Package interminebio :: Class RegionQuery
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Class RegionQuery

source code

       object --+    
                |    
SequenceDataQuery --+
                    |
                   RegionQuery

Class for querying InterMine Webservices for Features in Genomic Intervals

This module allows you to construct queries that retrieve data about sequences and sequence features in biologically relevant formats, where those features are located overlapping genomic intervals.

The currently supported formats are UCSC-BED, GFF3, and FASTA.

These queries may also be used to construct lists with.

Instance Methods [hide private]
 
__init__(self, service, organism, feature_types, regions, extension=0, is_interbase=False) source code
 
_get_region_query(self) source code
dict
to_query_params(self)
This method is a required part of the interface for creating lists.
source code
str
get_list_upload_uri(self)
This method is a required part of the interface for creating lists.
source code

Inherited from SequenceDataQuery: bed, fasta, gff3

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  LIST_PATH = '/regions/list'
  BED_PATH = '/regions/bed'
  FASTA_PATH = '/regions/fasta'
  GFF3_PATH = '/regions/gff3'
Properties [hide private]
  query

Inherited from object: __class__

Method Details [hide private]

__init__(self, service, organism, feature_types, regions, extension=0, is_interbase=False)
(Constructor)

source code 

Constructor

>>> s = Service("www.flymine.org/query", "API-KEY")
>>> org = "D. melanogaster"
>>> regions = ["2L:14614843..14619614"]
>>> feature_types = ["Exon", "Intron"]
>>> q = RegionQuery(s, org, feature_types, regions)
<interminebio.RegionQuery @xxx>
Parameters:
  • service (intermine.webservice.Service) - The service to connect to.
  • organism (str) - The short name of the organism to look within (eg: D. melanogaster)
  • feature_types (list[str]) - The types of features to look for
  • regions (list(str)) - The regions to search within, in chrX:start..end or chrX start end format
  • extension (int) - A number of base-pairs to extend each region on either side (default: 0)
  • is_interbase (boolean) - Whether to interpret the co-ordinates as interbase co-ordinates
Overrides: object.__init__

Property Details [hide private]

query

Get Method:
unreachable.query(self)