add_biosource
Add a BioSource to DeepBlue. A BioSource refers to a term describing the origin of a given sample, such as a tissue or cell line.
Parameters:
name
(string)
— biosource namedescription
(string)
— description of the biosourceextra_metadata
(struct)
— additional metadatauser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly inserted biosource
['error', error_message]
— Error. Verify the error message.
list_biosources
List BioSources included in DeepBlue. A BioSource refers to a term describing the origin of a given sample, such as a tissue or cell line. It is possible to filter the BioSources by their extra_metadata fields content. These fields vary depending on the original data source.
Parameters:
extra_metadata
(struct)
— Metadata that must be matcheduser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
biosources
(array)
— biosources names and IDS
['error', error_message]
— Error. Verify the error message.
list_similar_biosources
List all BioSources that have a similar name compared to the provided name. A BioSource refers to a term describing the origin of a given sample, such as a tissue or cell line. The similarity is calculated using the Levenshtein method.
Parameters:
name
(string)
— biosource nameuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
biosource
(string)
— biosource name
['error', error_message]
— Error. Verify the error message.
create_experiments_set
Create a set of experiments to be shared among others users
Parameters:
name
(string)
— experiments set namedescription
(string)
— experiments set descriptionpublic
(boolean)
— True is others users can access this listexperiment_name
(string)
— name(s) of selected experiment(s)user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the experiments set
['error', error_message]
— Error. Verify the error message.
get_biosource_children
A BioSource refers to a term describing the origin of a given sample, such as a tissue or cell line. These form a hierarchy in which children of a BioSource term can be fetched with this command. Children terms are more specific terms that are defined in the imported ontologies.
Parameters:
biosource
(string)
— biosource nameuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
biosources
(array)
— related biosources
['error', error_message]
— Error. Verify the error message.
get_biosource_parents
A BioSource refers to a term describing the origin of a given sample, such as a tissue or cell line. These form a hierarchy in which the parent of a BioSource term can be fetched with this command. Parent terms are more generic terms that are defined in the imported ontologies.
Parameters:
biosource
(string)
— biosource nameuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
biosources
(array)
— parents biosources
['error', error_message]
— Error. Verify the error message.
A BioSource refers to a term describing the origin of a given sample, such as a tissue or cell line. These form a hierarchy in which the children of a BioSource term and its synonyms can be fetched with this command. Children terms are more specific terms that are defined in the imported ontologies. Synonyms are different aliases for the same biosource.
Parameters:
biosource
(string)
— biosource nameuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
biosources
(array)
— related biosources
['error', error_message]
— Error. Verify the error message.
get_biosource_synonyms
Obtain the synonyms of the specified biosource. Synonyms are different aliases for the same biosource. A BioSource refers to a term describing the origin of a given sample, such as a tissue or cell line.
Parameters:
biosource
(string)
— name of the biosourceuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
synonyms
(array)
— synonyms of the biosource
['error', error_message]
— Error. Verify the error message.
set_biosource_parent
Define a BioSource as parent of another BioSource. This command is used to build the BioSources hierarchy. A BioSource refers to a term describing the origin of a given sample, such as a tissue or cell line.
Parameters:
parent
(string)
— parentchild
(string)
— childuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
['error', error_message]
— Error. Verify the error message.
set_biosource_synonym
Define a synonym for a BioSource. BioSources can have multiple synonyms. This command for can be used multiply to add several synonyms. A BioSource refers to a term describing the origin of a given sample, such as a tissue or cell line.
Parameters:
biosource
(string)
— biosource namesynonym_name
(string)
— name of the synonymuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
synonym_name
(string)
— inserted synonym_name
['error', error_message]
— Error. Verify the error message.
Column Types - Inserting and listing different column types
create_column_type_calculated
Create a calculated column type in DeepBlue.A calculated column can use existing columns and transform or summarize them through mathematical operations or string operations using the programming language LUA. Examples: the following 'code' parameter can be used to calculate the square root of the column VALUE: 'return math.sqrt(value_of('VALUE'))'. Another example is dividing the value of the column 'VALUE' by the region length: 'return value_of('VALUE') / (value_of('END') - value_of('END'))'.
