CheckM-1.0.18/bin/checkm

125     subparsers = parser.add_subparsers(help="--", dest='subparser_name')
132             help='''
141     tree_parser.add_argument('bin_dir', help="directory containing bins (fasta format)")
142     tree_parser.add_argument('output_dir', help="directory to write output files")
143 …tree_parser.add_argument('-r', '--reduced_tree', dest='bReducedTree', action="store_true", help="u…
144 …ument('--ali', dest='bKeepAlignment', action="store_true", default=False, help="generate HMMER ali…
145 …tree_parser.add_argument('--nt', dest='bNucORFs', action="store_true", default=False, help="genera…
146 …'-g', '--genes', dest='bCalledGenes', action="store_true", default=False, help="bins contain genes…
147 …tree_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (other files …
148     tree_parser.add_argument('-t', '--threads', type=int, default=1, help="number of threads")
149 …tree_parser.add_argument('--pplacer_threads', type=int, default=1, help="number of threads used by…
150 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
151 …tree_parser.add_argument('--tmpdir', action=ChangeTempAction, help="specify an alternative directo…
158     tree_qa_parser.add_argument('tree_dir', help="directory specified during tree command")
160                                     help='''desired output:
167     tree_qa_parser.add_argument('-f', '--file', default='stdout', help="print results to file")
168 …ment('--tab_table', dest='bTabTable', action="store_true", default=False, help="print tab-separate…
169 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
170 …tree_qa_parser.add_argument('--tmpdir', action=ChangeTempAction, help="specify an alternative dire…
177     lineage_set_parser.add_argument('tree_dir', help="directory specified during tree command")
178 …lineage_set_parser.add_argument('marker_file', help="output file describing marker set for each bi…
179 …lineage_set_parser.add_argument('-u', '--unique', type=int, default=10, help="minimum number of un…
180 …lineage_set_parser.add_argument('-m', '--multi', type=int, default=10, help="maximum number of mul…
181 …--force_domain', dest='bForceDomain', action="store_true", default=False, help="use domain-level s…
182 … dest='bNoLineageSpecificRefinement', action="store_true", default=False, help="do not perform lin…
183 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
184 …lineage_set_parser.add_argument('--tmpdir', action=ChangeTempAction, help="specify an alternative …
191 …taxon_list_parser.add_argument('--rank', help="restrict list to specified taxonomic rank", choices…
192 …taxon_list_parser.add_argument('--tmpdir', action=ChangeTempAction, help="specify an alternative d…
199     taxon_set_parser.add_argument('rank', help="taxonomic rank", choices=taxonomicRanks)
200     taxon_set_parser.add_argument('taxon', help="taxon of interest")
201 …taxon_set_parser.add_argument('marker_file', help="output file describing taxonomic-specific marke…
202 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
203 …taxon_set_parser.add_argument('--tmpdir', action=ChangeTempAction, help="specify an alternative di…
210 …analyze_parser.add_argument('marker_file', help="markers for assessing bins (marker set or HMM fil…
211     analyze_parser.add_argument('bin_dir', help="directory containing bins (fasta format)")
212     analyze_parser.add_argument('output_dir', help="directory to write output files")
213 …ument('--ali', dest='bKeepAlignment', action="store_true", default=False, help="generate HMMER ali…
214 …analyze_parser.add_argument('--nt', dest='bNucORFs', action="store_true", default=False, help="gen…
215 …'-g', '--genes', dest='bCalledGenes', action="store_true", default=False, help="bins contain genes…
216 …analyze_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (other fil…
217     analyze_parser.add_argument('-t', '--threads', type=int, default=1, help="number of threads")
218 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
220 …--ali_top_hits', dest='bAlignTopHit', action="store_true", default=False, help=argparse.SUPPRESS) …
221 …analyze_parser.add_argument('--tmpdir', action=ChangeTempAction, help="specify an alternative dire…
234     qa_parser.add_argument('marker_file', help="marker file specified during analyze command")
235     qa_parser.add_argument('analyze_dir', help="directory specified during analyze command")
237                                 help='''desired output:
249 …qa_parser.add_argument('--exclude_markers', default=None, help="file specifying markers to exclude…
250 …_markers', dest='bIndividualMarkers', action="store_true", default=False, help="treat marker as in…
251 …rrection', dest='bSkipAdjCorrection', action="store_true", default=False, help="do not exclude adj…
252 …n', dest='bSkipPseudoGeneCorrection', action="store_true", default=False, help="skip identificatio…
253 …qa_parser.add_argument('--aai_strain', type=float, default=0.9, help="AAI threshold used to identi…
