Python API to UCSC genome browser tables
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README.md

Python bindings to UCSC genome browser tables

pyucsc provides a way of accessing UCSC genome browser SQL tables and FASTA files. It provides the following features:

  • SQL table access via SqlAlchemy
  • FASTA file access via pyfasta & fastinterval
  • Python models and mappers that link together database information into python classes

Example

A really simple example session::

>>> import ucsc
>>> from ucsc.model import KnownGene
>>> session, genome = ucsc.use('hg19') 
>>> vhl = session.query(KnownGene).filter(KnownGene.geneSymbol=='VHL').one()
>>> vhl 
KnownGene(VHL, uc003bvc.2, chr3:10183318-10193744)
 >>> vhl.transcript
Interval(10183318, 10193744)
>>> vhl.transcript.sequence
'CCTCGCCTCCGTTACAACGGCCTACGGTGCTG...'

Documentation

Please see the pyucsc documentation