# commands[:body_start_1] +
# shift(commands[body_start_1:], int(self.x*40),int(self.y*40))
# )
start = body_start + int(self.percent/100.0*(body_end-body_start))
while True:
if start == body_start: break
if commands[start].startswith('Z'):
pos = map(int,item[1:].split(','))
if pos[2] >= 2420:
break
start -= 1
print 'commands ', len(commands)
print 'body_start', body_start
print 'start ', start
print 'body_end ', body_end
execute(commands[:body_start], self.port)
execute(shift(commands[body_start:],int(self.x*40),int(self.y*40)),
self.port, start-body_start)
if __name__ == '__main__':
nesoni.run_tool(Send)
# whistle_jaw_space = self.working.bore.copy()
#
# whistle_jaw.rotate(1,0,0, 90)
# whistle_jaw_space.rotate(1,0,0, 90)
#
# offset = -whistle_jaw.extent().zmin
# whistle_jaw.move(0,0,offset)
# whistle_jaw_space.move(0,0,offset)
#
# self.save(whistle_jaw, 'jaw')
# jaw_packable = [ pack.Packable([ whistle_jaw, whistle_jaw_space ], 90, self.mill_diameter) ]
#
# self.working.bore.add(whistle_jaw_clipper)
# self.working.outside.remove(whistle_jaw_clipper)
#
# pack.cut_and_pack(
# self.working.outside, self.working.bore,
# upper_segments, lower_segments,
# xsize=self.mill_length,
# ysize=self.mill_width,
# zsize=self.mill_thickness,
# bit_diameter=self.mill_diameter,
# save=self.save,
#
# extra_packables=[ jaw_packable ],
# )
if __name__ == '__main__':
nesoni.run_tool(Make_whistle)
# see also max_hole_spacing
# balance
# Very simple fingering system
initial_length = demakein.design.wavelength('D4') * 0.4
fingerings = [
('D4', [1, 1, 1, 1, 1, 1]),
('E4', [0, 1, 1, 1, 1, 1]),
('F#4', [0, 0, 1, 1, 1, 1]),
('G4', [0, 0, 0, 1, 1, 1]),
('A4', [0, 0, 0, 0, 1, 1]),
('B4', [0, 0, 0, 0, 0, 1]),
('C#5', [0, 0, 0, 0, 0, 0]),
('D5', [1, 1, 1, 1, 1, 1]),
('E5', [0, 1, 1, 1, 1, 1]),
('F#5', [0, 0, 1, 1, 1, 1]),
('G5', [0, 0, 0, 1, 1, 1]),
('A5', [0, 0, 0, 0, 1, 1]),
('B5', [0, 0, 0, 0, 0, 1]),
('C#6', [0, 0, 0, 0, 0, 0]),
]
if __name__ == '__main__':
nesoni.run_tool(Design_simple_shawm)
# or
#nesoni.run_toolbox([
# Design_simple_shawm,
# #...
# ])
import nesoni
class Tentacle(make.Make):
def run(self):
path = geom.path(
geom.XYZ(0.0, 0.0, 0.0),
geom.XYZ(0.0, 1.0, 0.0),
geom.XYZ(1.0, 0.0, 0.0),
geom.XYZ(0.0, 0.0, 100.0),
geom.XYZ(0.0, 0.0, 1.0),
geom.XYZ(1.0, 0.0, 0.0),
)
#geom.plot(path.position)
print path.get_length()
print path.find(90.0)
print path.get_point(90.0)
l = path.get_length()
prof = profile.make_profile([(0.0, 20.0), (l, 0.0)])
tentacle = shape.path_extrusion(path, shape.circle, prof)
self.save(tentacle, 'tentacle')
if __name__ == '__main__':
nesoni.run_tool(Tentacle)
#min_hole_spacing = [ 5,5,5,20,20 ]
# see also max_hole_spacing
# balance
# Very simple fingering system
initial_length = demakein.design.wavelength('D4') * 0.4
fingerings = [
('D4', [1,1,1,1,1,1]),
('E4', [0,1,1,1,1,1]),
('F#4', [0,0,1,1,1,1]),
('G4', [0,0,0,1,1,1]),
('A4', [0,0,0,0,1,1]),
('B4', [0,0,0,0,0,1]),
('C#5', [0,0,0,0,0,0]),
('D5', [1,1,1,1,1,1]),
('E5', [0,1,1,1,1,1]),
('F#5', [0,0,1,1,1,1]),
('G5', [0,0,0,1,1,1]),
('A5', [0,0,0,0,1,1]),
('B5', [0,0,0,0,0,1]),
('C#6', [0,0,0,0,0,0]),
]
if __name__ == '__main__':
nesoni.run_tool(Design_simple_shawm)
