Package: pygenome
pygenomeHarness the awesome power of yeast genetics through python! Pygenome provide access to theSaccharomyces cerevisiaegenome from Python.Genes,promoters,terminators, andintergenic, sequences
as well as the deletionlocicreated by thegenome wide deletion projectare available by their systematic names (likeYPR080w) or by
standard name (likeCYC1). DNA
sequences are returned as BiopythonSeqRecordobjects. Thanks toSGDfor letting me use the SuperYeast logotype above.Typical usage at theIPythoncommand line could look like this:frompygenomeimportsgmygene=sg.stdgene["XKS1"]mygeneGene XKS1/YGR194Cmygene.short_descriptionXylulokinase; converts D-xylulose and ATP to xylulose 5-phosphate and ADP; rate limiting step in fermentation of xylulose; required for xylose fermentation by recombinant S. cerevisiae strainssg.sysgene["YGR194C"]Gene XKS1/YGR194Cmygene.cdsSeqRecord(seq=Seq('ATGTTGTGTTCAGTAATTCAGAGACAGACAAGAGAGGTTTCCAACACAATGTCT...TAA'), id='BK006941.2', name='BK006941', description='BK006941 REGION: complement(887876..886072)', dbxrefs=[])mygene.locus()SeqRecord(seq=Seq('ATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATATGTTAA...GAA'), id='BK006941.2', name='BK006941', description='BK006941 REGION: complement(888876..885072)', dbxrefs=[])mygene.promoterSeqRecord(seq=Seq('ATGATGATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATA...TTA'), id='YGR195W_YGR194C', name='.', description='BK006941.2 REGION: complement(887876..888881)', dbxrefs=[])mygene.terminatorSeqRecord(seq=Seq('AATATGTTTGAATAATTTATCATGCCCTGACAAGTACACACAAACACAGACACA...AAA'), id='YGR194C_YGR195W', name='.', description='Intergenic sequence between upstream gene YGR194C and downstream gene Gene PDX1/YGR193C', dbxrefs=[])mygene.downstream_geneGene PDX1/YGR193Cmygene.upstream_geneGene SKI6/YGR195Wmygene.deletion_locusSeqRecord(seq=Seq('ATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATATGTTAA...GAA'), id='ygr194c::KanMX4 locus with 1000 bp up and 1000 bp downstream DNA', name='ygr194c::KanMX4', description='description', dbxrefs=[])http://www-sequence.stanford.edu/group/yeast_deletion_project/downloads.htmlverdatecomment2.0.02017-09-02split sg.gene dict into sg.stdgene and sg.sysgene1.0.02017-03-24Internal stuff, automativ build & test0.9.52017-01-01Python 3 release0.9.02015-05-01Changed interface to a more object oriented style0.5.02015-03-03Documentation, automatic build, test and deployment0.0.62014-06-17Bugfix0.0.52014-06-14Simpler api (see example above)0.0.12013-08-01first releaseInstallation using conda on AnacondaThe absolutely best way of installing and using pygenome is to use the
freeAnacondaorMinicondapython distributions.Anaconda is a large download (about 400 Mb) while Miniconda is about 40-50 Mb.Once Anaconda (or Miniconda) is installed, the conda package manager can be used to install pygenome
from theBjornFJohanssonpackage channel.The first step is to add the channel by typing the command below followed by return:conda config --append channels BjornFJohanssonThen pygenome can be installed by typing the command below followed by return:conda install pygenomeThis works on Windows, MacOSX and Linux, and installs all necessary dependencies automatically.RequirementsPython 3.6 or 3.7(pygenome version 0.9.0 was the last to support Python 2.7.)pydnarequestsappdirsInstall with pipThe second best way of installing pygenome is by usingpipsudo pip install pygenomeSource Code Repositorypydna source code is hosted onGithub.