def main(args):
mincov, args = grace.get_option_value(args, '--mincov', int, 1)
maxdiff, args = grace.get_option_value(args, '--maxdiff', int, 16)
minsize, args = grace.get_option_value(args, '--minsize', int, 200)
what, args = grace.get_option_value(args, '--what', as_core_or_unique, 'core')
is_core = (what == 'core')
grace.expect_no_further_options(args)
if len(args) < 2:
print >> sys.stderr, HELP
raise grace.Help_shown()
output_dir, working_dirs = args[0], args[1:]
assert not path.exists(path.join(output_dir, 'reference.fa')), \
'Output directory not given'
if not path.exists(output_dir):
os.mkdir(output_dir)
for name, seq in io.read_sequences(path.join(working_dirs[0],'reference.fa')):
print name
friendly_name = grace.filesystem_friendly_name(name)
good = [ True ] * len(seq)
for working_dir in working_dirs:
if is_core:
suffix = '-depth.userplot'
else:
suffix = '-ambiguous-depth.userplot'
data = trivia.read_unstranded_userplot(
os.path.join(working_dir, friendly_name+suffix)
)
assert len(seq) == len(data)
for i in xrange(len(seq)):
if good[i]:
if is_core:
good[i] = data[i] >= mincov
else:
good[i] = data[i] < mincov
#Close holes
start = -maxdiff-1
n_holes = 0
for i in xrange(len(seq)):
if good[i]:
if 0 < i-start <= maxdiff:
for j in xrange(start,i): good[j] = True
n_holes += 1
start = i+1
print 'Closed', grace.pretty_number(n_holes), 'holes'
f = open(path.join(output_dir, '%s-%s.fa' % (friendly_name,what)), 'wb')
io.write_fasta(f, name,
''.join([ (seq[i] if good[i] else 'N')
for i in xrange(len(seq)) ])
)
f.close()
f = open(path.join(output_dir, '%s-%s_masked.fa' % (friendly_name,what)), 'wb')
io.write_fasta(f, name,
''.join([ (seq[i] if good[i] else seq[i].lower())
for i in xrange(len(seq)) ])
)
f.close()
f_good = open(path.join(output_dir, '%s-%s_parts.fa' % (friendly_name,what)), 'wb')
f_nongood = open(path.join(output_dir, '%s-non%s_parts.fa' % (friendly_name,what)), 'wb')
start = 0
n_good = [0]
n_good_bases = [0]
def emit(i):
if i-start < minsize: return
if good[start]:
n_good[0] += 1
n_good_bases[0] += i-start
io.write_fasta(
f_good if good[start] else f_nongood,
'%s:%d..%d' % (name, start+1,i),
seq[start:i]
)
for i in xrange(1,len(seq)):
if good[i] != good[start]:
emit(i)
start = i
emit(len(seq))
f_nongood.close()
f_good.close()
print grace.pretty_number(sum(good)), 'bases are '+what+', of', grace.pretty_number(len(seq)), 'in reference sequence'
print grace.pretty_number(n_good[0]), 'parts at least', grace.pretty_number(minsize), 'bases long with', grace.pretty_number(n_good_bases[0]), 'total bases'
print
def run(self):
#mincov, args = grace.get_option_value(args, '--mincov', int, 1)
#maxdiff, args = grace.get_option_value(args, '--maxdiff', int, 16)
#minsize, args = grace.get_option_value(args, '--minsize', int, 200)
#what, args = grace.get_option_value(args, '--what', as_core_or_unique, 'core')
#is_core = (what == 'core')
#
#grace.expect_no_further_options(args)
#
#if len(args) < 2:
# print >> sys.stderr, HELP
# raise grace.Help_shown()
#
#output_dir, working_dirs = args[0], args[1:]
#
##assert not path.exists(path.join(output_dir, 'reference.fa')), \
#assert not path.exists(path.join(output_dir, 'parameters')), \
# 'Output directory not given'
#
#if not path.exists(output_dir):
# os.mkdir(output_dir)
assert self.what in (
'core',
'unique'), 'Expected --what to be either "core" or "unique".'
