def main():
nesoni.run_toolbox([
'tail-tools ' + VERSION,
'Tools:',
'These tools are used by the workflows below, you generally won\'t need to use these directly.',
Make_tt_reference,
Make_ucsc_reference,
Fasta_qual_merge,
Clip_runs_colorspace,
Clip_runs_basespace,
Extend_sam_colorspace,
Extend_sam_basespace,
Proportions,
Proportions_heatmap,
Tail_count,
Aggregate_tail_counts,
#Tail_stats,
Plot_pooled,
Plot_comparison,
Collapse_counts,
Compare_peaks,
Test,
Geneview_webapp,
'Workflows:',
Analyse_polya,
Analyse_tail_counts,
Analyse_polya_batch,
Call_peaks,
],
'tail-tools',
)
def main():
nesoni.run_toolbox([
'Semiautocount version '+VERSION,
Segment,
Configure,
Import,
Label,
Classify,
Report,
'https://github.com/Victorian-Bioinformatics-Consortium/semiautocount',
],
show_make_flags=False,
)
def main():
nesoni.run_toolbox(
[
'Semiautocount version ' + VERSION,
Segment,
Configure,
Import,
Label,
Classify,
Report,
'https://github.com/Victorian-Bioinformatics-Consortium/semiautocount',
],
show_make_flags=False,
)
def main():
nesoni.run_toolbox([
'tail-tools ' + VERSION,
'Tools:',
'These tools are used by the workflows below, you generally won\'t need to use these directly.',
Fasta_qual_merge,
Clip_runs_colorspace,
Clip_runs_basespace,
Extend_sam_colorspace,
Extend_sam_basespace,
Proportions,
Proportions_heatmap,
Tail_count,
Aggregate_tail_counts,
Plot_pooled,
#Plot_comparison,
Compare_peaks,
Call_utrs,
Test,
Geneview_webapp,
Shiny,
'Component workflows:',
Call_peaks,
Polya_bigwigs,
Analyse_polya,
Analyse_tail_counts,
'Primary workflow:',
Analyse_polya_batch,
'Reference directory creation:',
Make_tt_reference,
Make_ucsc_reference,
Make_ensembl_reference,
'RNA-Seq analysis:',
Make_rnaseq_reference,
Bam_to_bigwig,
Bam_ambiguity,
'Utilities:',
Primer_gff,
],
'tail-tools',
)
def main():
""" Command line interface. """
import nesoni
nesoni.run_toolbox([
'Demakein '+VERSION,
'Flutes',
Design_pflute,
Design_folk_flute,
Make_flute,
Make_cork,
'Whistles',
Design_folk_whistle,
Design_dorian_whistle,
Design_recorder,
Design_three_hole_whistle,
Make_whistle,
'Reed instruments',
Design_reed_drone,
Design_reedpipe,
Design_shawm,
Design_folk_shawm,
Make_reed_instrument,
Make_dock_extender,
Make_mouthpiece,
Make_windcap,
Make_bauble,
#Make_reed,
Make_reed_shaper,
'Panpipes',
Make_panpipe,
'Utilities',
Tune,
#'Everything',
#All,
#'"demakein all:" uses the nesoni make system, see flags below.',
],
show_make_flags=False,
)
def main():
nesoni.run_toolbox(
[
'tail-tools ' + VERSION,
'Tools:',
'These tools are used by the workflows below, you generally won\'t need to use these directly.',
Fasta_qual_merge,
Clip_runs_colorspace,
Clip_runs_basespace,
Extend_sam_colorspace,
Extend_sam_basespace,
Proportions,
Proportions_heatmap,
Tail_count,
Aggregate_tail_counts,
Plot_pooled,
#Plot_comparison,
Compare_peaks,
Call_utrs,
Test,
Geneview_webapp,
Shiny,
'Component workflows:',
Call_peaks,
Polya_bigwigs,
Analyse_polya,
Analyse_tail_counts,
'Primary workflow:',
Analyse_polya_batch,
'Reference directory creation:',
Make_tt_reference,
Make_ucsc_reference,
Make_ensembl_reference,
'RNA-Seq analysis:',
Make_rnaseq_reference,
Bam_to_bigwig,
Bam_ambiguity,
'Utilities:',
Primer_gff,
],
'tail-tools',
)
def main():
""" Command line interface. """
import nesoni
nesoni.run_toolbox(
[
'Demakein ' + VERSION,
'Flutes',
Design_pflute,
Design_folk_flute,
Make_flute,
Make_cork,
'Whistles',
Design_folk_whistle,
Design_dorian_whistle,
Design_recorder,
Design_three_hole_whistle,
Make_whistle,
'Reed instruments',
Design_reed_drone,
Design_reedpipe,
Design_shawm,
Design_folk_shawm,
Make_reed_instrument,
Make_dock_extender,
Make_mouthpiece,
Make_windcap,
Make_bauble,
#Make_reed,
Make_reed_shaper,
'Panpipes',
Make_panpipe,
'Utilities',
Tune,
#'Everything',
#All,
#'"demakein all:" uses the nesoni make system, see flags below.',
],
show_make_flags=False,
)
def run(self):
with nesoni.Stage() as stage:
for filename in self.stls:
