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',
)
