def fixpairs(args):
"""
%prog fixpairs pairsfile sep sd
Fix pairs library stats. This is sometime useful to modify library stats,
for example, the separation between paired reads after importing the data.
"""
p = OptionParser(fixpairs.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
pairsfile, sep, sd = args
newpairsfile = pairsfile.rsplit(".", 1)[0] + ".new.pairs"
sep = int(sep)
sd = int(sd)
p = PairsFile(pairsfile)
p.fixLibraryStats(sep, sd)
p.write(newpairsfile)
def fixpairs(args):
"""
%prog fixpairs pairsfile sep sd
Fix pairs library stats. This is sometime useful to modify library stats,
for example, the separation between paired reads after importing the data.
"""
p = OptionParser(fixpairs.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
pairsfile, sep, sd = args
newpairsfile = pairsfile.rsplit(".", 1)[0] + ".new.pairs"
sep = int(sep)
sd = int(sd)
p = PairsFile(pairsfile)
p.fixLibraryStats(sep, sd)
p.write(newpairsfile)
def main():
parser = OptionParser()
parser.add_option('--restore', dest='restore', action='store_true',
help='restore your simulation files and cache the current sampling results',
default=False)
parser.add_option('--radii', dest='radii', default='0.0,4.0,8.0',
action='store', type='string',
help='the displacement radii to sample, separated with commas and no spaces, e.g., --radius=0.0,4.0,8.0')
parser.add_option('--magnitudes', dest='magnitudes', default='0.1,0.2,0.4',
action='store', type='string',
help='the displacement magnitudes to sample, separated with commas and no spaces, e.g., --magnitude=0.1,0.2,0.4')
parser.add_option('--searches', dest='searches', default=50,
action='store', type=int,
help='the number of searches to perform per sample')
(options, args) = parser.parse_args()
if options.restore:
restore()
return
if not os.path.exists('original'):
if not os.path.exists('config.ini') or not os.path.exists('reactant.con'):
print('This does not appear to be an eon project directory. Either config.ini or reactant.con or both were not found. Aborting.')
sys.exit()
rads = [float(r) for r in options.radii.split(',')]
mags = [float(m) for m in options.magnitudes.split(',')]
searches = int(options.searches)
initialize(rads, mags, searches)
print 'Initialized new akmc displacement sampling with radii %s, magnitudes %s, and performing %s searches per sample.' % (options.radii, options.magnitudes, options.searches)
return
radi, rads, magi, mags, searches = read_metadata()
# Make sure we're not finished sampling before continuing.
if magi >= len(mags):
print_table()
print 'Sampling complete.'
sys.exit(1)
return
rad = rads[radi]
mag = mags[magi]
if not os.path.exists('config.ini') or not os.path.exists('reactant.con'):
# Initialize the next sample.
for thing in glob.glob('original/*'):
shutil.copy(thing, '.')
print 'Sampling with radius %f and magnitude %f' % (rad, mag)
parser = ConfigParser.SafeConfigParser()
parser.read('config.ini')
parser.set('Saddle Search', 'displace_radius', str(rad))
parser.set('Saddle Search', 'displace_magnitude', str(mag))
parser.set('AKMC', 'confidence', '1.1')
fob = open('config.ini', 'w')
parser.write(fob)
fob.close()
# Register any available results.
throwaway = commands.getoutput('eon -n')
# Check the number of completed searches.
n_completed_searches = 0
if os.path.exists('states/0/search_results.txt'):
n_completed_searches = len(open('states/0/search_results.txt').readlines()) - 2
print '%d searches have been completed for this sample.' % n_completed_searches
if n_completed_searches >= searches:
print 'Sample finished.'
store_sample('samples/sample-%f-%f' % (rad, mag))
# Increment the sample parameters
inc_attempt = inc_params()
return
print 'Executing eon...'
throwaway = commands.getoutput('eon')
print 'Done.'