stage.process(self.do_one, filename)
def do_one(self, filename):
prefix = os.path.splitext(filename)[0]
self.raster(filename).run()
self.path(prefix+'.raster').run()
if __name__ == '__main__':
nesoni.run_toolbox([
Raster,
Path,
All,
], show_make_flags=False)
#
#def do_cut(prefix, miller_name, filename):
# data = load(filename)
# if isinstance(data['raster'], str):
# data['raster'] = numpy.fromstring(data['raster'],data['dtype']).reshape(data['shape'])
#
# template = lambda: MILLERS[miller_name](res=data['res'])
# miller = template()
#
# height, width = data['raster'].shape
# resrad = miller.res_bit_radius
# for x,y,name in [
#!/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_toolbox(
[ Design_my_whistle, demakein.Make_whistle ],
show_make_flags=False)
('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]),
]
class Pentatonic(Reedpipe):
closed_top = True
inner_diameters = [6.0, 6.0]
outer_diameters = [6.0, 6.0]
min_hole_diameters = [4.0] * 5
max_hole_diameters = [4.0] * 5
initial_length = demakein.design.wavelength('C4') * 0.25 * 0.85
fingerings = [
('C4', [1, 1, 1, 1, 1]),
('D4', [0, 1, 1, 1, 1]),
('E4', [0, 0, 1, 1, 1]),
('G4', [0, 0, 0, 1, 1]),
('A4', [0, 0, 0, 0, 1]),
('C5', [0, 0, 0, 0, 0]),
]
if __name__ == '__main__':
nesoni.run_toolbox([Diatonic, Pentatonic])
('D5', [1,1,1,1, 0]),
('E5', [0,1,1,1, 0]),
('G5', [0,0,1,1, 0]),
('A5', [0,0,0,1, 0]),
('B5', [0,0,0,0, 0]),
]
initial_length = design.wavelength('D4') * 0.5
# Holes 1, 2 and 3 should be fairly evenly spaced
balance = [ None, 0.1, None ]
#Spacing of holes
# 0,1,2 1,2,3 2,3,4
hole_horiz_angles = [ 0.0, 5.0, 0.0, 0.0, 0.0 ]
# Ways in which the flute may be jointed
divisions = [
# A single joint above hole 3
[ (3, 0.0) ],
# A joint halfway between hole 0 and hole 1,
# and a joint above hole 3
[ (0, 0.5), (3, 0.0) ],
]
if __name__ == '__main__':
nesoni.run_toolbox(
[ Design_pentatonic_flute, demakein.Make_flute ],
show_make_flags=False)
('B4', [0, 0, 0, 0, 0]),
('D5', [1, 1, 1, 1, 0]),
('E5', [0, 1, 1, 1, 0]),
('G5', [0, 0, 1, 1, 0]),
('A5', [0, 0, 0, 1, 0]),
('B5', [0, 0, 0, 0, 0]),
]
initial_length = design.wavelength('D4') * 0.5
# Holes 1, 2 and 3 should be fairly evenly spaced
balance = [None, 0.1, None]
#Spacing of holes
# 0,1,2 1,2,3 2,3,4
hole_horiz_angles = [0.0, 5.0, 0.0, 0.0, 0.0]
# Ways in which the flute may be jointed
divisions = [
# A single joint above hole 3
[(3, 0.0)],
# A joint halfway between hole 0 and hole 1,
# and a joint above hole 3
[(0, 0.5), (3, 0.0)],
]
if __name__ == '__main__':
nesoni.run_toolbox([Design_pentatonic_flute, demakein.Make_flute],
show_make_flags=False)
#!/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_toolbox([Design_my_whistle, demakein.Make_whistle],
show_make_flags=False)
('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]),
]
class Pentatonic(Reedpipe):
closed_top = True
inner_diameters = [ 6.0, 6.0 ]
outer_diameters = [ 6.0, 6.0 ]
min_hole_diameters = [ 4.0 ]*5
max_hole_diameters = [ 4.0 ]*5
initial_length = demakein.design.wavelength('C4') * 0.25 * 0.85
fingerings = [
('C4', [1,1,1,1,1]),
('D4', [0,1,1,1,1]),
('E4', [0,0,1,1,1]),
('G4', [0,0,0,1,1]),
('A4', [0,0,0,0,1]),
('C5', [0,0,0,0,0]),
]
if __name__ == '__main__':
nesoni.run_toolbox([ Diatonic, Pentatonic ])
def run(self):
with nesoni.Stage() as stage:
for filename in self.stls:
stage.process(self.do_one, filename)
def do_one(self, filename):
prefix = os.path.splitext(filename)[0]
self.raster(filename).run()
self.path(prefix + '.raster').run()
if __name__ == '__main__':
nesoni.run_toolbox([
Raster,
Path,
All,
], show_make_flags=False)
#
#def do_cut(prefix, miller_name, filename):
# data = load(filename)
# if isinstance(data['raster'], str):
# data['raster'] = numpy.fromstring(data['raster'],data['dtype']).reshape(data['shape'])
#
# template = lambda: MILLERS[miller_name](res=data['res'])
# miller = template()
#
# height, width = data['raster'].shape
# resrad = miller.res_bit_radius
# for x,y,name in [