Parameters:
name
(string)
— column type namedescription
(string)
— description of the column typecode
(string)
— Lua code that will be executeduser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly created column type
['error', error_message]
— Error. Verify the error message.
create_column_type_category
Create a categoric column type in DeepBlue from a set of items. As example, the STRAND column is a category column that contain the items: '+', '-', and '.' .
Parameters:
name
(string)
— column type namedescription
(string)
— description of the column typeitems
(string)
— items that are accepted for this category setuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly created column type
['error', error_message]
— Error. Verify the error message.
create_column_type_range
Create a range column type in DeepBlue. For example, a METHYLATION_BETA_VALUE column where accepted values are from 0.0 to 1.0 .
Parameters:
name
(string)
— column type namedescription
(string)
— description of the column typeminimum
(double)
— minimum value for this range (inclusive)maximum
(double)
— maximum value for this range (inclusive)user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly created column type
['error', error_message]
— Error. Verify the error message.
create_column_type_simple
Create a simple column type (string, integer, double) in DeepBlue.
Parameters:
name
(string)
— column type namedescription
(string)
— description of the column typetype
(string)
— type of the column type (string, integer, double)user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly created column type
['error', error_message]
— Error. Verify the error message.
list_column_types
Lists the ColumnTypes included in DeepBlue.
Parameters:
user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
column_types
(array)
— column types names and IDS
['error', error_message]
— Error. Verify the error message.
Modify the extra metadata content of experiments, annotations, biosources, and samples. Use this command with an extra metadata key without value for removing this key. Extra metadata fields are optional non-standardized fields that are created during the import process. Only files uploaded by the user can me modified. The command 'clone_dataset' must be used if the user wants to modify a files that does not belong to him.
Parameters:
id
(string)
— id of the datakey
(string)
— extra_metadata keyvalue
(string)
— extra_metadata key (empty for delete this key)user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the modified data
['error', error_message]
— Error. Verify the error message.
clone_dataset
Clone a dataset optionally changing its metadata and extra_metadata values. This command must be used in data curation because users do not have permission to change the metadata values of the Annotations and Experiments that were not uploaded by them.
Parameters:
dataset_id
(string)
— ID of the dataset (experiment or annotation ID)new_name
(string)
— New dataset namenew_epigenetic_mark
(string)
— New epigenetic marknew_sample
(string)
— New sample IDnew_technique
(string)
— New techniquenew_project
(string)
— New projectdescription
(string)
— description of the experiment - empty to copy from the cloned datasetformat
(string)
— format of the provided data - empty to copy from the cloned datasetextra_metadata
(struct)
— additional metadatauser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the new dataset
['error', error_message]
— Error. Verify the error message.
add_epigenetic_mark
Include an Epigenetic Mark such as, for instance, a specific type of histone modification, in DeepBlue.
Parameters:
name
(string)
— name of the epigenetic markdescription
(string)
— description of the epigenetic markextra_metadata
(struct)
— additional metadatauser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly inserted epigenetic mark
['error', error_message]
— Error. Verify the error message.
list_epigenetic_marks
List Epigenetic Marks included in DeepBlue. This includes histone marks, DNA methylation, DNA sensitivity, etc. It is possible to filter the Epigenetic Marks by their extra_metadata field content.
Parameters:
extra_metadata
(struct)
— Metadata that must be matcheduser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
epigenetic_marks
(array)
— epigenetic mark names and IDS
['error', error_message]
— Error. Verify the error message.
list_similar_epigenetic_marks
List all Epigenetic Marks that have a similar name compared to the provided name. The similarity is calculated using the Levenshtein method.
Parameters:
name
(string)
— epigenetic mark nameuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
epigenetic_marks
(array)
— similar epigenetic mark names
['error', error_message]
— Error. Verify the error message.
add_experiment
Add an Experiment in DeepBlue. An Experiment describes the characteristics of a specific Epigenetic Mark with respect to a single sample. The technology used and project must be informed as well. Extra metadata can be specified in addition to the mandatory meta information.
Parameters:
name
(string)
— experiment namegenome
(string)
— the target genomeepigenetic_mark
(string)
— epigenetic mark of the experimentsample
(string)
— id of the used sampletechnique
(string)
— technique used by this experimentproject
(string)
— the project namedescription
(string)
— description of the experimentdata
(string)
— the BED formated dataformat
(string)
— format of the provided dataextra_metadata
(struct)
— additional metadatauser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly inserted experiment
['error', error_message]
— Error. Verify the error message.
collection_experiments_count
Count the number of experiments that match the selection criteria in each term of the selected controlled_vocabulary. The selection can be achieved through specifying a list of BioSources, experimental Techniques, Epigenetic Marks, Samples or Projects.
