Selecting Experiments

The select_regions command is used to access the experiments' data. The select_regions command is similar to select_annotations. The difference is that select_regions accepts epigenetic_mark, sample, technique, and project parameters.

Selecting Experiments Example

Example: Firstly, we use the get_biosource_related command to retrieve all biosources related to the term "blood" and then we select only the biosources names from the blood_related list. Them, we select all samples that use these biosources and get their IDs. Finally, we select all chromosome chr1 regions from the experiments that have genome hg19, epigenetic_mark methylation and the found samples and print the chromosome, start, and end of these regions:

(status, blood_related) = server.get_biosource_related("blood", user_key)
blood_related_names = server.extract_names(blood_related)[1]
(status, blood_samples) = server.list_samples(blood_related_names,
                                              {"karyotype":"cancer"}, user_key)
blood_samples_ids = server.extract_ids(blood_samples)[1]
(status, query_id) = server.select_regions(None, "hg19", "DNA Methylation",
                                           blood_samples_ids, None, None,
                                           "chr1", None, None, user_key)
(status, request_id) = server.get_regions(query_id,
                                          "CHROMOSOME, START, END", user_key)
(status, regions) = server.get_request_data(request_id, user_key)
print regions

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