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) args = parser.parse_args(["--infile","/net/eichler/vol8/home/nkrumm/EXOMES/ESP2000/SVD/ESP.BROAD.SVD70.QC.SampleQC.hdf5", "--outfile","test.SVD70sd.txt", "--plotfile","test.SVD70.png", "--verbose"]) p = ConiferPipeline(args.infile) #n_probes = sum([len(p.getProbesByChrom(x)) for x in range(1,24)]) 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 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)
import argparse 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("--chr", "-c", action="store", nargs="+", required=False, default="All") parser.add_argument("--samples", "-s", action="store", nargs="+", required=False, default="All") parser.add_argument("--ncpu", "--ncpus", action="store", type=int, required=False, default=10) parser.add_argument("--nretry", "--nretries", action="store", type=int, required=False, default=3) parser.add_argument("--verbose", "-v", action="store_true", required=False, default=False) args = parser.parse_args() p = ConiferPipeline(args.infile) if args.chr == "All": chromosomes = None # process all print "All Chromosomes" else: chromosomes = args.chr print "Chromosomes: %s" % ", ".join(chromosomes) if args.samples == "All": samples = None # process all print "All samples" else: samples = args.samples print "Samples: ", ", ".join(samples) calls = p.makeCallsMPI(chromosomes=chromosomes, samples=samples,