Parameters:
controlled_vocabulary
(string)
— controlled vocabulary namegenome
(string)
— the target genometype
(string)
— type of the experiment: peaks or signalepigenetic_mark
(string)
— name(s) of selected epigenetic mark(s)biosource
(string)
— name(s) of selected biosource(s)sample
(string)
— id(s) of selected sample(s)technique
(string)
— name(s) of selected technique(s)project
(string)
— name(s) of selected projectsuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
terms
(array)
— controlled_vocabulary terms with count
['error', error_message]
— Error. Verify the error message.
faceting_experiments
Summarize the controlled_vocabulary fields, from experiments that match the selection criteria. It is similar to the 'collection_experiments_count' command, but this command return the summarization for all controlled_vocabulary terms.
Parameters:
genome
(string)
— the target genometype
(string)
— type of the experiment: peaks or signalepigenetic_mark
(string)
— name(s) of selected epigenetic mark(s)biosource
(string)
— name(s) of selected biosource(s)sample
(string)
— id(s) of selected sample(s)technique
(string)
— name(s) of selected technique(s)project
(string)
— name(s) of selected projectsuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
faceting
(struct)
— Map with the mandatory fields of the experiments metadata, where each contains a list of terms that appears.
['error', error_message]
— Error. Verify the error message.
list_experiments
List the DeepBlue Experiments that matches the search criteria defined by this command parameters.
Parameters:
genome
(string)
— the target genometype
(string)
— type of the experiment: peaks or signalepigenetic_mark
(string)
— name(s) of selected epigenetic mark(s)biosource
(string)
— name(s) of selected biosource(s)sample
(string)
— id(s) of selected sample(s)technique
(string)
— name(s) of selected technique(s)project
(string)
— name(s) of selected projectsuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
experiments
(array)
— experiment names and IDS
['error', error_message]
— Error. Verify the error message.
list_recent_experiments
List the latest Experiments included in DeepBlue that match criteria defined in the parameters. The returned experiments are sorted by insertion date.
Parameters:
days
(double)
— maximum days ago the experiments were addedgenome
(string)
— the target genomeepigenetic_mark
(string)
— name(s) of selected epigenetic mark(s)sample
(string)
— id(s) of selected sample(s)technique
(string)
— name(s) of selected technique(es)project
(string)
— name(s) of selected projectsuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
experiments
(array)
— names of recent experiments
['error', error_message]
— Error. Verify the error message.
list_similar_experiments
List all Experiments that have a similar name compared to the provided name. The similarity is calculated using the Levenshtein method.
Parameters:
name
(string)
— experiment namegenome
(string)
— the target genomeuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
experiments
(array)
— similar experiment names
['error', error_message]
— Error. Verify the error message.
preview_experiment
List the DeepBlue Experiments that matches the search criteria defined by this command parameters.
Parameters:
experiment_name
(string)
— name(s) of selected experiment(s)user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
experiment
(string)
— experiment's regions
['error', error_message]
— Error. Verify the error message.
cancel_request
Stop, cancel, and remove request data. The request processed data is remove if its processing was finished.
Parameters:
id
(string)
— Request ID to be canceled, stopped or removed.user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— ID of the canceled request
['error', error_message]
— Error. Verify the error message.
info
Information about a DeepBlue data identifier (ID). Any DeepBlue data ID can be queried with this command. For example, it is possible to obtain all available information about an Experiment using its ID, to obtain the actual Request processing status or the information about a Sample. A user can obtain information about him- or herself using the value 'me' in the parameter 'id'. Multiple IDs can be queried in the same operation.
Parameters:
id
(string)
— ID or an array of IDsuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
information
(array)
— List of Maps, where each map contains the info of an object.
['error', error_message]
— Error. Verify the error message.
is_biosource
Verify if the name is an existing and valid DeepBlue BioSource name. A BioSource refers to a term describing the origin of a given sample, such as a tissue or cell line.
Parameters:
biosource
(string)
— biosource nameuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
information
(string)
— A string containing the biosource name
['error', error_message]
— Error. Verify the error message.
list_in_use
List all terms used by the Experiments mandatory metadata that have at least one Experiment or Annotation using them.