raw_text_split = raw_text.splitlines()
insert_counter = 0
for (i,rt) in zip(range(0,len(raw_text_split)),raw_text_split):
if rt.find("video::") >= 0:
video_text = rt.split(" ")
for (j,vt) in zip(range(0,len(video_text)),video_text):
if vt.find("video::") >= 0:
tmp_text = os.path.basename(video_text[j + 1])
raw_text_split.insert(i + 1 + insert_counter, " :url: http://jenkins.jsk.imi.i.u-tokyo.ac.jp:8080/job/agentsystem-test/lastSuccessfulBuild/artifact/%s-example/_images/%s"%(args[0],tmp_text))
insert_counter = insert_counter + 1
raw_text = "\n".join(raw_text_split)
sphinxdoc += raw_text+'\n\n'
parser.getroot().remove(tag)
tf = tempfile.TemporaryFile()
parser.write(tf)
tf.seek(0)
sxml = tf.read()
sphinxdoc += """Contents
########
.. code-block:: xml
%s
"""%re.sub('\\n','\n ',sxml)
try:
os.mkdir(os.path.join(pkgdir,options.output_dir))
except OSError:
pass
def main():
parser = OptionParser()
parser.add_option(
'--restore',
dest='restore',
action='store_true',
help=
'restore your simulation files and cache the current sampling results',
default=False)
parser.add_option(
'--radii',
dest='radii',
default='0.0,4.0,8.0',
action='store',
type='string',
help=
'the displacement radii to sample, separated with commas and no spaces, e.g., --radius=0.0,4.0,8.0'
)
parser.add_option(
'--magnitudes',
dest='magnitudes',
default='0.1,0.2,0.4',
action='store',
type='string',
help=
'the displacement magnitudes to sample, separated with commas and no spaces, e.g., --magnitude=0.1,0.2,0.4'
)
parser.add_option('--searches',
dest='searches',
default=50,
action='store',
type=int,
help='the number of searches to perform per sample')
(options, args) = parser.parse_args()
if options.restore:
restore()
return
if not os.path.exists('original'):
if not os.path.exists('config.ini') or not os.path.exists(
'reactant.con'):
print(
'This does not appear to be an eon project directory. Either config.ini or reactant.con or both were not found. Aborting.'
)
sys.exit()
rads = [float(r) for r in options.radii.split(',')]
mags = [float(m) for m in options.magnitudes.split(',')]
searches = int(options.searches)
initialize(rads, mags, searches)
print 'Initialized new akmc displacement sampling with radii %s, magnitudes %s, and performing %s searches per sample.' % (
options.radii, options.magnitudes, options.searches)
return
radi, rads, magi, mags, searches = read_metadata()
# Make sure we're not finished sampling before continuing.
if magi >= len(mags):
print_table()
print 'Sampling complete.'
sys.exit(1)
return
rad = rads[radi]
mag = mags[magi]
if not os.path.exists('config.ini') or not os.path.exists('reactant.con'):
# Initialize the next sample.
for thing in glob.glob('original/*'):
shutil.copy(thing, '.')
print 'Sampling with radius %f and magnitude %f' % (rad, mag)
parser = ConfigParser.SafeConfigParser()
parser.read('config.ini')
parser.set('Saddle Search', 'displace_radius', str(rad))
parser.set('Saddle Search', 'displace_magnitude', str(mag))
parser.set('AKMC', 'confidence', '1.1')
fob = open('config.ini', 'w')
parser.write(fob)
fob.close()
# Register any available results.
throwaway = commands.getoutput('eon -n')
# Check the number of completed searches.
n_completed_searches = 0
if os.path.exists('states/0/search_results.txt'):
n_completed_searches = len(
open('states/0/search_results.txt').readlines()) - 2
print '%d searches have been completed for this sample.' % n_completed_searches
if n_completed_searches >= searches:
print 'Sample finished.'
store_sample('samples/sample-%f-%f' % (rad, mag))
# Increment the sample parameters
inc_attempt = inc_params()
return
print 'Executing eon...'
throwaway = commands.getoutput('eon')
print 'Done.'
video_text = rt.split(" ")
for (j, vt) in zip(range(0, len(video_text)), video_text):
if vt.find("video::") >= 0:
tmp_text = os.path.basename(video_text[j + 1])
raw_text_split.insert(
i + 1 + insert_counter,
" :url: http://jenkins.jsk.imi.i.u-tokyo.ac.jp:8080/job/agentsystem-test/lastSuccessfulBuild/artifact/%s-example/_images/%s"
% (args[0], tmp_text),
)
insert_counter = insert_counter + 1
raw_text = "\n".join(raw_text_split)
sphinxdoc += raw_text + "\n\n"
parser.getroot().remove(tag)
tf = tempfile.TemporaryFile()
parser.write(tf)
tf.seek(0)
sxml = tf.read()
sphinxdoc += """Contents
########
.. code-block:: xml
%s
""" % re.sub(
"\\n", "\n ", sxml
)
try:
os.mkdir(os.path.join(pkgdir, options.output_dir))
