def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.addarg_mvf() parser.addarg_out() parser.addarg_sample_indices(nmin=2) parser.addarg_sample_labels(nmin=2) parser.addarg_windowsize() parser.addarg_mincoverage() parser.add_argument("--data-type", "--datatype", choices=("dna", "prot"), help=("Data type to compare." "(This option is only needed for codon " " MVF files, others will default.)")) parser.add_argument("--ambig", choices=("random2", "random3"), help=("By default, ambiguous nucleotides are " "excluded. This option will include " "sets of ambiguous characters by " "randomly choosing one of the options " "for: RYMKWS ('random2') or " "RYMKWS+BDHV ('random3')")) parser.add_argument( "--emit-counts", action="store_true", help=("output additional file that presents " "the raw counts of pairwise patterns for " "each sample pair tested for each window")) return parser
def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.addarg_mvf() parser.addarg_out() parser.addarg_sample_indices() parser.addarg_sample_labels() parser.addarg_windowsize() parser.addarg_mincoverage() return parser
def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.addarg_mvf() parser.addarg_out() parser.addarg_sample_indices() parser.addarg_sample_labels() parser.addarg_windowsize() parser.addarg_mincoverage() parser.add_argument("--output-lists", action="store_true") return parser
def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.addarg_mvf() parser.addarg_out() parser.addarg_contig_ids() parser.addarg_contig_labels() parser.addarg_sample_indices() parser.addarg_sample_labels() parser.addarg_mincoverage() parser.addarg_windowsize() parser.add_argument( "--base-match", "--basematch", help="String of bases to match (i.e. numerator).") parser.add_argument( "--base-total", "--basetotal", help="String of bases for total (i.e. denominator).") return parser
def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.addarg_mvf() parser.addarg_gff() parser.addarg_out() parser.addarg_samples() parser.addarg_windowsize() parser.addarg_mincoverage() parser.add_argument( "--allele-groups", "--allelegroups", nargs='*', help=("GROUP1:LABEL,LABEL GROUP2:LABEL,LABEL ")) parser.add_argument("--species-groups", "--speciesgroups", nargs='*') parser.add_argument( "--chi-test", "--chitest", help=("Input two number values for expected " "Nonsynonymous and Synonymous expected values.")) parser.add_argument( "--target", nargs="*", help=("Specify the taxa labels that define the " "target lineage-specific branch to be tested.")) parser.add_argument("--num-target-species", "--targetspec", type=int, default=1, help=("Specify the minimum number of " "taxa in the target set " "that are required to conduct analysis")) parser.add_argument("--output-align", "--outputalign", help=("Output alignment to this file path in " "phylip format.")) parser.add_argument( "--outgroup", help=("Specify sample name with which to root trees.")) parser.add_argument( "--use-labels", "--uselabels", action="store_true", help="Use contig labels instead of IDs in output.") parser.add_argument("--codeml-path", "--codemlpath", default="codeml", type=os.path.abspath, help="Full path for PAML codeml executable.") parser.add_argument("--raxml-path", "--raxmlpath", type=os.path.abspath, default="raxml", help="Full path to RAxML program executable.") parser.add_argument("--start-contig", "--startcontig", type=int, default=0, help="Numerical ID for the starting contig.") parser.add_argument("--end-contig", "--endcontig", type=int, default=100000000, help="Numerical id for the ending contig.") parser.add_argument( "--paml-tmp", "--pamltmp", default="pamltmp", type=os.path.abspath, help="path for temporary folder for PAML output files") parser.add_argument( "--all-sample-trees", "--allsampletrees", action="store_true", help=("Makes trees from all samples instead of " "only the most complete sequence from " "each species")) parser.add_argument( "--branch-lrt", "--branchlrt", type=os.path.abspath, help=("Specify the output file for and turn on the " "RAxML-PAML format LRT test scan for " "selection on the target branch in addition " "to the basic patterns scan")) parser.add_argument("--verbose", action="store_true", help="additional screen output") return parser