def main():
actions = (
('wgsim', 'sample paired end reads using dwgsim'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('prepare', 'parse list of count files and group per family'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('fragment', 'extract upstream and downstream seq of particular RE'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
# Compile population data - pipeline: compilevcf->mergecsv->meta->data->mask
('bin', 'convert tsv to binary format'),
('filtervcf', 'filter lobSTR VCF'),
('compilevcf', "compile vcf results into master spreadsheet"),
('mergecsv', "combine csv into binary array"),
('meta', 'compute allele frequencies and write to meta'),
('data', 'filter data based on the meta calls'),
('mask', 'compute P-values based on meta calls and data'),
('treds', 'compile allele_frequency for TRED results'),
# lobSTR related
('lobstrindex', 'make lobSTR index'),
('batchlobstr', "run batch lobSTR"),
('lobstr', 'run lobSTR on a big BAM'),
('batchhtt', "run batch HTT caller"),
('htt', 'extract HTT region and run lobSTR'),
('stutter', 'extract info from lobSTR vcf file'),
# Specific markers
('liftover', 'liftOver CODIS/Y-STR markers'),
('trf', 'run TRF on FASTA files'),
('ystr', 'print out Y-STR info given VCF'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
# OM guided approach
('refine', 'find gaps within or near breakpoint regions'),
('patcher', 'given om alignment, prepare the patchers'),
# Gap filling through sequence matching
('fill', 'perform gap filling using one assembly vs the other'),
('install', 'install patches into backbone'),
# Placement through mates and manual insertions and deletions
('bambus', 'find candidate scaffolds to insert based on mates'),
('insert', 'insert scaffolds into assembly'),
('eject', 'eject scaffolds from assembly'),
('closest', 'find the nearest gaps flanking suggested regions'),
# Misc
('tips', 'append telomeric sequences based on patchers and complements'),
('gaps', 'create patches around OM gaps'),
# Touch-up
('pasteprepare', 'prepare sequences for paste'),
('paste', 'paste in good sequences in the final assembly'),
('pastegenes', 'paste in zero or low coverage genes'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('blast', 'run blastn using query against reference'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('bed', 'get gene bed from phytozome'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('bed', 'Convert del.txt to del.bed'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('table', 'convert HTML tables to csv'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('posmap', 'QC based on indexed posmap file'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('names', 'convert a list of names to sbt blocks'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('summary', 'provide summary on id% and cov%'),
('completeness', 'print completeness statistics for each query'),
('annotation', 'create tabular file with the annotations'),
('top10', 'count the most frequent 10 hits'),
('filter', 'filter BLAST file (based on score, id%, alignlen)'),
('covfilter', 'filter BLAST file (based on id% and cov%)'),
('cscore', 'calculate C-score for BLAST pairs'),
('best', 'get best BLAST hit per query'),
('pairs', 'print paired-end reads of BLAST tabular file'),
('bed', 'get bed file from BLAST tabular file'),
('condense', 'group HSPs together for same query-subject pair'),
('chain', 'chain adjacent HSPs together'),
('swap', 'swap query and subjects in BLAST tabular file'),
('sort', 'sort lines so that query grouped together and scores desc'),
('subset', 'extract hits from some query and subject chrs'),
('mismatches', 'print out histogram of mismatches of HSPs'),
('annotate', 'annotate overlap types in BLAST tabular file'),
('score', 'add up the scores for each query seq'),
('rbbh', 'find reciprocal-best blast hits'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('connect', 'connect contigs using long reads'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('bed', 'convert xml format into bed format'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('fetch', 'fetch records from uniprot. input is a list of query terms'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('patch', 'run PBJelly with reference and reads'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('prepare', 'prepare shell script to run trinity-dn/gg on a folder of reads'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('cat', 'concatenate pages from pdf files into a single pdf file'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('depth', 'calculate average depth per feature using coverageBed'),
('sort', 'sort bed file'),
('merge', 'merge bed files'),
('index', 'index bed file using tabix'),
('bins', 'bin bed lengths into each window'),
('summary', 'summarize the lengths of the intervals'),
('evaluate', 'make truth table and calculate sensitivity and specificity'),
('pile', 'find the ids that intersect'),
