import sys import os from hivwholeseq.utils.generic import mkdirs from hivwholeseq.patients.samples import itersample from hivwholeseq.sequencing.samples import load_samples_sequenced as lss from hivwholeseq.patients.samples import load_samples_sequenced as lssp from hivwholeseq.sequencing.filenames import get_sample_foldername # Script if __name__ == '__main__': samples_pat = lssp() samples_seq = lss() for samplename, sample in itersample(samples_pat): root_foldername = sample.get_foldername()+'samples_sequencing/' mkdirs(root_foldername) for samplenameseq, sampleseq in samples_seq.iterrows(): if sampleseq['patient sample'] == samplename: src_folder = get_sample_foldername(samplenameseq) dst_folder = root_foldername+samplenameseq if not os.path.islink(dst_folder): os.symlink(src_folder, dst_folder) print 'Symlink:', src_folder, dst_folder else: print 'Esists:', dst_folder
samples = lssp() if pnames is not None: samples = samples.loc[samples.patient.isin(pnames)] elif samplenames is not None: samples = samples.loc[samples.index.isin(samplenames)] if VERBOSE >= 2: print "samples", samples.index.tolist() if use_plot: fig, ax = plt.subplots() for ir, region in enumerate(regions): for isam, (samplename, sample) in enumerate(itersample(samples)): if VERBOSE >= 1: print samplename, region cov = sample.get_coverage(region) if use_plot: color = cm.jet(1.0 * (isam + ir * len(samples)) / (len(regions) * len(samples))) ax.plot(cov + 0.1, lw=2, c=color, label=samplename + ", " + region) if use_plot: ax.set_xlabel("Position [bp]") ax.set_ylabel("Coverage") ax.set_yscale("log") ax.set_ylim(0.1, 1e6)
samples = lssp() if pnames is not None: samples = samples.loc[samples.patient.isin(pnames)] elif samplenames is not None: samples = samples.loc[samples.index.isin(samplenames)] if VERBOSE >= 2: print 'samples', samples.index.tolist() if use_plot: fig, ax = plt.subplots() for ir, region in enumerate(regions): for isam, (samplename, sample) in enumerate(itersample(samples)): if VERBOSE >= 1: print samplename, region cov = sample.get_coverage(region) if use_plot: color = cm.jet(1.0 * (isam + ir * len(samples)) / (len(regions) * len(samples))) ax.plot(cov + 0.1, lw=2, c=color, label=samplename + ', ' + region) if use_plot: ax.set_xlabel('Position [bp]')
author: Fabio Zanini date: 18/05/15 content: Get days since infection from dates. ''' # Globals import pandas as pd from hivwholeseq.patients.patients import load_patients from hivwholeseq.patients.samples import load_samples_sequenced, itersample # Script if __name__ == '__main__': samples = load_samples_sequenced(include_empty=True) patients = load_patients() dsi = [] for samplename, sample in itersample(samples): t = sample.date t0 = patients.loc[sample.patient]['infect date best'] dt = (t - t0).days dsi.append({'sample': samplename, 'dsi': dt, }) dsi = pd.DataFrame(dsi).set_index('sample') print dsi