254 …qa_parser.add_argument('-a', '--alignment_file', default=None, help="produce file showing alignmen…
255 …hresholds', dest='bIgnoreThresholds', action="store_true", default=False, help="ignore model-speci…
256 …qa_parser.add_argument('-e', '--e_value', type=float, default=DefaultValues.E_VAL, help="e-value c…
257 …qa_parser.add_argument('-l', '--length', type=float, default=DefaultValues.LENGTH, help="percent o…
258 …qa_parser.add_argument('-c', '--coverage_file', default=None, help="file containing coverage of ea…
259     qa_parser.add_argument('-f', '--file', default='stdout', help="print results to file")
260 …ment('--tab_table', dest='bTabTable', action="store_true", default=False, help="print tab-separate…
261     qa_parser.add_argument('-t', '--threads', type=int, default=1, help="number of threads")
262 …qa_parser.add_argument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="s…
263 …qa_parser.add_argument('--tmpdir', action=ChangeTempAction, help="specify an alternative directory…
270     lineage_wf_parser.add_argument('bin_dir', help="directory containing bins (fasta format)")
271     lineage_wf_parser.add_argument('output_dir', help="directory to write output files")
272 …rgument('-r', '--reduced_tree', dest='bReducedTree', action="store_true", help="use reduced tree (…
273 …ument('--ali', dest='bKeepAlignment', action="store_true", default=False, help="generate HMMER ali…
274 …add_argument('--nt', dest='bNucORFs', action="store_true", default=False, help="generate nucleotid…
275 …'-g', '--genes', dest='bCalledGenes', action="store_true", default=False, help="bins contain genes…
276 …lineage_wf_parser.add_argument('-u', '--unique', type=int, default=10, help="minimum number of uni…
277 …lineage_wf_parser.add_argument('-m', '--multi', type=int, default=10, help="maximum number of mult…
278 …--force_domain', dest='bForceDomain', action="store_true", default=False, help="use domain-level s…
279 … dest='bNoLineageSpecificRefinement', action="store_true", default=False, help="do not perform lin…
280 …_markers', dest='bIndividualMarkers', action="store_true", default=False, help="treat marker as in…
281 …rrection', dest='bSkipAdjCorrection', action="store_true", default=False, help="do not exclude adj…
282 …n', dest='bSkipPseudoGeneCorrection', action="store_true", default=False, help="skip identificatio…
283 …lineage_wf_parser.add_argument('--aai_strain', type=float, default=0.9, help="AAI threshold used t…
284 …lineage_wf_parser.add_argument('-a', '--alignment_file', default=None, help="produce file showing …
285 …hresholds', dest='bIgnoreThresholds', action="store_true", default=False, help="ignore model-speci…
286 …lineage_wf_parser.add_argument('-e', '--e_value', type=float, default=DefaultValues.E_VAL, help="e…
287 …lineage_wf_parser.add_argument('-l', '--length', type=float, default=DefaultValues.LENGTH, help="p…
288     lineage_wf_parser.add_argument('-f', '--file', default='stdout', help="print results to file")
289 …ment('--tab_table', dest='bTabTable', action="store_true", default=False, help="print tab-separate…
290 …lineage_wf_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (other …
291     lineage_wf_parser.add_argument('-t', '--threads', type=int, default=1, help="number of threads")
292 …lineage_wf_parser.add_argument('--pplacer_threads', type=int, default=1, help="number of threads u…
293 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
294 …lineage_wf_parser.add_argument('--tmpdir', action=ChangeTempAction, help="specify an alternative d…
302 …taxonomy_wf_parser.add_argument('rank', help="taxonomic rank", choices=['life', 'domain', 'phylum'…
303     taxonomy_wf_parser.add_argument('taxon', help="taxon of interest")
304     taxonomy_wf_parser.add_argument('bin_dir', help="directory containing bins (fasta format)")
305     taxonomy_wf_parser.add_argument('output_dir', help="directory to write output files")
306 …ument('--ali', dest='bKeepAlignment', action="store_true", default=False, help="generate HMMER ali…
307 …add_argument('--nt', dest='bNucORFs', action="store_true", default=False, help="generate nucleotid…
308 …'-g', '--genes', dest='bCalledGenes', action="store_true", default=False, help="bins contain genes…
309 …_markers', dest='bIndividualMarkers', action="store_true", default=False, help="treat marker as in…
310 …rrection', dest='bSkipAdjCorrection', action="store_true", default=False, help="do not exclude adj…
311 …n', dest='bSkipPseudoGeneCorrection', action="store_true", default=False, help="skip identificatio…
312 …taxonomy_wf_parser.add_argument('--aai_strain', type=float, default=0.9, help="AAI threshold used …
313 …taxonomy_wf_parser.add_argument('-a', '--alignment_file', default=None, help="produce file showing…
314 …hresholds', dest='bIgnoreThresholds', action="store_true", default=False, help="ignore model-speci…
315 …er.add_argument('-e', '--e_value', type=float, default=DefaultValues.E_VAL, help="e-value cut off")
