list = gene_source
if (isinstance(gene_source, str)): # It can be a string.
if (os.path.isfile(gene_source)
): # The string may represent a path to a gtf file.
self.load_gene_list(gene_source, filter_havana=False)
else: # The string may represent an organism which points to a gtf file within data.config.
genome_data = GenomeData(gene_source)
self.load_gene_list(genome_data.get_gencode_annotation(),
filter_havana=False)
# Initializing Optional Field - TF List
if (tf_source):
if (isinstance(tf_source, list)):
if (isinstance(tf_source[0], list)): # It can be a matrix
self.tf_list = tf_source
else:
mtf_file_list = []
motif_data = MotifData()
for e in tf_source:
if (os.path.isfile(e)
): # It can be a path to a mtf file.
mtf_file_list.append(e)
else: # It can represent an organism which points to an mtf file within data.config.
mtf_file = motif_data.get_mtf_path(e)
mtf_file_list.append(mtf_file)
self.tf_list = self.load_tf_list(mtf_file_list)
else:
pass # TODO Throw error.
# Initializing Optional Field - Alias Dictionary
if (alias_source):
if (isinstance(alias_source, dict)
): # It can be a dictionary - Used by internal methods.
self.alias_dict = alias_source
if (isinstance(alias_source, str)): # It can be a string.
if (os.path.isfile(alias_source)
): # The string may represent a path to a txt alias file.
self.load_alias_dict(alias_source)
else: # The string may represent an organism which points to a txt alias file within data.config.
genome_data = GenomeData(alias_source)
self.load_alias_dict(genome_data.get_gene_alias())
else:
pass # TODO Throw error
def __init__(self, gene_source, tf_source=None, alias_source=None):
"""
Initializes AnnotationSet.
Keyword arguments:
gene_source -- Gene source annotation. It will be used to create the gene_list
element. It can be:
* A matrix (list of lists): An AnnotationSet will be created based on such
matrix.
* A string representing a gtf file: An AnnotationSet will be created based
on such gtf file.
* A string representing an organism: An AnnotationSet will be created based
on the gtf file for that organism in data.config file.
tf_source -- TF source annotation. After initialization, this object is mapped with
gene_list. It can be:
* A matrix (list of lists): Represents a final tf_list element.
* A list of mtf files: The tf_list will be created based on all mtf files.
* A list of repositories: The tf_list will be created based on the mtf files
associated with such repositories in data.config.
alias_source -- Alias dictionary source annotation. It can be:
* A dictionary: An alias dictionary will be created based on such dictionary.
* A string representing a alias (txt) file: An alias dictionary will be created
based on such txt file.
* A string representing an organism: An alias dictionary will be created based
on the txt file for that organism in data.config file.
"""
# Class Objects
self.gene_list = [] # Represents gene annotation.
self.tf_list = [] # Represents TF PWM annotation.
self.alias_dict = dict() # Gene Symbol or other IDs -> ENSEMBL ID
self.symbol_dict = dict() # ENSEMBL ID -> Official gene symbol
# Initializing Required Field - Gene List
if(isinstance(gene_source,list)): # It can be a matrix - Used by internal methods.
self.gene_list = gene_source
if(isinstance(gene_source,str)): # It can be a string.
if(os.path.isfile(gene_source)): # The string may represent a path to a gtf file.
self.load_gene_list(gene_source, filter_havana=False, protein_coding=True,
known_only=True)
else: # The string may represent an organism which points to a gtf file within data.config.
genome_data = GenomeData(gene_source)
self.load_gene_list(genome_data.get_gencode_annotation(), filter_havana=False, protein_coding=True,
known_only=True)
# Initializing Optional Field - TF List
if(tf_source):
if(isinstance(tf_source,list)):
if(isinstance(tf_source[0],list)): # It can be a matrix
self.tf_list = tf_source
else:
mtf_file_list = []
motif_data = MotifData()
for e in tf_source:
if(os.path.isfile(e)): # It can be a path to a mtf file.
mtf_file_list.append(e)
else: # It can represent an organism which points to an mtf file within data.config.
mtf_file = motif_data.get_mtf_path(e)
mtf_file_list.append(mtf_file)
self.tf_list = self.load_tf_list(mtf_file_list)
else: pass # TODO Throw error.
# Initializing Optional Field - Alias Dictionary
if(alias_source):
if(isinstance(alias_source,dict)): # It can be a dictionary - Used by internal methods.
self.alias_dict = alias_source
if(isinstance(alias_source,str)): # It can be a string.
if(os.path.isfile(alias_source)): # The string may represent a path to a txt alias file.
self.load_alias_dict(alias_source)
else: # The string may represent an organism which points to a txt alias file within data.config.
genome_data = GenomeData(alias_source)
self.load_alias_dict(genome_data.get_gene_alias())
else: pass # TODO Throw error