Parameters:
controlled_vocabulary
(string)
— controlled vocabulary nameuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
terms
(array)
— controlled_vocabulary terms with count
['error', error_message]
— Error. Verify the error message.
name_to_id
Obtain the data ID(s) from the informed data name(s).
Parameters:
name
(string)
— ID or an array of IDscollection
(string)
— Collection where the data name is inuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
information
(array)
— List of IDs.
['error', error_message]
— Error. Verify the error message.
remove
Remove a DeepBlue data by using its ID.
Parameters:
id
(string)
— Data ID to be removed.user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the removed data
['error', error_message]
— Error. Verify the error message.
search
Search all data of all types for the given keyword. A minus (-) character in front of a keyword searches for data without the given keyword. The search can be restricted to the following data types are: Annotations, Biosources, Column_types, Epigenetic_marks, Experiments, Genomes, Gene_models, Gene_expressions, Genes, Gene_ontology, Projects, Samples, Techniques, Tilings.
Parameters:
keyword
(string)
— keyword to search bytype
(string)
— type of data to search for - Annotations, Biosources, Column_types, Epigenetic_marks, Experiments, Genomes, Gene_models, Gene_expressions, Genes, Gene_ontology, Projects, Samples, Techniques, Tilingsuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
results
(array)
— search results as [id, name, type]
['error', error_message]
— Error. Verify the error message.
add_gene_model
Include a Gene Model in DeepBlue. The data must be in the GTF format. Important: this command will include only the lines where the column 'feature' is 'genes'.
Parameters:
gene_model
(string)
— the gene modelgenome
(string)
— the target genomedescription
(string)
— description of the gene modeldata
(string)
— data in the GTF formatformat
(string)
— data format - currently, only the GTF format is supported.extra_metadata
(struct)
— additional metadatauser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly inserted gene model
['error', error_message]
— Error. Verify the error message.
add_gene_ontology_term
Add a Gene Ontology Term to DeepBlue. A Gene Ontology Term refers to a term use to describe the genes functions.
Parameters:
go_id
(string)
— GO identifiergo_label
(string)
— GO labeldescription
(string)
— description of the Gene Ontology Termnamespace
(string)
— term namespace: cellular component, biological process or molecular functionuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly inserted Gene Ontology Term
['error', error_message]
— Error. Verify the error message.
annotate_gene
Annotate a Gene with a Gene Ontology Term.
Parameters:
gene_ensb_id
(string)
— Gene ENSB ID (ENSGXXXXXXXXXXX identifiergo_term_id
(string)
— GO Term IDuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly inserted Gene Ontology Term
['error', error_message]
— Error. Verify the error message.
count_gene_ontology_terms
Count how many times a GO term appears.
Parameters:
genes
(string)
— Name(s) or ENSEMBL ID (ENSGXXXXXXXXXXX.X ) of the gene(s).go_terms
(string)
— gene ontology terms - ID or labelchromosome
(string)
— chromosome name(s)start
(int)
— minimum start regionend
(int)
— maximum end regiongene_model
(string)
— the gene modeluser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
faceting
(struct)
— Map with the mandatory fields of the experiments metadata, where each contains a list of terms that appears.
['error', error_message]
— Error. Verify the error message.
list_gene_models
List all the Gene Models currently available in DeepBlue. A gene model is a set of genes usually imported from GENCODE. For example Gencode v22.
Parameters:
user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
gene_models
(array)
— gene models names and IDS
['error', error_message]
— Error. Verify the error message.
list_genes
List the Genes currently available in DeepBlue.
Parameters:
genes
(string)
— Name(s) or ENSEMBL ID (ENSGXXXXXXXXXXX.X ) of the gene(s).go_terms
(string)
— gene ontology terms - ID or labelchromosome
(string)
— chromosome name(s)start
(int)
— minimum start regionend
(int)
— maximum end regiongene_model
(string)
— the gene modeluser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
genes
(array)
— genes names and its content
['error', error_message]
— Error. Verify the error message.
select_genes
Select genes (by their name or ID) as genomic regions from the specified gene model.