316 ….add_argument('-l', '--length', type=float, default=DefaultValues.LENGTH, help="percent overlap be…
317 …taxonomy_wf_parser.add_argument('-c', '--coverage_file', default=None, help="file containing cover…
318     taxonomy_wf_parser.add_argument('-f', '--file', default='stdout', help="print results to file")
319 …ment('--tab_table', dest='bTabTable', action="store_true", default=False, help="print tab-separate…
320 …taxonomy_wf_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (other…
321 …  taxonomy_wf_parser.add_argument('-t', '--threads', type=int, default=1, help="number of threads")
322 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
323 …taxonomy_wf_parser.add_argument('--tmpdir', action=ChangeTempAction, help="specify an alternative …
327 …plot_need_qa_results_parser.add_argument('results_dir', help="directory specified during qa comman…
330     plot_parser.add_argument('bin_dir', help="directory containing bins to plot (fasta format)")
331     plot_parser.add_argument('output_dir', help="directory to hold plots")
332 …--image_type', default='png', choices=['eps', 'pdf', 'png', 'ps', 'svg'], help='desired image type…
333     plot_parser.add_argument('--dpi', type=int, default=600, help='desired DPI of output image')
334     plot_parser.add_argument('--font_size', type=int, default=8, help='Desired font size')
335 …plot_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (other files …
339 …  plot_single_parser.add_argument('--width', type=float, default=6.5, help='width of output image')
340 …plot_single_parser.add_argument('--height', type=float, default=6.5, help='height of output image')
344 …  plot_double_parser.add_argument('--width', type=float, default=6.5, help='width of output image')
345 …plot_double_parser.add_argument('--height', type=float, default=3.5, help='height of output image')
349     plot_rows_parser.add_argument('--width', type=float, default=6.5, help='width of output image')
350 …plot_rows_parser.add_argument('--row_height', type=float, default=0.3, help='height of each row in…
355                                         help='Create GC histogram and delta-GC plot.',
360 …plot_gc_parser.add_argument('distributions', help='reference distribution(s) to plot; integer betw…
361 …plot_gc_parser.add_argument('-w', '--gc_window_size', help="window size used to calculate GC histo…
362 …plot_gc_parser.add_argument('-b', '--gc_bin_width', help="width of GC bars in histogram", type=flo…
363 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
372 …plot_coding_parser.add_argument('distributions', help='reference distribution(s) to plot; integer …
373 …plot_coding_parser.add_argument('-w', '--cd_window_size', help="window size used to calculate CD h…
374 …plot_coding_parser.add_argument('-b', '--cd_bin_width', help="width of CD bars in histogram", type…
375 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
383 …plot_tetra_parser.add_argument('tetra_profile', help='tetranucleotide profiles for each bin (see t…
384 …plot_tetra_parser.add_argument('distributions', help='reference distribution(s) to plot; integer b…
385 …plot_tetra_parser.add_argument('-w', '--td_window_size', help="window size used to calculate TD hi…
386 …plot_tetra_parser.add_argument('-b', '--td_bin_width', help="width of TD bars in histogram", type=…
387 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
394     plot_dist_parser.add_argument('results_dir', help="directory specified during analyze command")
395 …  plot_dist_parser.add_argument('bin_dir', help="directory containing bins to plot (fasta format)")
396     plot_dist_parser.add_argument('output_dir', help="directory to hold plots")
397 …plot_dist_parser.add_argument('tetra_profile', help='tetranucleotide profiles for each sequence (s…
398 …plot_dist_parser.add_argument('distributions', help='reference distribution(s) to plot; integer be…
400 …--image_type', default='png', choices=['eps', 'pdf', 'png', 'ps', 'svg'], help='desired image type…
401 …  plot_dist_parser.add_argument('--dpi', type=int, default=600, help='desired DPI of output image')
402     plot_dist_parser.add_argument('--font_size', type=int, default=8, help='Desired font size')
403 …plot_dist_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (other f…
404     plot_dist_parser.add_argument('--width', type=float, default=6.5, help='width of output image')
405     plot_dist_parser.add_argument('--height', type=float, default=8, help='height of output image')
407 …plot_dist_parser.add_argument('-a', '--gc_window_size', help="window size used to calculate GC his…
408 …plot_dist_parser.add_argument('-b', '--td_window_size', help="window size used to calculate TD his…
409 …plot_dist_parser.add_argument('-c', '--cd_window_size', help="window size used to calculate CD his…
410 …plot_dist_parser.add_argument('-1', '--gc_bin_width', help="width of GC bars in histogram", type=f…
411 …plot_dist_parser.add_argument('-2', '--td_bin_width', help="width of TD bars in histogram", type=f…
