GroopM-0.3.4/bin/groopm

111     subparsers = parser.add_subparsers(help="--", dest='subparser_name')
121                                         help='parse raw data and save to disk',
123     file_parser.add_argument('dbname', help="name of the database being created")
124     file_parser.add_argument('reference', help="fasta file containing bam reference sequences")
125     file_parser.add_argument('bamfiles', nargs='+', help="bam files to parse")
126 …file_parser.add_argument('-t', '--threads', type=int, default=1, help="number of threads to use du…
127 …file_parser.add_argument('-f', '--force', action="store_true", default=False, help="overwrite exis…
128 …file_parser.add_argument('-c', '--cutoff', type=int, default=500, help="cutoff contig size during …
134                                         help='load saved data and make bin cores',
136     core_builder.add_argument('dbname', help="name of the database to open")
137 …core_builder.add_argument('-c', '--cutoff', type=int, default=1500, help="cutoff contig size for c…
138 …core_builder.add_argument('-s', '--size', type=int, default=10, help="minimum number of contigs wh…
139 …core_builder.add_argument('-b', '--bp', type=int, default=1000000, help="cumulative size of contig…
140 …core_builder.add_argument('-f', '--force', action="store_true", default=False, help="overwrite exi…
141     core_builder.add_argument('-g', '--graphfile', help="output graph of micro bin mergers")
142 …core_builder.add_argument('-p', '--plot', action="store_true", default=False, help="create plots o…
143 …core_builder.add_argument('-m', '--multiplot', default=0, help="create plots during core creation …
149                                         help='merge similar bins / split chimeric ones',
151     bin_refiner.add_argument('dbname', help="name of the database to open")
153 …bin_refiner.add_argument('-a', '--auto', action="store_true", default=False, help="automatically r…
154 …bin_refiner.add_argument('-r', '--no_transform', action="store_true", default=False, help="skip da…
155 …bin_refiner.add_argument('-p', '--plot', action="store_true", default=False, help="create plots of…
161                                         help='load saved data and enlarge bins',
163     bin_expander.add_argument('dbname', help="name of the database to open")
164     bin_expander.add_argument('-c', '--cutoff', type=int, default=500, help="cutoff contig size")
165 …bin_expander.add_argument('-f', '--force', action="store_true", default=False, help="overwrite exi…
166 …bin_expander.add_argument('-s', '--step', default=200, type=int, help="step size for iterative rec…
167 …bin_expander.add_argument('-i', '--inclusivity', default=2.5, type=float, help="make recruitment m…
173                                         help='extract contigs or reads based on bin affiliations',
175     bin_extractor.add_argument('dbname', help="name of the database to open")
176     bin_extractor.add_argument('data', nargs='+', help="data file(s) to extract from, bam or fasta")
177 …bin_extractor.add_argument('-b', '--bids', nargs='+', type=int, default=None, help="bin ids to use…
178 …bin_extractor.add_argument('-m', '--mode', default="contigs", help="what to extract [reads, contig…
179 …bin_extractor.add_argument('-o', '--out_folder', default="", help="write to this folder (None for …
180     bin_extractor.add_argument('-p', '--prefix', default="", help="prefix to apply to output files")
182 …bin_extractor.add_argument('-c', '--cutoff', type=int, default=0, help=">>CONTIG MODE ONLY<< cutof…
184 …bin_extractor.add_argument('--mix_bams', action="store_true", default=False, help=">>READ MODE ONL…
185 …bin_extractor.add_argument('--mix_groups', action="store_true", default=False, help=">>READ MODE O…
186 …bin_extractor.add_argument('--mix_reads', action="store_true", default=False, help=">>READ MODE ON…
187 …bin_extractor.add_argument('--interleave', action="store_true", default=False, help=">>READ MODE O…
188 …bin_extractor.add_argument('--headers_only', action="store_true", default=False, help=">>READ MODE…
189 …bin_extractor.add_argument('--no_gzip', action="store_true", default=False, help="do not gzip outp…
191 …bin_extractor.add_argument('--mapping_quality', type=int, default=0, help=">>READ MODE ONLY<< mapp…
192 …bin_extractor.add_argument('--use_secondary', action="store_true", default=False, help=">>READ MOD…
193 …bin_extractor.add_argument('--use_supplementary', action="store_true", default=False, help=">>READ…
194 …bin_extractor.add_argument('--max_distance', type=int, default=1000, help=">>READ MODE ONLY<< maxi…
196 …bin_extractor.add_argument('-v', '--verbose', action="store_true", default=False, help=">>READ MOD…
197 …bin_extractor.add_argument('-t', '--threads', type=int, default=1, help=">>READ MODE ONLY<< maximu…
207                                         help='merge 2 or more bins')
208     bin_merger.add_argument('dbname', help="name of the database to open")
209     bin_merger.add_argument('bids', nargs='+', type=int, help="bin ids to merge.")
