from conifertools import ConiferPipeline
import argparse
import numpy as np
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--infile", "-i", action="store", required=True)
parser.add_argument("--outfile", "-o", action="store", required=True)
parser.add_argument("--plotfile", action="store", required=False, default=None)
parser.add_argument("--verbose", action="store_true", required=False, default=False)
p = ConiferPipeline(args.infile)
out_sd_values = []
with open(args.outfile, 'w') as out_file:
for sampleID in p.samples:
sample_data = []
for c in xrange(1,24):
sample_data.extend(p.getConiferData(sampleID, c).rpkm)
sample_sd = np.std(np.array(sample_data))
out_sd_values.append(sample_sd)
if args.verbose:
print sampleID, sample_sd
out_file.write("%s\t%f\n" % (sampleID, sample_sd))
if args.plotfile:
from conifertools.plotting import QC_SampleSD_Plot
kwargs = {"bins": 20, "color":'r'}
QC_SampleSD_Plot(out_sd_values, title='SD values', outfile=args.plotfile, logscale=True, **kwargs)
from conifertools import ConiferPipeline, CallTable, CallFilterTemplate
import argparse
import numpy as np
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--conifer_file", action="store", required=True)
parser.add_argument("--call_file", action="store", required=True)
parser.add_argument("--outfile", "-o", action="store", required=True)
args = parser.parse_args()
p = ConiferPipeline(args.conifer_file)
SDFilter = CallFilterTemplate(
p,
"/net/eichler/vol8/home/nkrumm/REFERENCE_INFO/hg19genomicSuperDups.bed",
name="SegDupProbeOverlap",
filter_type="overlap",
func=lambda x: x < 0.5)
SDCount = CallFilterTemplate(
p,
"/net/eichler/vol8/home/nkrumm/REFERENCE_INFO/hg19genomicSuperDups.bed",
name="SegDupProbeCount",
filter_type="count")
PPGFilter = CallFilterTemplate(
p,
"/net/eichler/vol8/home/nkrumm/REFERENCE_INFO/pp_genes.hg19.spans.bed",
name="PPG_overlap",
filter_type="overlap",
func=lambda x: x < 0.9)