# or
#nesoni.run_toolbox([
# Design_simple_shawm,
# #...
# ])
def _find_spans(self, depth):
result = [ ]
i = 0
while i < len(depth):
j = i+1
while j < len(depth) and depth[j] == depth[i]:
j += 1
lap = max(0,self.lap-(j-i)+1)
lap_back = lap//2
lap_forward = lap-lap_back
if depth[i] >= self.min_depth:
for k in xrange(max(0,i-self.radius),min(len(depth),j+self.radius)):
if depth[k] > depth[i] or (depth[k] == depth[i] and k < i): #Resolve ties arbitrarily
break
else:
result.append((i-lap_back,j+lap_forward))
i = j
return result
if __name__ == '__main__':
nesoni.run_tool(Peaks)
class Reedpipe(demakein.design.Instrument_designer):
closed_top = True
inner_diameters = [ 6.0, 6.0 ]
outer_diameters = [ 10.0, 10.0 ]
min_hole_diameters = [ 3.0 ]*7
max_hole_diameters = [ 5.0 ]*7
#min_hole_spacing = [ 15.0 ]*6
#and/or
balance = [ 0.07 ]*5
initial_length = demakein.design.wavelength('C4') * 0.25
fingerings = [
('C4', [1,1,1,1,1,1,1]),
('D4', [0,1,1,1,1,1,1]),
('E4', [0,0,1,1,1,1,1]),
('F4', [0,0,0,1,1,1,1]),
('G4', [0,0,0,0,1,1,1]),
('A4', [0,0,0,0,0,1,1]),
('B4', [0,0,0,0,0,0,1]),
('C5', [0,0,0,0,0,1,0]),
]
if __name__ == '__main__':
nesoni.run_tool(Reedpipe)
#commands = (
# commands[:body_start_1] +
# shift(commands[body_start_1:], int(self.x*40),int(self.y*40))
# )
start = body_start + int(self.percent / 100.0 *
(body_end - body_start))
while True:
if start == body_start: break
if commands[start].startswith('Z'):
pos = map(int, commands[start][1:].split(','))
if pos[2] >= 2400:
break
start -= 1
print 'commands ', len(commands)
print 'body_start', body_start
print 'start ', start
print 'body_end ', body_end
execute(commands[:body_start], self.port)
execute(
shift(commands[body_start:], int(self.x * 40), int(self.y * 40),
self.v), self.port, start - body_start)
if __name__ == '__main__':
nesoni.run_tool(Send)
min_hole_diameters = [ 3.0 ]*6
max_hole_diameters = [ 8.0 ]*6
#min_hole_spacing = [ 15.0 ]*5
#and/or
balance = [ 0.05, None, None, 0.05 ]
initial_length = demakein.design.wavelength('D5') * 0.5
fingerings = [
('D5', [1,1,1,1,1,1]),
('E5', [0,1,1,1,1,1]),
('F#5', [0,0,1,1,1,1]),
('G5', [0,0,0,1,1,1]),
('A5', [0,0,0,0,1,1]),
('B5', [0,0,0,0,0,1]),
('C#6', [0,0,0,0,0,0]),
('D6', [1,1,1,1,1,1]),
('E6', [0,1,1,1,1,1]),
('F#6', [0,0,1,1,1,1]),
('G6', [0,0,0,1,1,1]),
('A6', [0,0,0,0,1,1]),
('B6', [0,0,0,0,0,1]),
('C#7', [0,0,0,0,0,0]),
('D8', [1,1,1,1,1,1]),
]
if __name__ == '__main__':
nesoni.run_tool(Flute)
peak = analysis.peaks_asis[candidates[0][1]].copy()
peak.attr['Parent'] = utr.attr['Parent']
peak.attr['Name'] = utr.attr.get('Name','')
peak.attr['Product'] = utr.attr.get('Product','')
called_peaks.append(peak)
called_utr = utr.five_prime().span_with(peak.three_prime())
called_utr.attr['Peak'] = peak.get_id()
called_utrs.append(called_utr)
called_gene = ref.genes[utr.attr['Parent']].five_prime().span_with(peak.three_prime())
called_gene.attr['Peak'] = peak.get_id()