('pairs', 'estimate insert size between paired reads from bedfile'),
('mates', 'print paired reads from bedfile'),
('sizes', 'infer the sizes for each seqid'),
('uniq', 'remove overlapping features with higher scores'),
('longest', 'select longest feature within overlapping piles'),
('bedpe', 'convert to bedpe format'),
('distance', 'calculate distance between bed features'),
('sample', 'sample bed file and remove high-coverage regions'),
('refine', 'refine bed file using a second bed file'),
('flanking', 'get n flanking features for a given position'),
('some', 'get a subset of bed features given a list'),
('fix', 'fix non-standard bed files'),
('filter', 'filter the bedfile to retain records between size range'),
('random', 'extract a random subset of features'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
# Compile population data
('bin', 'convert tsv to binary format'),
('mask', 'compute P-values based on meta and data'),
('filterloci', 'select subset of loci based on allele counts'),
('filterdata', 'select subset of data based on filtered loci'),
('filtervcf', 'filter lobSTR VCF'),
('compilevcf', "compile vcf results into master spreadsheet"),
('mergecsv', "combine csv into binary array"),
# lobSTR related
('lobstrindex', 'make lobSTR index'),
('batchlobstr', "run batch lobSTR"),
('lobstr', 'run lobSTR on a big BAM'),
('batchhtt', "run batch HTT caller"),
('htt', 'extract HTT region and run lobSTR'),
('stutter', 'extract info from lobSTR vcf file'),
# Specific markers
('liftover', 'liftOver CODIS/Y-STR markers'),
('trf', 'run TRF on FASTA files'),
('ystr', 'print out Y-STR info given VCF'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('longest', 'label longest transcript per gene as full-length'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
# Alter read names
('append', 'append or prepend string to read names'),
# Extract info
('bed', 'convert bam files to bed'),
('fastq', 'convert bam files to paired fastq'),
('pair', 'parse sam file and get pairs'),
('pairs', 'print paired-end reads from BAM file'),
('chimera', 'parse sam file from `bwasw` and list multi-hit reads'),
('noclip', 'remove clipped reads from bam'),
('ace', 'convert sam file to ace'),
('consensus', 'convert bam alignments to consensus FASTA'),
('fpkm', 'calculate FPKM values from BAM file'),
('coverage', 'calculate depth for BAM file'),
('vcf', 'call SNPs on a set of bam files'),
('mapped', 'extract mapped/unmapped reads from samfile'),
('count', 'count the number of reads mapped using htseq'),
('merge', 'merge bam files'),
# Convenience function
('index', 'convert to bam, sort and then index'),
('mini', 'extract mini-bam for a single region'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('prepare', 'prepare meraculous input'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('prepare', 'prepare TASSEL pipeline'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('bed', 'parse gff and produce bed file for particular feature type'),
('bed12', 'produce bed12 file for coding features'),
('fromgtf', 'convert gtf to gff3 format'),
('gtf', 'convert gff3 to gtf format'),
('sort', 'sort the gff file'),
('filter', 'filter the gff file based on Identity and Coverage'),
('format', 'format the gff file, change seqid, etc.'),
('rename', 'change the IDs within the gff3'),
('uniq', 'remove the redundant gene models'),
('liftover', 'adjust gff coordinates based on tile number'),
('script', 'parse gmap gff and produce script for sim4db to refine'),
('note', 'extract certain attribute field for each feature'),
('load', 'extract the feature (e.g. CDS) sequences and concatenate'),
('extract', 'extract a particular contig from the gff file'),
('split', 'split the gff into one contig per file'),
('merge', 'merge several gff files into one'),
('parents', 'find the parents given a list of IDs'),
('children', 'find all children that belongs to the same parent'),
('fromgb', 'convert from gb format to gff3'),
('frombed', 'convert from bed format to gff3'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('rdotplot', 'dot plot based on lastz rdotplot output'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('libsvm', 'convert csv file to LIBSVM format'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('rnaseq', 'evaluate completeness, contiguity, and chimer of RNAseq'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('needle', 'take protein pairs and needle them'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('n50', "Given FASTA or a list of contig sizes, calculate N50"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('patch', 'run PBJelly with reference and reads'),
('spancount', 'count support for each gap'),
('filterm4', 'filter .m4 file after blasr is run'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("batchseeds", "extract seed metrics for each image in a directory"),
("seeds", "extract seed metrics from one image"),
("calibrate", "calibrate pixel-inch ratio and color adjustment"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('libs', 'get list of lib_ids to to run by pull'),
