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def main():
actions = (
('connect', 'connect contigs using long reads'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('prepare', 'prepare TASSEL pipeline'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
('epoch', 'show the methods used in epoch paper'),
# Cotton paper (Paterson et al., 2012 Nature)
('cotton', 'plot cotton macro- and micro-synteny (requires data)'),
# Amborella paper (Albert et al., 2013 Science)
('amborella', 'plot amborella macro- and micro-synteny (requires data)'),
# Mt4.0 paper (Tang et al., 2014 BMC Genomics)
('mtdotplots', 'plot Mt3.5 and Mt4.0 side-by-side'),
# Oropetium paper (Vanburen et al., 2015 Nature)
('oropetium', 'plot oropetium micro-synteny (requires data)'),
# Unpublished
('birch', 'plot birch macro-synteny (requires data)'),
('litchi', 'plot litchi micro-synteny (requires data)'),
('pomegranate', 'plot pomegranate macro- and micro-synteny (requires data)'),
('utricularia', 'plot utricularia micro-synteny (requires data)'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('lms', 'ALLMAPS cartoon to illustrate LMS metric'),
('estimategaps', "illustrate ALLMAPS gap estimation algorithm"),
('simulation', 'plot ALLMAPS accuracy across a range of simulated data'),
('comparebed', 'compare the scaffold links indicated in two bed files'),
('resamplestats', 'prepare resample results table'),
('resample', 'plot ALLMAPS performance across resampled real data'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('nucmer', 'select specific chromosome region based on MTR mapping'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('index', 'wraps bowtie2-build'),
('align', 'wraps bowtie2'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
actions = (
('rename', 'rename genes for annotation release'),
# perform following actions on list files
('reindex', 'reindex isoforms per gene locus'),
('publocus', 'create pub_locus identifiers according to GenBank specs'),
# Medicago gene renumbering
('annotate', 'annotation new bed file with features from old'),
('renumber', 'renumber genes for annotation updates'),
('instantiate', 'instantiate NEW genes tagged by renumber'),
('plot', 'plot gene identifiers along certain chromosome'),
# External gene prediction programs
('augustus', 'convert augustus output into gff3'),
('tRNAscan', 'convert tRNAscan-SE output into gff3'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('prepare', 'convert vcf and bam to variant list'),
('counts', 'collect allele counts from RO/AO fields'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
('compare', 'compare callers on fake HD patients'),
('compare2', 'compare TREDPARSE and lobSTR on fake HD patients'),
('power', 'compare TREDPARSE on fake HD patients adding evidence'),
('tredparse', 'compare TREDPARSE on fake HD patients adding coverage'),
('allelefreq', 'plot the allele frequencies of some STRs'),
('allelefreqall', 'plot all 30 STR allele frequencies'),
('depth', 'plot read depths across all TREDs'),
# Diagram
('diagram', 'plot the predictive power of various evidences'),
# Extra analysis for reviews
('mendelian', 'calculate Mendelian errors based on trios and duos'),
('mendelian2', 'second iteration of Mendelian error calculation'),
('mendelian_errors', 'plot Mendelian errors calculated by mendelian'),
('mendelian_errors2', 'plot Mendelian errors calculated by mendelian2'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())