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)
