def clip_refseq_enrichment_statistics(inputfiles, outputfile): inputfilesarg = ' '.join('%s:%s' % ( smp, Paths.genomespace_refseq_counts(smp)) for smp in Options.ALLCLIP_SAMPLES) refsample = Options.CLIPCTL_SAMPLES[0] # XXX fix this to support multiple controls clipsamples = ','.join(Options.CLIP_SAMPLES) runproc(""" $STATS_CLIP_NRREFSEQ_ENRICHED \ $nr_refseq_db $refsample $clipsamples $inputfilesarg \ > $outputfile""", outputfile)
def clip_refseq_enrichment_statistics(inputfiles, outputfile): inputfilesarg = ' '.join('%s:%s' % (smp, Paths.genomespace_refseq_counts(smp)) for smp in Options.ALLCLIP_SAMPLES) refsample = Options.CLIPCTL_SAMPLES[ 0] # XXX fix this to support multiple controls clipsamples = ','.join(Options.CLIP_SAMPLES) runproc( """ $STATS_CLIP_NRREFSEQ_ENRICHED \ $nr_refseq_db $refsample $clipsamples $inputfilesarg \ > $outputfile""", outputfile)
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR # OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, # ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR # OTHER DEALINGS IN THE SOFTWARE. # from ruffus import * import os from rnarry.nrclip import (Paths, Options, DerivedDatabaseBuilding, SequenceAnnotation, ContaminantFilter, SequenceProcessing) from rnarry.nrclip.PipelineControl import * @files([ Paths.genomespace_refseq_counts(sample) for sample in Options.ALLCLIP_SAMPLES ], Paths.clip_enrichment_summary) @follows(DerivedDatabaseBuilding.quantitate_refseq_in_gspace) def clip_refseq_enrichment_statistics(inputfiles, outputfile): inputfilesarg = ' '.join('%s:%s' % (smp, Paths.genomespace_refseq_counts(smp)) for smp in Options.ALLCLIP_SAMPLES) refsample = Options.CLIPCTL_SAMPLES[ 0] # XXX fix this to support multiple controls clipsamples = ','.join(Options.CLIP_SAMPLES) runproc( """ $STATS_CLIP_NRREFSEQ_ENRICHED \ $nr_refseq_db $refsample $clipsamples $inputfilesarg \
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR # OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, # ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR # OTHER DEALINGS IN THE SOFTWARE. # from ruffus import * import os from rnarry.nrclip import ( Paths, Options, DerivedDatabaseBuilding, SequenceAnnotation, ContaminantFilter, SequenceProcessing) from rnarry.nrclip.PipelineControl import * @files([Paths.genomespace_refseq_counts(sample) for sample in Options.ALLCLIP_SAMPLES], Paths.clip_enrichment_summary) @follows(DerivedDatabaseBuilding.quantitate_refseq_in_gspace) def clip_refseq_enrichment_statistics(inputfiles, outputfile): inputfilesarg = ' '.join('%s:%s' % ( smp, Paths.genomespace_refseq_counts(smp)) for smp in Options.ALLCLIP_SAMPLES) refsample = Options.CLIPCTL_SAMPLES[0] # XXX fix this to support multiple controls clipsamples = ','.join(Options.CLIP_SAMPLES) runproc(""" $STATS_CLIP_NRREFSEQ_ENRICHED \ $nr_refseq_db $refsample $clipsamples $inputfilesarg \ > $outputfile""", outputfile)