def main():
""" Only called if run not interactively
"""
import optparse
import shutil
import glob
import dec
# parse command line
optparser = optparse.OptionParser()
optparser.add_option("-b", "--bam", help="sorted bam format alignment file.",
default="", type="string", dest="b")
optparser.add_option("-f", "--fasta", help="reference genome in fasta format.",
default="", type="string", dest="f")
optparser.add_option("-a", "--alpha", help="alpha in dpm sampling <0.01>", default=0.01,
type="float", dest="a")
optparser.add_option("-w", "--windowsize", help="window size <201>", default=201,
type="int", dest="w")
optparser.add_option("-s", "--winshifts", help="number of window shifts <3>", default=3,
type="int", dest="s") # window shiftings, such that each base is covered up to win_shifts times
optparser.add_option("-i", "--sigma", help="value of sigma to use when calling SNVs", default = 0.01,
type="float", dest="i")
optparser.add_option("-x", "--maxcov", help="approximate maximum coverage allowed", default=10000,
type="int", dest="x")
optparser.add_option("-r", "--region", help="region in format 'chr:start-stop', eg 'ch3:1000-3000'", default='',
type="string", dest="r")
optparser.add_option("-k","--keep_files",help="keep intermediate files (Gibbs sampling)", default=False,
action="store_true", dest="k")
(options, args) = optparser.parse_args()
sholog.info(' '.join(sys.argv))
in_bam = options.b
in_fasta = options.f
keep_all_files = options.k
step = options.w
win_shifts = options.s
max_coverage = options.x
sigma = options.i
alpha = options.a
region = options.r
in_stem=os.path.split(in_bam)[1].split('.')[0]
if not os.path.exists('snv/SNV.txt'):
# run dec.py
sholog.debug('running dec.py')
dec.main(in_bam,in_fasta, step, win_shifts, max_coverage, sigma, region, keep_all_files, alpha)
# copy file and run fas2reads
shutil.move('%s.cor.fas' % in_stem, '%s_cor.fas' % in_stem)
sholog.debug('running fas2reads')
retcode = run_f2r('%s_cor.fas' % in_stem)
if retcode is not 0:
sholog.error('fas2reads did not return 0')
sys.exit()
# run contain
retcode = run_contain('%s_cor' % in_stem)
if retcode is not 0:
sys.exit()
# run mm.py (this might become a module)
retcode = run_mm('%s_cor' % in_stem)
if retcode is not 0:
sys.exit()
# run EM freqEst
retcode = run_freqEst('%s_cor' % in_stem)
if retcode is not 0:
sys.exit()
# run snv.py
sholog.debug('running snv.py')
retcode = run_snv(in_fasta, in_bam, sigma, step/win_shifts)
if retcode is not 0:
sholog.error('snv calling failed')
# tidy snvs
try:
os.mkdir('snv')
except:
pass
for snv_file in glob.glob('./SNV*'):
shutil.move(snv_file, 'snv/')
def main():
""" Only called if run not interactively
"""
import optparse
import shutil
import dec
import s2f
# parse command line
optparser = optparse.OptionParser()
optparser.add_option("-f",
"--readsfile",
help="file with reads <.fas or .far format>",
default="",
type="string",
dest="f")
optparser.add_option("-j",
"--iterations",
help="iterations in dpm sampling <1000>",
default=1000,
type="int",
dest="j")
optparser.add_option("-a",
"--alpha",
help="alpha in dpm sampling <0.01>",
default=0.01,
type="float",
dest="a")
optparser.add_option("-w",
"--windowsize",
help="window size in <201>",
default=201,
type="int",
dest="w")
optparser.add_option(
"-t",
"--threshold",
help="if similarity is less, throw reads away... <default=0.7>",
type="float",
dest="threshold",
default=0.7)
optparser.add_option("-n",
"--no_pad_insert",
help="do not insert padding gaps <default=insert>",
action="store_false",
default=True,
dest="pad")
optparser.add_option("-r", "--ref", type="string", default="", dest="ref")
optparser.add_option(
"-o",
"--output",
help="output suffix for alignment: must be '.far' or none for stdout",
type="string",
dest="o")
optparser.add_option(
"-s",
"--winshifts",
help="number of window shifts <3>",
default=3,
type="int",
dest="s"
