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object --+ | 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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Constructor
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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. |
Get results as BEDReturn a BedIterator object, which stringifies to the BED results, and works as an iterator over the lines. After iteration the header information is accessible with the iter.header() method |
Get results as GFF3Return a GFF3Iterator object, which stringifies to the GFF3 results, and works as an iterator over the lines. After iteration the header information is accessible with the iter.header() method |
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