parser.add_argument('--qualmin', type=int, default=30, help='Minimal quality of base to call') parser.add_argument('--PCR', type=int, default=1, help='Analyze only reads from this PCR (e.g. 1)') args = parser.parse_args() pnames = args.patients samplenames = args.samples fragments = args.fragments submit = args.submit VERBOSE = args.verbose save_to_file = args.save qual_min = args.qualmin PCR = args.PCR 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 not fragments: fragments = ['F'+str(i) for i in xrange(1, 7)] if VERBOSE >= 3: print 'fragments', fragments for fragment in fragments: inses = []
default=1, help='Analyze only reads from this PCR (1 or 2)') args = parser.parse_args() pnames = args.patients samplenames = args.samples fragments = args.fragments VERBOSE = args.verbose maxreads = args.maxreads use_tests = args.tests submit = args.submit save_to_file = args.save qual_min = args.qualmin PCR = args.PCR 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 not fragments: fragments = ['F' + str(i) for i in xrange(1, 7)] if VERBOSE >= 3: print 'fragments', fragments if submit: for fragment in fragments:
# Modules 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
fragment = 'F1' VERBOSE = 2 username = os.path.split(os.getenv('HOME'))[-1] foldername = get_figure_folder(username, 'first') fn_data = foldername+'data/' mkdirs(fn_data) fn_data = fn_data + 'minor_alleles_example.pickle' if not os.path.isfile(fn_data) or params.redo: samplename = 'NL4-3' sample = lss(samplename) counts = sample.get_allele_counts(fragment, merge_read_types=True) data = compress_data(counts, samplename, fragment) samplename = '27134' sample = lssp(samplename) counts = sample.get_allele_counts(fragment, merge_read_types=True) data = compress_data(counts, samplename, fragment, data=data) store_data(data, fn_data) else: data = load_data(fn_data) plot_minor_allele_example(data, VERBOSE=VERBOSE, fig_filename=foldername+'freq_minor_alleles_example', )
fragment = 'F1' VERBOSE = 2 username = os.path.split(os.getenv('HOME'))[-1] foldername = get_figure_folder(username, 'first') fn_data = foldername + 'data/' mkdirs(fn_data) fn_data = fn_data + 'minor_alleles_example.pickle' if not os.path.isfile(fn_data) or params.redo: samplename = 'NL4-3' sample = lss(samplename) counts = sample.get_allele_counts(fragment, merge_read_types=True) data = compress_data(counts, samplename, fragment) samplename = '27134' sample = lssp(samplename) counts = sample.get_allele_counts(fragment, merge_read_types=True) data = compress_data(counts, samplename, fragment, data=data) store_data(data, fn_data) else: data = load_data(fn_data) plot_minor_allele_example( data, VERBOSE=VERBOSE, fig_filename=foldername + 'freq_minor_alleles_example', )