) # window shiftings, such that each base is covered up to win_shifts times
optparser.add_option(
"-k",
"--keep_files",
help="keep intermediate files (Gibbs sampling) <default=False>",
default=False,
action="store_true",
dest="k")
(options, args) = optparser.parse_args()
sholog.info(' '.join(sys.argv))
in_file = options.f
keep_all_files = options.k
step = options.w
win_shifts = options.s
fas_reads = options.f
iters = options.j
alpha = options.a
try:
[in_stem, in_format] = [
os.path.split(in_file)[1].split('.')[0],
os.path.split(in_file)[1].split('.')[1]
]
except IndexError:
print 'The input file must be filestem.format'
sholog.error('The input file must be filestem.format')
sys.exit()
if in_format != 'far':
ref_file = options.ref
out_file = os.path.join(os.getcwd(), in_stem + '.far')
thresh = options.threshold
pad_insert = options.pad
sholog.debug('running s2f.py')
s2f.main(ref_file, in_file, out_file, thresh, pad_insert,
keep_all_files)
# run dec.py
sholog.debug('running dec.py')
dec.main(out_file, step, win_shifts, keep_all_files, iters, alpha)
else:
# run dec.py
sholog.debug('running dec.py')
dec.main(in_file, step, win_shifts, keep_all_files, iters, alpha)
# copy file and run fas2reads
shutil.move('%s.cor.fas' % in_stem, '%s_cor.fas' % in_stem)
sholog.debug('running fas2reads')
retcode = run_f2r('%s_cor.fas' % in_stem)
if retcode is not 0:
sholog.error('fas2reads did not return 0')
sys.exit()
# run contain
retcode = run_contain('%s_cor' % in_stem)
if retcode is not 0:
sys.exit()
# run mm.py (this might become a module)
retcode = run_mm('%s_cor' % in_stem)
if retcode is not 0:
sys.exit()
# run EM freqEst
retcode = run_freqEst('%s_cor' % in_stem)
if retcode is not 0:
sys.exit()
(options, args) = optparser.parse_args()
del(args)
sholog.info(' '.join(sys.argv))
in_stem = '.'.join(os.path.split(options.b)[1].split('.')[:-1])
if options.p:
# amplicon_mode, run only diri_sampler and snv.py
amplian.main(in_bam=options.b, in_fasta=options.f,
max_coverage=options.x, alpha=options.a)
if not os.path.exists('snv/SNV.txt'):
# 1. run dec.py
sholog.debug('running dec.py')
dec.main(in_bam=options.b, in_fasta=options.f, win_length=options.w,
win_shifts=options.s, max_coverage=options.x,
region=options.r, keep_files=options.k, alpha=options.a)
# 2. copy file and run fas2read to convert from fasta
shutil.move('%s.cor.fas' % in_stem, '%s_cor.fas' % in_stem)
sholog.debug('running fas2reads')
my_prog = 'perl -I %s %s' % (dn + '/perllib',
os.path.join(dn, 'fas2read.pl'))
my_arg = " -f %s_cor.fas" % in_stem
assert os.path.isfile("%s_cor.fas" % in_stem), \
'File %s_cor.fas not found' % in_stem
retcode_f2r = run_child(my_prog, my_arg)
if retcode_f2r:
sholog.error('fas2read did not return 0')
sys.exit('Something went wrong in fas2read')
else:
in_stem = '.'.join(os.path.split(options.b)[1].split('.')[:-1])
if options.p:
# amplicon_mode, run only diri_sampler and snv.py
amplian.main(in_bam=options.b,
in_fasta=options.f,
max_coverage=options.x,
alpha=options.a)
if not os.path.exists('snv/SNV.txt'):
# 1. run dec.py
sholog.debug('running dec.py')
dec.main(in_bam=options.b,
in_fasta=options.f,
win_length=options.w,
win_shifts=options.s,
max_coverage=options.x,
region=options.r,
keep_files=options.k,
alpha=options.a)
# 2. copy file and run fas2read to convert from fasta
shutil.move('%s.cor.fas' % in_stem, '%s_cor.fas' % in_stem)
sholog.debug('running fas2reads')
my_prog = 'perl -I %s %s' % (dn + '/perllib',
os.path.join(dn, 'fas2read.pl'))
my_arg = " -f %s_cor.fas" % in_stem
assert os.path.isfile("%s_cor.fas" % in_stem), \
'File %s_cor.fas not found' % in_stem
retcode_f2r = run_child(my_prog, my_arg)
if retcode_f2r:
sholog.error('fas2read did not return 0')
def install_dependencies():
os.system('pip install pillow')
os.system('pip3 install pillow')
return
def raise_err():
help_content = '''
Unknown argument: "{}"
Type "python {} -h" to see the usage.
