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object --+ | SequenceDataQuery --+ | SequenceQuery
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.
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Inherited from Inherited from |
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Inherited from |
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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>
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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 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. |
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