called_genes.append(called_gene)
n_good += 1
print n_good, 'UTR called'
print n_bad, 'no UTR called'
annotation.write_gff3(self.prefix + '-peaks.gff', called_peaks)
annotation.write_gff3(self.prefix + '-utrs.gff', called_utrs)
annotation.write_gff3(self.prefix + '-genes.gff', called_genes)
if __name__ == '__main__':
nesoni.run_tool(Call_utrs)
for accession in self.accessions:
Fetch_sra(work / 'sra', accession).process_make(stage)
nesoni.Make_reference(
output_dir=work / 'TW20',
filenames=[
work / ('genbank', accession + '.gbk')
for accession in self.genbanks
],
genome=True,
bowtie=True,
ls=True,
snpeff=True,
).make()
analyser = nesoni.Analyse_samples
analyser(work / 'analysis',
work / 'TW20',
samples=[
nesoni.Analyse_sample(
accession,
pairs=[[
work / ('sra', accession + '_1.fastq.bz2'),
work / ('sra', accession + '_2.fastq.bz2')
]]) for accession in self.accessions
]).make()
if __name__ == '__main__':
nesoni.run_tool(Test_analyse_samples(output_dir='output'))
import nesoni
from demakein import make
from design_horn import Design_horn
class Make_horn(make.Make_millable_instrument):
def run(self):
spec = self.working.spec
self.make_instrument(inner_profile=spec.inner,
outer_profile=spec.outer,
hole_positions=[],
hole_diameters=[],
hole_vert_angles=[],
hole_horiz_angles=[],
xpad=[],
ypad=[],
with_fingerpad=[])
self.make_parts(up=True, flip_top=True)
#l = spec.length
#self.segment([l*0.333,l*0.666], spec.length, up=True)
if __name__ == '__main__':
nesoni.run_tool(Make_horn)
#!/usr/bin/env python
import demakein, nesoni
class Design_my_whistle(demakein.Design_folk_whistle):
transpose = 12
# ... and any other things you want to change ...
if __name__ == '__main__':
nesoni.run_tool(Design_my_whistle)
for item in inner_diameters[1:-1]
]
outer_diameters = [ 8.0, 8.0 ]
outer_add = True
initial_length = demakein.design.wavelength('C4') * 0.5
fingerings = [
('C4', []),
('C4*2', []),
('C4*3', []),
('C4*4', []),
('C4*5', []),
('C4*6', []),
('C4*7', []),
('C4*8', []),
('C4*9', []),
#('C4*10', []),
#('C4*11', []),
#('C4*12', []),
]
divisions = [
#[(-1,0.333),(-1,0.6666)],
#[(-1,0.25),(-1,0.5),(-1,0.75)],
[(-1,i/8.0) for i in xrange(1,8) ],
]
if __name__ == '__main__':
nesoni.run_tool(Design_horn)
# whistle_jaw_space.rotate(1,0,0, 90)
#
# offset = -whistle_jaw.extent().zmin
# whistle_jaw.move(0,0,offset)
# whistle_jaw_space.move(0,0,offset)
#
# self.save(whistle_jaw, 'jaw')
# jaw_packable = [ pack.Packable([ whistle_jaw, whistle_jaw_space ], 90, self.mill_diameter) ]
#
# self.working.bore.add(whistle_jaw_clipper)
# self.working.outside.remove(whistle_jaw_clipper)
#
# pack.cut_and_pack(
# self.working.outside, self.working.bore,
# upper_segments, lower_segments,
# xsize=self.mill_length,
# ysize=self.mill_width,
# zsize=self.mill_thickness,
# bit_diameter=self.mill_diameter,
# save=self.save,
#
# extra_packables=[ jaw_packable ],
# )
if __name__ == '__main__':