is_core = (self.what == 'core')
workspace = self.get_workspace()
for name, seq in io.read_sequences(
working_directory.Working(self.working_dirs[0]).get_reference(
).reference_fasta_filename()):
self.log.log(name + '\n')
friendly_name = grace.filesystem_friendly_name(name)
good = [True] * len(seq)
for working_dir in self.working_dirs:
if is_core:
suffix = '-depth.userplot'
else:
suffix = '-ambiguous-depth.userplot'
data = trivia.read_unstranded_userplot(
os.path.join(working_dir, friendly_name + suffix))
assert len(seq) == len(data)
for i in xrange(len(seq)):
if good[i]:
if is_core:
good[i] = data[i] >= self.mincov
else:
good[i] = data[i] < self.mincov
#Close holes
start = -self.maxdiff - 1
n_holes = 0
for i in xrange(len(seq)):
if good[i]:
if 0 < i - start <= self.maxdiff:
for j in xrange(start, i):
good[j] = True
n_holes += 1
start = i + 1
self.log.log('Closed ' + grace.pretty_number(n_holes) + ' holes\n')
f = open(workspace / ('%s-%s.fa' % (friendly_name, self.what)),
'wb')
io.write_fasta(
f, name, ''.join([(seq[i] if good[i] else 'N')
for i in xrange(len(seq))]))
f.close()
f = open(
workspace / ('%s-%s_masked.fa' % (friendly_name, self.what)),
'wb')
io.write_fasta(
f, name, ''.join([(seq[i] if good[i] else seq[i].lower())
for i in xrange(len(seq))]))
f.close()
f_good = open(
workspace / ('%s-%s_parts.fa' % (friendly_name, self.what)),
'wb')
f_nongood = open(
workspace / ('%s-non%s_parts.fa' % (friendly_name, self.what)),
'wb')
start = 0
n_good = [0]
n_good_bases = [0]
def emit(i):
if i - start < self.minsize: return
if good[start]:
n_good[0] += 1
n_good_bases[0] += i - start
io.write_fasta(f_good if good[start] else f_nongood,
'%s:%d..%d' % (name, start + 1, i),
seq[start:i])
for i in xrange(1, len(seq)):
if good[i] != good[start]:
emit(i)
start = i
emit(len(seq))
f_nongood.close()
f_good.close()
self.log.log(
grace.pretty_number(sum(good)) + ' bases are ' + self.what +
', of ' + grace.pretty_number(len(seq)) +
' in reference sequence\n')
self.log.log(
grace.pretty_number(n_good[0]) + ' parts at least ' +
grace.pretty_number(self.minsize) + ' bases long with ' +
grace.pretty_number(n_good_bases[0]) + ' total bases\n')
self.log.log('\n')
def run(self):
#mincov, args = grace.get_option_value(args, '--mincov', int, 1)
#maxdiff, args = grace.get_option_value(args, '--maxdiff', int, 16)
#minsize, args = grace.get_option_value(args, '--minsize', int, 200)
#what, args = grace.get_option_value(args, '--what', as_core_or_unique, 'core')
#is_core = (what == 'core')
#
#grace.expect_no_further_options(args)
#
#if len(args) < 2:
# print >> sys.stderr, HELP
# raise grace.Help_shown()
#
#output_dir, working_dirs = args[0], args[1:]
#
##assert not path.exists(path.join(output_dir, 'reference.fa')), \
#assert not path.exists(path.join(output_dir, 'parameters')), \
# 'Output directory not given'
#
#if not path.exists(output_dir):
# os.mkdir(output_dir)
assert self.what in ('core','unique'), 'Expected --what to be either "core" or "unique".'
