def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.addarg_mvf() parser.addarg_out() parser.add_argument("--gff", type=os.path.abspath, help=("Input GFF3 file. If GFF3 not provided, " "alignments are assumed to be " "in-frame coding sequences.")) parser.add_argument("--output-data", "--outputdata", choices=['protein', 'codon'], default="codon", help=("protein=single data column " "of protein alleles; " "codon=four columns with: " "protein frame1 frame2 frame3")) parser.add_argument("--filter-annotation", "--filterannotation", help=("skip GFF entries with text " "matching this in their 'Notes' field")) parser.addarg_linebuffer() parser.addarg_overwrite() return parser
def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.add_argument("--mvf", nargs="*", type=os.path.abspath, required=True, help="One or more mvf files.") parser.addarg_out() parser.add_argument( "--new-contigs", "--newcontigs", action="store_true", help=("By default, contigs are matched between files " "using their text labels in the header. " "Use this option to turn matching off and treat " "each file's contigs as distinct.")) parser.add_argument( "--newsamples", action="store_true", help=("By default, samples are matched between files " "using their text labels in the header. " "Use this option to turn matching off and treat " "each file's sample columns as distinct.")) parser.add_argument( "--main_header_file", "--mainheaderfile", help=("Output file will use same headers as " "this input file (default=first in list).")) parser.addarg_linebuffer() parser.addarg_overwrite() return parser
def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.addarg_mvf() parser.addarg_out() parser.addarg_gff() parser.add_argument("--filter-annotation", "--filterannotation", help=("Skip entries in the GFF file that " "contain this string in their 'Notes'")) parser.add_argument( "--nongenic-mode", "--nongenicmode", action="store_true", help=("Instead of returning annotated genes, " "return the non-genic regions without " "without changing contigs or coordinates")) parser.add_argument( "--nongenic-margin", "--nongenicmargin", type=int, default=0, help=("for --unnanotated-mode, only retain " "positions that are this number of bp away " "from an annotated region boundary")) parser.addarg_linebuffer() parser.addarg_overwrite() return parser
def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.addarg_mvf() parser.addarg_out() parser.add_argument( "--actions", nargs='*', help=("set of actions:args to perform, " "note these are done in order as listed")) parser.add_argument("--labels", action="store_true", help="use sample labels instead of indices") parser.add_argument("--test", help="manually input a line for testing") parser.add_argument("--test-nchar", "--textnchar", type=int, help="total number of samples for test string") parser.add_argument( "--more-help", "--morehelp", action="store_true", help="prints full module list and descriptions") parser.addarg_linebuffer() parser.add_argument("--verbose", action="store_true", help="report every line (for debugging)") parser.addarg_overwrite() return parser
def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.add_argument( "--maf", help="input MAF file", required=True, type=os.path.abspath, ) parser.add_argument("--out", help="output MVF file", type=os.path.abspath, required=True) parser.add_argument("--ref-tag", "--reftag", help="old reference tag") parser.add_argument( "--mvf-ref-label", "--mvfreflabel", default="REF", help=("new label for reference sample (default='REF')")) parser.add_argument( "--sample-tags", "--sampletags", nargs="*", required=True, help=("one or more TAG:NEWLABEL or TAG, items, " "if TAG found in sample label, replace with " "NEW (or TAG if NEW not specified) " "NEW and TAG must each be unique.")) parser.addarg_linebuffer() parser.addarg_overwrite() return parser
def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.addarg_mvf() parser.addarg_out() parser.add_argument("--gff", type=os.path.abspath, help=("Input GFF3 file. If GFF3 not provided, " "alignments are assumed to be " "in-frame coding sequences.")) parser.add_argument("--output-data", "--outputdata", choices=['protein', 'codon'], default="codon", help=("protein=single data column " "of protein alleles; " "codon=four columns with: " "protein frame1 frame2 frame3")) parser.add_argument("--filter-annotation", "--filterannotation", help=("skip GFF entries with text " "matching this in their 'Notes' field")) parser.add_argument("--parent-gene-prefix", "--parentgeneprefix", default="gene:", help=("Parent genes prefix when interpreting" "GFF files. For GFF3 files, 'gene:' " "is standard, but for older or custom " "GFF files this may vary. Use 'none' " "to make empty.")) parser.addarg_linebuffer() parser.addarg_overwrite() parser.add_argument( "--verbose", action="store_true", help="""Output excessive data to screen for debugging""") return parser
def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.addarg_mvf() parser.addarg_out() parser.addarg_gff() parser.add_argument("--filter-annotation", "--filterannotation", help=("Skip entries in the GFF file that " "contain this string in their 'Notes'")) parser.add_argument( "--nongenic-mode", "--nongenicmode", action="store_true", help=("Instead of returning annotated genes, " "return the non-genic regions without " "without changing contigs or coordinates")) parser.add_argument( "--nongenic-margin", "--nongenicmargin", type=int, default=0, help=("for --unnanotated-mode, only retain " "positions that are this number of bp away " "from an annotated region boundary")) parser.add_argument("--gene-prefix", "--geneprefix", default="mRNA:", help=("Gene entry prefix when interpreting" "GFF files. For GFF3 files, 'mRNA:' " "is standard, but for older or custom " "GFF files this may vary. Use 'none' " "to make empty.")) parser.addarg_linebuffer() parser.addarg_overwrite() return parser
def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.add_argument("--vcf", type=os.path.abspath, help="VCF input file") parser.add_argument("--out", required=True, help="output MVF file") parser.add_argument( "--out-flavor", "--outflavor", default="dna", choices=['dna', 'dnaqual', 'dnaqual-indel', 'dna-indel'], help=("choose output MVF flavor to include " "quality scores and/or indels")) parser.add_argument("--mask-depth", "--maskdepth", type=int, default=1, help="below this read depth mask with N/n") parser.add_argument( "--low-depth", "--lowdepth", type=int, default=3, help=("below this read depth coverage, " "convert to lower case set to 0 to disable")) parser.add_argument( "--mask-qual", "--maskqual", type=int, default=3, help=("low quality cutoff, bases replaced by N/- " "set to 0 to disable")) parser.add_argument( "--low-qual", "--lowqual", type=int, default=20, help=("below this quality convert to lower case " "set to 0 to disable")) parser.add_argument( "--contig-ids", "--contigids", nargs='*', help=("manually specify one or more contig ids " "as ID;VCFLABE;MVFLABEL, note that " "VCFLABEL must match EXACTLY the contig string " "labels in the VCF file")) parser.add_argument( "--sample-replace", "--samplereplace", nargs="*", help=("one or more TAG:NEWLABEL or TAG, items, " "if TAG found in sample label, replace with " "NEW (or TAG if NEW not specified) " "NEW and TAG must each be unique")) parser.add_argument( "--ref-label", "--reflabel", default="REF", help="label for reference sample (default='REF')") parser.add_argument("--alleles-from", "--allelesfrom", default=None, help="""get additional alignment columns from INFO fields (:-separated)""") parser.addarg_linebuffer() parser.add_argument( "--no-autoindex", "--noautoindex", action="store_true", help="do not automatically index contigs from the VCF") parser.add_argument( "--field-sep", "--fieldsep", default="TAB", choices=['TAB', 'SPACE', 'DBLSPACE', 'COMMA', 'MIXED'], help="""VCF field separator (default='TAB')""") parser.add_argument( "--qual", action="store_true", help="""Include Phred genotype quality (GQ) scores""") parser.addarg_overwrite() return parser