nesoni.run_tool(Make_whistle)
import nesoni
from demakein import make
from design_horn import Design_horn
class Make_horn(make.Make_millable_instrument):
def run(self):
spec = self.working.spec
self.make_instrument(
inner_profile=spec.inner,
outer_profile=spec.outer,
hole_positions=[],
hole_diameters=[],
hole_vert_angles=[],
hole_horiz_angles=[],
xpad=[],
ypad=[],
with_fingerpad=[],
)
self.make_parts(up=True, flip_top=True)
# l = spec.length
# self.segment([l*0.333,l*0.666], spec.length, up=True)
if __name__ == "__main__":
nesoni.run_tool(Make_horn)
for accession in self.accessions:
Fetch_sra(
work/'sra',
accession
).process_make(stage)
nesoni.Make_reference(
output_dir=work/'TW20',
filenames=[ work/('genbank',accession+'.gbk') for accession in self.genbanks ],
genome=True, bowtie=True, ls=True, snpeff=True,
).make()
analyser = nesoni.Analyse_samples
analyser(
work/'analysis',
work/'TW20',
samples=[
nesoni.Analyse_sample(
accession,
pairs=[[ work/('sra',accession+'_1.fastq.bz2'),work/('sra',accession+'_2.fastq.bz2') ]]
)
for accession in self.accessions
]
).make()
if __name__ == '__main__':
nesoni.run_tool(Test_analyse_samples(output_dir='output'))
for item in inner_diameters[1:-1]
]
outer_diameters = [ 8.0, 8.0 ]
outer_add = True
initial_length = demakein.design.wavelength('C4') * 0.5
fingerings = [
('C4', []),
('C4*2', []),
('C4*3', []),
('C4*4', []),
('C4*5', []),
('C4*6', []),
('C4*7', []),
('C4*8', []),
('C4*9', []),
#('C4*10', []),
#('C4*11', []),
#('C4*12', []),
]
divisions = [
#[(-1,0.333),(-1,0.6666)],
#[(-1,0.25),(-1,0.5),(-1,0.75)],
[(-1,i/8.0) for i in xrange(1,8) ],
]
if __name__ == '__main__':
nesoni.run_tool(Design_horn)
min_hole_diameters = [3.0] * 6
max_hole_diameters = [8.0] * 6
#min_hole_spacing = [ 15.0 ]*5
#and/or
balance = [0.05, None, None, 0.05]
initial_length = demakein.design.wavelength('D5') * 0.5
fingerings = [
('D5', [1, 1, 1, 1, 1, 1]),
('E5', [0, 1, 1, 1, 1, 1]),
('F#5', [0, 0, 1, 1, 1, 1]),
('G5', [0, 0, 0, 1, 1, 1]),
('A5', [0, 0, 0, 0, 1, 1]),
('B5', [0, 0, 0, 0, 0, 1]),
('C#6', [0, 0, 0, 0, 0, 0]),
('D6', [1, 1, 1, 1, 1, 1]),
('E6', [0, 1, 1, 1, 1, 1]),
('F#6', [0, 0, 1, 1, 1, 1]),
('G6', [0, 0, 0, 1, 1, 1]),
('A6', [0, 0, 0, 0, 1, 1]),
('B6', [0, 0, 0, 0, 0, 1]),
('C#7', [0, 0, 0, 0, 0, 0]),
('D8', [1, 1, 1, 1, 1, 1]),
]
if __name__ == '__main__':
nesoni.run_tool(Flute)
from demakein import shape, geom, make, profile
import nesoni
class Tentacle(make.Make):
def run(self):
path = geom.path(
geom.XYZ(0.0,0.0,0.0),
geom.XYZ(0.0,1.0,0.0),
geom.XYZ(1.0,0.0,0.0),
geom.XYZ(0.0,0.0,100.0),
geom.XYZ(0.0,0.0,1.0),
geom.XYZ(1.0,0.0,0.0),
)
#geom.plot(path.position)
print path.get_length()
print path.find(90.0)
print path.get_point(90.0)
l = path.get_length()
prof = profile.make_profile([(0.0,20.0),(l,0.0)])
tentacle = shape.path_extrusion(path,shape.circle,prof)
self.save(tentacle, 'tentacle')
if __name__ == '__main__':
nesoni.run_tool(Tentacle)
