Package interminebio :: Class SequenceQuery

Class SequenceQuery

       object --+    
                |    
SequenceDataQuery --+
                    |
                   SequenceQuery

Class for querying InterMine Webservices for Sequence based data

This module allows you to construct queries that retrieve data about sequences and sequence features in biologically relevant formats.

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

Instance Methods

[hide private]

__init__(self, service_or_query, root=None)

source code

add_sequence_feature(self, *features)
Fasta, GFF3 and BED queries all can read information from SequenceFeatures.

source code

where(self, *args, **kwargs)
Add a constraint to the query, and return self for chaining.

source code

set_sequence(self, f)
Add a sequence holding object to the query.

source code

Inherited from SequenceDataQuery: bed, fasta, gff3

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, service_or_query, root=None)
(Constructor)

source code

Constructor

>>> s = Service("www.flymine.org/query")
>>> bio_query = SequenceQuery(s, "Gene")
<interminebio.SequenceQuery xxx>
>>> q = s.new_query("Gene").where(s.model.Gene.symbol == ["h", "r", "eve", "zen"])
>>> bio_query = SequenceQuery(q)
<interminebio.SequenceQuery yyy>

Parameters:

service_or_query (intermine.webservice.Service or intermine.query.Query) - The service to connect to, or a query to wrap.
root (str) - The root class of the query

Overrides: object.__init__

add_sequence_feature(self, *features)

source code

Add an arbitrarily long list of sequence features to the query.

Fasta, GFF3 and BED queries all can read information from SequenceFeatures. For Fasta you are advised to use the set_sequence method instead, as unlike the GFF3 and BED services, the Fasta service can only handle queries with one output column.

set_sequence(self, f)

source code

Set the sequence column to retrieve.

Add a sequence holding object to the query. It can be a SequenceFeature, Protein or Sequence object.

Fasta queries, which read sequences rather than sequence features, currently only permit one output column.

Class SequenceQuery

Class for querying InterMine Webservices for Sequence based data

__init__(self, service_or_query, root=None) (Constructor)

Constructor

add_sequence_feature(self, *features)

Add an arbitrarily long list of sequence features to the query.

set_sequence(self, f)

Set the sequence column to retrieve.

init(self, service_or_query, root=None)
(Constructor)