Parameters:
genes
(string)
— Name(s) or ENSEMBL ID (ENSGXXXXXXXXXXX.X ) of the gene(s).go_terms
(string)
— gene ontology terms - ID or labelgene_model
(string)
— the gene modelchromosome
(string)
— chromosome name(s)start
(int)
— minimum start regionend
(int)
— maximum end regionuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
['error', error_message]
— Error. Verify the error message.
set_gene_ontology_term_parent
Define a BioSource as parent of another BioSource. This command is used to build the BioSources hierarchy. A BioSource refers to a term describing the origin of a given sample, such as a tissue or cell line.
Parameters:
parent_go_id
(string)
— parent GO identifierparent_go_id
(string)
— parent GO identifieruser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
['error', error_message]
— Error. Verify the error message.
add_genome
Add a (reference) Genome assembly to DeepBlue.
Parameters:
name
(string)
— genome namedescription
(string)
— description of the genomedata
(string)
— genome datauser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly inserted genome
['error', error_message]
— Error. Verify the error message.
chromosomes
List the chromosomes of a given Genome.
Parameters:
genome
(string)
— the target genomeuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
chromosomes
(array)
— A list containing all chromosomes, with theirs names and sizes
['error', error_message]
— Error. Verify the error message.
list_genomes
List Genomes assemblies that are registered in DeepBlue.
Parameters:
user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
genomes
(array)
— genome names
['error', error_message]
— Error. Verify the error message.
list_similar_genomes
Lists all Genomes that have a similar name compared to the provided name. The similarity is calculated using the Levenshtein method.
Parameters:
name
(string)
— genome nameuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
genomes
(array)
— similar genome names
['error', error_message]
— Error. Verify the error message.
upload_chromosome
Upload the DNA sequence of a chromosome.
Parameters:
genome
(string)
— the target genomechromosome
(string)
— chromosome namedata
(string)
— chromosome sequence datauser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
['error', error_message]
— Error. Verify the error message.
aggregate
Summarize the data_id content using the regions specified in ranges_id as boundaries. Use the fields @AGG.MIN, @AGG.MAX, @AGG.SUM, @AGG.MEDIAN, @AGG.MEAN, @AGG.VAR, @AGG.SD, @AGG.COUNT in 'get_regions' command 'format' parameter to retrieve the computed values minimum, maximum, median, mean, variance, standard deviation and number of regions, respectively.
Parameters:
data_id
(string)
— id of the query with the dataranges_id
(string)
— id of the query with the regions rangecolumn
(string)
— name of the column that will be used in the aggregationuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
regions
(string)
— query id of this aggregation operation
['error', error_message]
— Error. Verify the error message.
binning
Bin results according to counts.
Parameters:
query_data_id
(string)
— query data that will made by the binning.column
(string)
— name of the column that will be used in the aggregationbins
(int)
— number of of binsuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
request_id
(string)
— Request ID - Use it to retrieve the result with info() and get_request_data()
['error', error_message]
— Error. Verify the error message.
count_regions
Return the number of genomic regions present in the query.
Parameters:
query_id
(string)
— Query IDuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
request_id
(string)
— Request ID - Use it to retrieve the result with info() and get_request_data()
['error', error_message]
— Error. Verify the error message.
coverage
Send a request to count the number of regions in the result of the given query.
Parameters:
query_id
(string)
— Query IDgenome
(string)
— Genome where the coverage will be calculated touser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
request_id
(string)
— Request ID - Use it to retrieve the result with info() and get_request_data()
['error', error_message]
— Error. Verify the error message.
distinct_column_values
Obtain the distict values of the field.
Parameters:
query_id
(string)
— Query IDfield
(string)
— field that is filtered byuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of filtered query
['error', error_message]
— Error. Verify the error message.
extend
Extend the genomic regions included in the query. It is possible to extend downstream, upstream or in both directions.
Parameters:
query_id
(string)
— Query IDlength
(int)
— The new region lengthdirection
(string)
— The direction that the region will be extended: 'BACKWARD', 'FORWARD', 'BOTH'. (Empty value will be used for both direction.use_strand
(boolean)
— Use the region column STRAND to define the region directionuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the new query
['error', error_message]
— Error. Verify the error message.
filter_by_motif
Filter the genomic regions by a regular expression motif.
Parameters:
query_id
(string)
— Query IDmotif
(string)
— motif (PERL regular expression)user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of filtered query
['error', error_message]
— Error. Verify the error message.
filter_regions
Filter the genomic regions by their content.