210 …bin_merger.add_argument('-f', '--force', action="store_true", default=False, help="merge without p…
216                                         help='split a bin into n pieces')
217     bin_splitter.add_argument('dbname', help="name of the database to open")
218     bin_splitter.add_argument('bid', type=int, help="bin id to split")
219     bin_splitter.add_argument('parts', type=int, help="number of parts to split the bin into")
220 …  bin_splitter.add_argument('-m', '--mode', default="kmer", help="profile to split on [kmer, cov]")
221 …bin_splitter.add_argument('-f', '--force', action="store_true", default=False, help="split without…
227                                         help='delete bins')
228     bin_deleter.add_argument('dbname', help="name of the database to open")
229     bin_deleter.add_argument('bids', nargs='+', type=int, help="bin ids to delete")
230 …bin_deleter.add_argument('-f', '--force', action="store_true", default=False, help="delete without…
240                                         help='explore and validate bins')
241     bin_explorer.add_argument('dbname', help="name of the database to open")
242 …bin_explorer.add_argument('-b', '--bids', nargs='+', type=int, default=None, help="bin ids to plot…
243     bin_explorer.add_argument('-c', '--cutoff', type=int, default=1000, help="cutoff contig size")
244 …bin_explorer.add_argument('-m', '--mode', default="binids", help="Exploration mode [binpoints, bin…
245 …bin_explorer.add_argument('-r', '--no_transform', action="store_true", default=False, help="skip d…
246 …bin_explorer.add_argument('-k', '--kmers', action="store_true", default=False, help="include kmers…
247 …bin_explorer.add_argument('-p', '--points', action="store_true", default=False, help="ignore conti…
248 …bin_explorer.add_argument('-C', '--cm', default="HSV", help="set colormap [HSV, Accent, Blues, Spe…
254                                       help='create a purdy flyover plot of the bins you made')
255     bin_pilot.add_argument('dbname', help="name of the database to open")
256 …bin_pilot.add_argument('-b', '--bids', nargs='+', type=int, default=None, help="bin ids to concent…
257     bin_pilot.add_argument('-c', '--cutoff', type=int, default=1000, help="cutoff contig size")
258 …bin_pilot.add_argument('-p', '--points', action="store_true", default=False, help="ignore contig l…
259 …bin_pilot.add_argument('-P', '--prefix', default="file", help="prefix to append to start of output…
260     bin_pilot.add_argument('-t', '--title', default="", help="title to add to output images")
261 …bin_pilot.add_argument('-B', '--colorbar', action="store_true", default=False, help="show the colo…
262     bin_pilot.add_argument('-f', '--format', default="jpeg", help="file format output images")
263     bin_pilot.add_argument('--fps', type=float, default=10, help="frames per second")
264 …bin_pilot.add_argument('--totalTime', type=float, default=120., help="how long the movie should go…
265 …bin_pilot.add_argument('--firstFade', type=float, default=0.05, help="what percentage of the movie…
271                                         help='plot bins')
272     bin_plotter.add_argument('dbname', help="name of the database to open")
273 …bin_plotter.add_argument('-b', '--bids', nargs='+', type=int, default=None, help="bin ids to plot …
274     bin_plotter.add_argument('-t', '--tag', default="BIN", help="tag to add to output filename")
275     bin_plotter.add_argument('-f', '--folder', default="", help="save plots in folder")
276 …bin_plotter.add_argument('-p', '--points', action="store_true", default=False, help="ignore contig…
277 …bin_plotter.add_argument('-C', '--cm', default="HSV", help="set colormap [HSV, Accent, Blues, Spec…
283                                             help='highlight specific bins')
284     bin_highlighter.add_argument('dbname', help="name of the database to open")
285 …bin_highlighter.add_argument('-P', '--place', action="store_true", default=False, help="use this t…
286 …bin_highlighter.add_argument('-L', '--binlabels', default="", help="replace bin IDs with user spec…
287     bin_highlighter.add_argument('-C', '--contigcolors', default="", help="specify contig colors")
288 …bin_highlighter.add_argument('-r', '--radius', action="store_true", default=False, help="draw plac…
289 …  bin_highlighter.add_argument('-c', '--cutoff', type=int, default=1000, help="cutoff contig size")
290 …bin_highlighter.add_argument('-e', '--elevation', type=float, default=25.0, help="elevation in pri…
291 …bin_highlighter.add_argument('-a', '--azimuth', type=float, default=-45.0, help="azimuth in printe…
292 …bin_highlighter.add_argument('-f', '--file', default="gmview", help="name of image file to produce…
293     bin_highlighter.add_argument('-t', '--filetype', default="jpg", help="Type of file to produce")
294     bin_highlighter.add_argument('-d', '--dpi', default=300, help="Image resolution")
295 …bin_highlighter.add_argument('-s', '--show', action="store_true", default=False, help="load image …
296 …bin_highlighter.add_argument('-p', '--points', action="store_true", default=False, help="ignore co…
297 …bin_highlighter.add_argument('-b', '--bids', nargs='+', type=int, default=None, help="bin ids to p…
303                                         help='print bin information')
304     bin_printer.add_argument('dbname', help="name of the database to open")
305 …bin_printer.add_argument('-b', '--bids', nargs='+', type=int, default=None, help="bin ids to print…
306     bin_printer.add_argument('-o', '--outfile', default="", help="print to file not STDOUT")
307     bin_printer.add_argument('-f', '--format', default='bins', help="output format [bins, contigs]")
308 …bin_printer.add_argument('-u', '--unbinned', action="store_true", default=False, help="print unbin…
318                                         help='write database to text file')
319     data_dumper.add_argument('dbname', help="name of the database to open")
320 …data_dumper.add_argument('-f', '--fields', default="names,bins", help="fields to extract: Build a …
321 …  data_dumper.add_argument('-o', '--outfile', default="GMdump.csv", help="write data to this file")
322     data_dumper.add_argument('-s', '--separator', default=",", help="data separator")
323 …data_dumper.add_argument('--no_headers', action="store_true", default=False, help="don't add heade…
330                                               help='import information from ')
331         data_importer.add_argument('dbname', help="name of the database to open")
332         data_importer.add_argument('infile', help="file with data to import")
333 …   data_importer.add_argument('-t', '--fields', default="bins", help="data type to import. [bins]")
334         data_importer.add_argument('-s', '--separator', default=",", help="data separator")
335 …data_importer.add_argument('--has_headers', action="store_true", default=False, help="file contain…