'''.format(sys.argv[1], sys.argv[0])
print(help_content)
return
if __name__ == '__main__':
if len(args) == 1 or (len(args) == 2 and args[1] == '-h'):
layout_help()
elif len(args) == 2 and args[1] == '-i':
install_dependencies()
elif len(args) == 3 and args[1] in rds:
import enc
import dec
if args[1] == rds[0]:
enc.main(args[2])
else:
dec.main(args[2])
else:
raise_err()
def main():
start_time = time.time()
latitude = 45.0619883 # latitude N
longitude = 7.6602814 # longitude E
elevation = 250 # meters above the sea
df = pd.read_csv('/home/bottaccioli/per_sara/2013.csv',
sep=";",
index_col='Date Time',
decimal=',')
df.index = pd.to_datetime(df.index)
df.index = df.index.tz_localize('Europe/Rome', ambiguous='infer')
models = ['Karatasou']
#models = ['Engerer2','Skartevit2','Skartevit1','Erbs','Reindl']
#models=['Karatasou','Ruiz','Skartevit1','Engerer2','Erbs','Reindl']
for model in models:
print(model)
i = 0
df = dec.main(latitude, longitude, elevation, model, df)
geodf = gpd.read_file("/home/bottaccioli/per_sara/primo/primo.shp",
crs='4326')
geodf = geodf.set_index(['FID'])
radiation = geodf.copy()
rad = geodf.copy()
radiation = radiation.drop(['geometry'], axis=1)
month = {
1: '17',
2: '47',
3: '75',
4: '105',
5: '135',
6: '162',
7: '198',
8: '228',
9: '258',
10: '288',
11: '318',
12: '344'
}
hour = {
4: '04',
5: '05',
6: '06',
7: '07',
8: '08',
9: '09',
10: '10',
11: '11',
12: '12',
13: '13',
14: '14',
15: '15',
16: '16',
17: '17',
18: '18',
19: '19',
20: '20',
21: '21',
22: '22'
}
minute = {0: '00', 15: '25', 30: '50', 45: '75'}
Linke = {
1: 3.5,
2: 4.3,
3: 4,
4: 4.2,
5: 4.6,
6: 4.6,
7: 4.4,
8: 4.5,
9: 4.3,
10: 4,
11: 4.4,
12: 4.4
}
directory = '/home/bottaccioli/raster_crocetta/'
for dfix in df.index:
i = i + 1
print model, str(i) + "of" + str(len(df))
if df.ix[dfix]['zenith'] < 85:
index = dfix
if index.dst().seconds != 0:
if dfix < pd.to_datetime('27/03/2013').tz_localize(
'Europe/Rome'):
index = dfix - pd.DateOffset(hours=1.25)
else:
index = dfix - pd.DateOffset(hours=1.00)
beam = directory + 'beam_' + month[
index.month] + '_' + hour[index.hour] + '.' + minute[
index.minute]
diff = directory + 'diff_' + month[
index.month] + '_' + hour[index.hour] + '.' + minute[
index.minute]
glob, gt = glob_real(beam, diff, df.ix[index, 'k_b'],
df.ix[index, 'k_d'])
stats = point_value(geodf, glob, gt)
radiation[index] = stats.values()
else:
beam = directory + 'beam_' + month[
index.month] + '_' + hour[index.hour] + '.' + minute[
index.minute]
diff = directory + 'diff_' + month[
index.month] + '_' + hour[index.hour] + '.' + minute[
index.minute]
glob, gt = glob_real(beam, diff, df.ix[index, 'k_b'],
df.ix[index, 'k_d'])
stats = point_value(geodf, glob, gt)
if dfix < pd.to_datetime('27/03/2013').tz_localize(
'Europe/Rome'):
radiation[index -
pd.DateOffset(hours=0.25)] = stats.values()
else:
print 'fava'
radiation[index] = stats.values()
glob = None
radiation = radiation.transpose()
print("--- %s seconds ---" % (time.time() - start_time))
radiation = radiation.join(df['T_ex'])
radiation.to_csv('primo_rad.csv')