Parameters:
query_id
(string)
— Query IDfield
(string)
— field that is filtered byoperation
(string)
— operation used for filtering. For 'string' must be '==' or '!=' and for 'number' must be one of these: ==,!=,>,>=,<,<=value
(string)
— value the operator is applied totype
(string)
— type of the value: 'number' or 'string'user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of filtered query
['error', error_message]
— Error. Verify the error message.
flank
Create a set of genomic regions that flank the query regions. The original regions are removed from the query. Use the merge command to combine flanking regions with the original query.
Parameters:
query_id
(string)
— Query IDstart
(int)
— Number of base pairs after the end of the region. Use a negative number to denote the number of base pairs before the start of the region.length
(int)
— The new region lengthuse_strand
(boolean)
— Use the region column STRAND to define the region directionuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the new query
['error', error_message]
— Error. Verify the error message.
get_experiments_by_query
List the experiments and annotations that have at least one genomic region in the final query result.
Parameters:
query_id
(string)
— Query IDuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
experiments
(array)
— List containing experiments names and ids
['error', error_message]
— Error. Verify the error message.
get_regions
Trigger the processing of the query's genomic regions. The output is a column based format with columns as defined in the 'output_format' parameter. Use the command 'info' for verifying the processing status. The 'get_request_data' command is used to download the regions using the programmatic interface. Alternatively, results can be download using the URL: http://deepblue.mpi-inf.mpg.de/download?r_id=&key=.
Parameters:
query_id
(string)
— Query IDoutput_format
(string)
— Output formatuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
request_id
(string)
— Request ID - Use it to retrieve the result with info() and get_request_data()
['error', error_message]
— Error. Verify the error message.
Upload a set of genomic regions that can be accessed through a query ID. An interesting use case for this command is to upload a set of custom regions for intersecting with genomic regions in DeepBlue to specifically select regions of interest.
Parameters:
genome
(string)
— the target genomeregion_set
(string)
— Regions in CHROMOSOME START END formatuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
['error', error_message]
— Error. Verify the error message.
intersection
Select genomic regions that intersect with at least one region of the second query. This command is a simplified version of the 'overlap' command.
Parameters:
query_data_id
(string)
— query data that will be filtered.query_filter_id
(string)
— query containing the regions that the regions of the query_data_id must overlap.user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the new query
['error', error_message]
— Error. Verify the error message.
merge_queries
Merge regions from two queries in a new query.
Parameters:
query_a_id
(string)
— id of the first queryquery_b_id
(string)
— id of the second query (or use an array to include multiple queries)user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— new query id
['error', error_message]
— Error. Verify the error message.
overlap
Select genomic regions that overlap or not overlap with with the specified number of regions of the second query. Important: This command is still experimental and changes may occour.
Parameters:
query_data_id
(string)
— query data that will be filtered.query_filter_id
(string)
— query containing the regions that the regions of the query_data_id must overlap.overlap
(boolean)
— True if must overlap, or false if must not overlap.amount
(int)
— Amount of regions that must overlap. Use the parameter 'amount_type' ('bp' or '%') to specify the unit. For example, use the value '10' with the amount_type '%' to specify that 10% of the bases in both regions must overlap, or use '10' with the amount_type 'bp' to specify that at least 10 bases must or must not overlap.amount_type
(string)
— Type of the amount: 'bp' for base pairs and '%' for percentage.user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the new query
['error', error_message]
— Error. Verify the error message.
query_cache
Cache a query result in DeepBlue memory. This command is useful when the same query ID is used multiple times in different requests. The command is an advice for DeepBlue to cache the query result and there is no guarantee that this query data access will be faster.
Parameters:
query_id
(string)
— Query IDcache
(boolean)
— set or unset this query cachinguser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
information
(string)
— New query ID.
['error', error_message]
— Error. Verify the error message.
query_experiment_type
Filter the query ID for regions associated with experiments of a given type. For example, it is possible to select only peaks using this command with the 'peaks' parameter.
Parameters:
query_id
(string)
— Query IDtype
(string)
— experiment type (peaks or signal)user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
information
(string)
— New query ID.
['error', error_message]
— Error. Verify the error message.
score_matrix
Build a matrix containing the aggregation result of the the experiments data by the aggregation boundaries.