('pull', 'pull the sequences from the TIGR database'),
('query', 'run query using input from datafile'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('align', 'align reads to reference'),
('prepare', 'prepare to run clc_novo_assemble'),
('trim', 'wrapper around clc quality_trim'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("demo",
"run a demo to showcase some common usages of various glyphs"),
("gff", "draw exons for genes based on gff files"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("libs", "get list of lib_ids to to run by pull"),
("pull", "pull the sequences from the TIGR database"),
("query", "run query using input from datafile"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('batchseeds', 'extract seed metrics for each image in a directory'),
('seeds', 'extract seed metrics from one image'),
('calibrate', 'calibrate pixel-inch ratio and color adjustment'),
)
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'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('batch', 'batch run AHRD'),
('merge', 'merge AHRD run results'),
('fix', 'fix AHRD names'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("prepare", "prepare cds sequences from .mcscan"),
("build", "build NJ and ML trees from cds"),
("draw", "draw Newick formatted trees"),
)
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'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("table", "convert HTML tables to csv"),
("links", "extract all links from web page"),
("gallery", "convert a folder of figures to a HTML table"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("index", "wraps bwa index"),
("align", "wraps bwa aln|mem|bwasw"),
("batch", "run bwa in batch mode"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('prepare', 'prepare cds sequences from .mcscan'),
('build', 'build NJ and ML trees from cds'),
('draw', 'draw Newick formatted trees'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('agp', 'write to AGP format from sizes file'),
('extract', 'extract the lines containing only the given IDs'),
('histogram', 'plot read/contig length distribution'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('index', 'wraps bwa index'),
('align', 'wraps bwa aln|mem|bwasw'),
('batch', 'run bwa in batch mode'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('blast', 'convert btab to BLAST -m8 format'),
('bed', 'convert btab to bed format'),
('gff', 'convert from btab (generated by AAT) to gff3 format'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('table', 'convert HTML tables to csv'),
('links', 'extract all links from web page'),
('gallery', 'convert a folder of figures to a HTML table'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('bed', 'convert read membership to bed format'),
('frombed', 'convert read placement to contig format'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('extract', 'extract contigs from ace file'),
('report', 'generate report of read location, consensus location or quality segment per contig'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('overlap', 'build larger contig set by fishing additional seqs'),
('overlapbatch', 'call overlap on a set of sequences'),
('scaffold', 'build scaffolds based on the ordering in the AGP file'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('bed', 'index bed file'),
('fasta', 'index fasta file'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('demo',
'run a demo to showcase some common usages of various glyphs'),
('gff', 'draw exons for genes based on gff files'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('extract', 'extract the lines containing only the given IDs'),
('agp', 'write to AGP format from sizes file'),
('lft', 'write to liftUp format from sizes file'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('excision', 'show intra-chromosomal recombination'),
('bites', 'show the bites calling pipeline'),
('scenario', 'show step-wise genome merger events in brapa'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
("excision", "show intra-chromosomal recombination"),
("bites", "show the bites calling pipeline"),
("scenario", "show step-wise genome merger events in brapa"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('mergechrom', 'merge synteny blocks on the same chrom'),
('pairs', 'convert anchorsfile to pairsfile'),
('fillrbh', 'fill syntelog block with RBH orthologs'),
)
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 = (
('stats', 'collect gene statistics based on gff file'),
('histogram', 'plot gene statistics based on output of stats'),
('summary', 'print gene statistics table'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
def main():
actions = (
('stack', 'create landscape plote with genic/te composition'),
('heatmap', 'similar to stack but adding heatmap'),
('composite', 'combine line plots, feature bars and alt-bars'),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
