def main():
actions = (
('bed', 'convert xml format into bed format'),
('condense', 'condense split alignments in om bed'),
('fasta', 'use the OM bed to scaffold and create pseudomolecules'),
('chimera', 'scan the bed file to break scaffolds that multi-maps'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('deletion', 'find IES based on mapping MAC reads'),
('insertion', 'find IES excision points based on mapping MIC reads'),
('insertionpairs', 'pair up the candidate insertions'),
('variation', 'associate IES in parents and progeny'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('location', 'given SNP locations characterize the locations'),
('mstmap', 'convert vcf format to mstmap input'),
('summary', 'summarize the genotype calls in table'),
('refallele', 'make refAllele file'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('cp', 'copy files with support for wildcards'),
('ls', 'list files with support for wildcards'),
('rm', 'remove files with support for wildcards'),
('role', 'change aws role'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("bed", "Convert del.txt to del.bed"),
("mito", "Find mito deletions in BAM"),
("mitosomatic", "Find mito mosaic somatic mutations in piledriver results"),
("mitocompile", "Compile mito deletions from multiple VCF files"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("flanks", "create sequences flanking the gaps"),
("sizes", "compile gap sizes"),
("estimate", "estimate gap sizes based on mates"),
("annotate", "annotate AGP v2 file with linkage info"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('blat', 'generate PSL file using BLAT'),
('frompsl', 'generate chain file from PSL format'),
('fromagp', 'generate chain file from AGP format'),
('summary', 'provide stats of the chain file'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("pasa", "extract terminal exons"),
("tigrprepare", "run EVM in TIGR-only mode"),
("tigrload", "load EVM results into TIGR db"),
("maker", "run EVM based on MAKER output"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('assemble', 'run pasa alignment assembly pipeline'),
('compare', 'run pasa annotation comparison pipeline'),
('longest', 'label longest transcript per gene as full-length'),
('consolidate', 'generate consolidated annotation set from 2 or more annot compare results')
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("index", "wraps gmap_build"),
("align", "wraps gsnap"),
("gmap", "wraps gmap"),
("bam", "convert GSNAP output to BAM"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('index', 'wraps gmap_build'),
('align', 'wraps gsnap'),
('gmap', 'wraps gmap'),
('bam', 'convert GSNAP output to BAM'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('A50', 'compare A50 graphics for a set of FASTA files'),
('coverage', 'plot coverage from a set of BED files'),
('qc', 'performs QC graphics on given contig/scaffold'),
('scaffold', 'plot the alignment of the scaffold to other evidences'),
('covlen', 'plot coverage vs length'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("run", "run a normal command on grid"),
("array", "run an array job"),
("kill", "wrapper around the `qdel` command"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('tofasta', 'generate fasta file for multiple gb records'),
('getgenes', 'extract protein coding genes from Genbank file'),
('gff', 'convert Genbank file to GFF file'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("deletion", "find IES based on mapping MAC reads"),
("insertion", "find IES excision points based on mapping MIC reads"),
("insertionpairs", "pair up the candidate insertions"),
("variation", "associate IES in parents and progeny"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("augustus", "run parallel AUGUSTUS"),
("cufflinks", "run cufflinks following tophat"),
("star", "run star alignment"),
("tophat", "run tophat on a list of inputs"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('pasa', 'extract pasa training models'),
('snap', 'train snap model'),
('augustus', 'train augustus model'),
('genemark', 'train genemark model'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('ids', 'get the representative ids from clstr file'),
('deduplicate', 'use `cd-hit-454` to remove duplicate reads'),
('summary',
'parse cdhit.clstr file to get distribution of cluster sizes'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('flanks', 'create sequences flanking the gaps'),
('sizes', 'compile gap sizes'),
('estimate', 'estimate gap sizes based on mates'),
('annotate', 'annotate AGP v2 file with linkage info'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("clean", "clean and dedup paired FASTQ files"),
("correct", "correct reads using ErrorCorrection"),
("prepare", "prepare SOAP config files and run script"),
("fillstats", "build stats on .fill file from GapCloser"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('frg', 'extract fasta sequences from frg'),
('asm', 'extract fasta sequences from asm'),
('filter', 'remove duplicate reads from frg'),
('count', 'count each type of messages'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('scaffold', 'run SSPACE scaffolding'),
('close', 'run GapFiller to fill gaps'),
('agp', 'convert SSPACE scaffold structure to AGP format'),
('embed', 'embed contigs to upgrade existing structure'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("trimUTR", "remove UTRs in the annotation set"),
("uniq", "remove overlapping gene models"),
("nmd",
"identify transcript variant candidates for nonsense-mediated decay"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('pasa', 'extract terminal exons'),
('tigrprepare', 'run EVM in TIGR-only mode'),
('tigrload', 'load EVM results into TIGR db'),
('maker', 'run EVM based on MAKER output'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('fetch', 'fetch records from a list of GenBank accessions'),
('bisect', 'determine the version of the accession'),
('phytozome', 'retrieve genomes and annotations from phytozome'),
('ensembl', 'retrieve genomes and annotations from ensembl'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('augustus', 'run parallel AUGUSTUS'),
('cufflinks', 'run cufflinks following tophat'),
('star', 'run star alignment'),
('tophat', 'run tophat on a list of inputs'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('fromblast', 'Generate path from BLAST file'),
('happy', 'Make graph from happy mapping data'),
('partition', 'Make individual graphs partitioned by happy mapping'),
('merge', 'Merge multiple graphs together and visualize'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('bed', 'Convert del.txt to del.bed'),
('mito', 'Find mito deletions in BAM'),
('mitosomatic', 'Find mito mosaic somatic mutations in piledriver results'),
('mitocompile', 'Compile mito deletions from multiple VCF files'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('run', 'run a normal command on grid'),
('array', 'run an array job'),
('kill', 'wrapper around the `qdel` command'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('stack', 'create landscape plot with genic/te composition'),
('heatmap', 'similar to stack but adding heatmap'),
('composite', 'combine line plots, feature bars and alt-bars'),
('multilineplot', 'combine multiple line plots in one vertical stack'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