Parameters:
experiments_columns
(struct)
— map with experiments names and columns to be processed. Example : {'wgEncodeBroadHistoneDnd41H3k27acSig.wig':'VALUE', 'wgEncodeBroadHistoneCd20ro01794H3k27acSig.wig':'VALUE'}aggregation_function
(string)
— aggregation function name: min, max, sum, mean, var, sd, median, count, booleanaggregation_regions_id
(string)
— query ID of the regions that will be used as the aggregation boundariesuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
score_matrix
(string)
— the score matrix containing the summarized data
['error', error_message]
— Error. Verify the error message.
select_annotations
Select regions from the Annotations that match the selection criteria.
Parameters:
annotation_name
(string)
— name(s) of selected annotation(s)genome
(string)
— the target genomechromosome
(string)
— chromosome name(s)start
(int)
— minimum start regionend
(int)
— maximum end regionuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
['error', error_message]
— Error. Verify the error message.
select_experiments
Selects regions from Experiments by the experiments names.
Parameters:
experiment_name
(string)
— name(s) of selected experiment(s)chromosome
(string)
— chromosome name(s)start
(int)
— minimum start regionend
(int)
— maximum end regionuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
['error', error_message]
— Error. Verify the error message.
select_regions
Selects Experiment regions that matches the criteria informed by the operation parameters.
Parameters:
experiment_name
(string)
— name(s) of selected experiment(s)genome
(string)
— the target genomeepigenetic_mark
(string)
— name(s) of selected epigenetic mark(s)sample_id
(string)
— id(s) of selected sample(s)technique
(string)
— name(s) of selected technique(es)project
(string)
— name(s) of selected projectschromosomes
(string)
— chromosome name(s)start
(int)
— minimum start regionend
(int)
— maximum end regionuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
['error', error_message]
— Error. Verify the error message.
tiling_regions
Generate tiling regions across the genome chromosomes. The idea is to "bin" genomic regions systematically in order to obtain discrete regions over which one can aggregate. Using the 'score_matrix' command, these bins (tiles) can be compared directly across experiments.
Parameters:
size
(int)
— tiling sizegenome
(string)
— the target genomechromosome
(string)
— chromosome name(s)user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
['error', error_message]
— Error. Verify the error message.
add_project
Add a Project to DeepBlue. A Project is used to group Experiments and to define their origin.
Parameters:
name
(string)
— projectnamedescription
(string)
— description of the projectuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the newly inserted project
['error', error_message]
— Error. Verify the error message.
add_user_to_project
Add a user as Project member.
Parameters:
user
(string)
— User name or IDproject
(string)
— Project name or IDset
(boolean)
— True to include the user or false to removeuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
user_id
(string)
— id of the user
['error', error_message]
— Error. Verify the error message.
list_projects
List Projects included in DeepBlue.
Parameters:
user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
projects
(array)
— project names
['error', error_message]
— Error. Verify the error message.
list_similar_projects
List Projects that have a similar name compared to the provided name. The similarity is calculated using the Levenshtein method.
Parameters:
name
(string)
— project nameuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
projects
(array)
— similar project names
['error', error_message]
— Error. Verify the error message.
set_project_public
Define a project as public. This means that all DeepBlue users can then access its data. You must be the project owner to perform this operation.
Parameters:
project
(string)
— Project name or IDset
(boolean)
— True to set the project as public of false for unsetuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— id of the project
['error', error_message]
— Error. Verify the error message.
get_request_data
Download the requested data. The output can be (i) a string (get_regions, score_matrix, and count_regions), or (ii) a list of ID and names (get_experiments_by_query), or (iii) a struct (coverage).
Parameters:
request_id
(string)
— ID of the requestuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
data
(string)
— the request data
['error', error_message]
— Error. Verify the error message.
list_requests
List the Requests made by the user. It is possible to obtain only the requests of a given state.
Parameters:
request_state
(string)
— Name of the state to get requests for. The valid states are: new, running, done, and failed.user_key
(string)
— users token key
Response:
['okay', result]
— result consists of
data_state
(array)
— Request-IDs and their state
['error', error_message]
— Error. Verify the error message.
reprocess
Reprocess the request. Useful when the request was cancelled or removed.
Parameters:
request_id
(string)
— ID of the requestuser_key
(string)
— users token key
Response:
['okay', result]
— result consists of
id
(string)
— ID of the reprocessed request
['error', error_message]
— Error. Verify the error message.