Get Regions

The command get_regions is used for requesting sequences from the server. The result can be retrieved using get_request_data. The command parameters are the query_id and the format.

The format is the name of the fields that were given in the add_experiment and add_annotations.

Example: Retrieving all regions from chromosome 1 with blood as biosource, methylation as epigenetic mark and containing the key karyotype with the value cancer in the sample:

(status, blood_related) = server.get_biosource_related("blood", user_key)
blood_related_names = [x[1] for x in blood_related]

(status, blood_samples) = server.list_samples(blood_related_names,
                                         {"karyotype":"cancer"}, user_key)
blood_samples_ids = [x[0] for x in blood_samples]

(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

Metafields

Metafields are fields used to obtain more information about the retrieved region. It is possible to obtain the region length and the name of the experiment of the given region. The following table shows all metafields in the regions experiment metadata:

The next example works as the previous one, but now returning the experiment name, length and BioSource name:

(status, regions) = server.get_regions(query_id,
                                       "CHROMOSOME,START,END,@NAME,@LENGTH,@BIOSOURCE",
                                       user_key)