How to use the jcvi.apps.base.ActionDispatcher function in jcvi

To help you get started, we’ve selected a few jcvi examples, based on popular ways it is used in public projects.

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github tanghaibao / jcvi / assembly / scaffold.py View on Github external
def main():

    actions = (
        ('connect', 'connect contigs using long reads'),
            )
    p = ActionDispatcher(actions)
    p.dispatch(globals())
github tanghaibao / jcvi / jcvi / variation / tassel.py View on Github external
def main():

    actions = (
        ('prepare', 'prepare TASSEL pipeline'),
            )
    p = ActionDispatcher(actions)
    p.dispatch(globals())
github tanghaibao / jcvi / jcvi / projects / misc.py View on Github external
('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        # Unpublished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())
github tanghaibao / jcvi / projects / allmaps.py View on Github external
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())
github tanghaibao / jcvi / jcvi / projects / alfalfa.py View on Github external
def main():

    actions = (
        ('nucmer', 'select specific chromosome region based on MTR mapping'),
            )
    p = ActionDispatcher(actions)
    p.dispatch(globals())
github tanghaibao / jcvi / jcvi / apps / bowtie.py View on Github external
def main():

    actions = (
        ('index', 'wraps bowtie2-build'),
        ('align', 'wraps bowtie2'),
            )
    p = ActionDispatcher(actions)
    p.dispatch(globals())
github tanghaibao / jcvi / jcvi / annotation / reformat.py View on Github external
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())
github tanghaibao / jcvi / jcvi / variation / phase.py View on Github external
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())
github tanghaibao / jcvi / jcvi / projects / str.py View on Github external
('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())