is_core = (self.what == 'core')
workspace = self.get_workspace()
for name, seq in io.read_sequences(working_directory.Working(self.working_dirs[0]).get_reference().reference_fasta_filename()):
self.log.log(name + '\n')
friendly_name = grace.filesystem_friendly_name(name)
good = [ True ] * len(seq)
for working_dir in self.working_dirs:
if is_core:
suffix = '-depth.userplot'
else:
suffix = '-ambiguous-depth.userplot'
data = trivia.read_unstranded_userplot(
os.path.join(working_dir, friendly_name+suffix)
)
assert len(seq) == len(data)
for i in xrange(len(seq)):
if good[i]:
if is_core:
good[i] = data[i] >= self.mincov
else:
good[i] = data[i] < self.mincov
#Close holes
start = -self.maxdiff-1
n_holes = 0
for i in xrange(len(seq)):
if good[i]:
if 0 < i-start <= self.maxdiff:
for j in xrange(start,i): good[j] = True
n_holes += 1
start = i+1
self.log.log('Closed '+grace.pretty_number(n_holes)+' holes\n')
f = open( workspace/('%s-%s.fa' % (friendly_name,self.what)), 'wb')
io.write_fasta(f, name,
''.join([ (seq[i] if good[i] else 'N')
for i in xrange(len(seq)) ])
)
f.close()
f = open( workspace/('%s-%s_masked.fa' % (friendly_name,self.what)), 'wb')
io.write_fasta(f, name,
''.join([ (seq[i] if good[i] else seq[i].lower())
for i in xrange(len(seq)) ])
)
f.close()
f_good = open( workspace/('%s-%s_parts.fa' % (friendly_name,self.what)), 'wb')
f_nongood = open( workspace/('%s-non%s_parts.fa' % (friendly_name,self.what)), 'wb')
start = 0
n_good = [0]
n_good_bases = [0]
def emit(i):
if i-start < self.minsize: return
if good[start]:
n_good[0] += 1
n_good_bases[0] += i-start
io.write_fasta(
f_good if good[start] else f_nongood,
'%s:%d..%d' % (name, start+1,i),
seq[start:i]
)
for i in xrange(1,len(seq)):
if good[i] != good[start]:
emit(i)
start = i
emit(len(seq))
f_nongood.close()
f_good.close()
self.log.log(grace.pretty_number(sum(good))+' bases are '+self.what+', of '+grace.pretty_number(len(seq))+' in reference sequence\n')
self.log.log(grace.pretty_number(n_good[0])+' parts at least '+grace.pretty_number(self.minsize)+' bases long with '+grace.pretty_number(n_good_bases[0])+' total bases\n')
self.log.log('\n')
def main(args):
mincov, args = grace.get_option_value(args, '--mincov', int, 1)
maxdiff, args = grace.get_option_value(args, '--maxdiff', int, 16)
minsize, args = grace.get_option_value(args, '--minsize', int, 200)
what, args = grace.get_option_value(args, '--what', as_core_or_unique,
'core')
is_core = (what == 'core')
grace.expect_no_further_options(args)
if len(args) < 2:
print >> sys.stderr, HELP
raise grace.Help_shown()
output_dir, working_dirs = args[0], args[1:]
assert not path.exists(path.join(output_dir, 'reference.fa')), \
'Output directory not given'
if not path.exists(output_dir):
os.mkdir(output_dir)
for name, seq in io.read_sequences(
path.join(working_dirs[0], 'reference.fa')):
print name
friendly_name = grace.filesystem_friendly_name(name)
good = [True] * len(seq)
for working_dir in working_dirs:
if is_core:
suffix = '-depth.userplot'
else:
suffix = '-ambiguous-depth.userplot'
data = trivia.read_unstranded_userplot(
os.path.join(working_dir, friendly_name + suffix))
assert len(seq) == len(data)
for i in xrange(len(seq)):
if good[i]:
if is_core:
good[i] = data[i] >= mincov
else:
good[i] = data[i] < mincov
#Close holes
start = -maxdiff - 1
n_holes = 0
for i in xrange(len(seq)):
if good[i]:
if 0 < i - start <= maxdiff:
for j in xrange(start, i):
good[j] = True
n_holes += 1
start = i + 1
print 'Closed', grace.pretty_number(n_holes), 'holes'
f = open(path.join(output_dir, '%s-%s.fa' % (friendly_name, what)),
'wb')
io.write_fasta(
f, name,
''.join([(seq[i] if good[i] else 'N') for i in xrange(len(seq))]))
f.close()
f = open(
path.join(output_dir, '%s-%s_masked.fa' % (friendly_name, what)),
'wb')
io.write_fasta(
f, name, ''.join([(seq[i] if good[i] else seq[i].lower())
for i in xrange(len(seq))]))
f.close()
f_good = open(
path.join(output_dir, '%s-%s_parts.fa' % (friendly_name, what)),
'wb')
f_nongood = open(
path.join(output_dir, '%s-non%s_parts.fa' % (friendly_name, what)),
'wb')
start = 0
n_good = [0]
n_good_bases = [0]
def emit(i):
if i - start < minsize: return
if good[start]:
n_good[0] += 1
n_good_bases[0] += i - start
io.write_fasta(f_good if good[start] else f_nongood,
'%s:%d..%d' % (name, start + 1, i), seq[start:i])
for i in xrange(1, len(seq)):
if good[i] != good[start]:
emit(i)
start = i
emit(len(seq))
f_nongood.close()
f_good.close()
print grace.pretty_number(
sum(good)), 'bases are ' + what + ', of', grace.pretty_number(
len(seq)), 'in reference sequence'
print grace.pretty_number(
n_good[0]), 'parts at least', grace.pretty_number(
minsize), 'bases long with', grace.pretty_number(
n_good_bases[0]), 'total bases'
print