412 …plot_dist_parser.add_argument('-3', '--cd_bin_width', help="width of CD bars in histogram", type=f…
413 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
421 …plot_tetra_pca_parser.add_argument('tetra_profile', help='tetranucleotide profiles for each sequen…
422 …plot_tetra_pca_parser.add_argument('--width', type=float, default=6.5, help='width of output image…
423 …plot_tetra_pca_parser.add_argument('--height', type=float, default=6.5, help='height of output ima…
424 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
432 …plot_gc_bias_parser.add_argument('bam_file', help="BAM file to interrogate for coverage informatio…
433 …plot_gc_bias_parser.add_argument('-w', '--window_size', help="window size used to calculate plot s…
434 …plot_gc_bias_parser.add_argument('-r', '--all_reads', action='store_true', help="use all reads to …
435 …plot_gc_bias_parser.add_argument('-a', '--min_align', help='minimum alignment length as percentage…
436 …plot_gc_bias_parser.add_argument('-e', '--max_edit_dist', help='maximum edit distance as percentag…
437 … plot_gc_bias_parser.add_argument('-t', '--threads', type=int, default=1, help="number of threads")
438 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
446 …plot_cov_pca_parser.add_argument('coverage_file', help="file indicating coverage of each sequence …
447 … plot_cov_pca_parser.add_argument('--width', type=float, default=6.5, help='width of output image')
448 …plot_cov_pca_parser.add_argument('--height', type=float, default=6.5, help='height of output image…
449 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
458 …plot_nx_parser.add_argument('-s', '--step_size', help="x step size for calculating Nx", type=float…
459 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
468 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
477 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
486 …marker_plot_parser.add_argument('--fig_padding', type=float, default=0.2, help='white space to pla…
487 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
495 …parallel_coord_plot_parser.add_argument('coverage_file', help="file indicating coverage of each se…
496 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
504 …dd_argument('--ignore_hetero', dest='bIgnoreHetero', action="store_true", help="do not plot strain…
505 …bin_qa_plot_parser.add_argument('--aai_strain', type=float, default=0.9, help="AAI threshold used …
506 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
513     unbinned_parser.add_argument('bin_dir', help="directory containing bins (fasta format)")
514     unbinned_parser.add_argument('seq_file', help="sequences used to generate bins (fasta format)")
515     unbinned_parser.add_argument('output_seq_file', help="write unbinned sequences to file")
516 …unbinned_parser.add_argument('output_stats_file', help="write unbinned sequence statistics to file…
517 …unbinned_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (other fi…
518 …unbinned_parser.add_argument('-s', '--min_seq_len', type=int, default=0, help="required length of …
519 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
527     coverage_parser.add_argument('bin_dir', help="directory containing bins (fasta format)")
528     coverage_parser.add_argument('output_file', help="print results to file")
529     coverage_parser.add_argument('bam_files', nargs='+', help="BAM files to parse")
530 …coverage_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (other fi…
531 …coverage_parser.add_argument('-r', '--all_reads', action='store_true', help="use all reads to esti…
532 …coverage_parser.add_argument('-a', '--min_align', help='minimum alignment length as percentage of …
533 …coverage_parser.add_argument('-e', '--max_edit_dist', help='maximum edit distance as percentage of…
534 …coverage_parser.add_argument('-m', '--min_qc', help='minimum quality score (in phred)', type=int, …
535     coverage_parser.add_argument('-t', '--threads', type=int, default=1, help="number of threads")
536 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
544     tetra_parser.add_argument('seq_file', help="sequences used to generate bins (fasta format)")
545     tetra_parser.add_argument('output_file', help="print results to file")
546     tetra_parser.add_argument('-t', '--threads', type=int, default=1, help="number of threads")
547 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
554 …profile_parser.add_argument('coverage_file', help="file indicating coverage of each sequence (see …
555     profile_parser.add_argument('-f', '--file', default='stdout', help="print results to file")
556 …ment('--tab_table', dest='bTabTable', action="store_true", default=False, help="print tab-separate…
557 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
564 …join_parser.add_argument('tables', nargs='+', help="tab-separated table files with bin ids as thei…
565     join_parser.add_argument('-f', '--file', default='stdout', help="print results to file")
566 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
573 …  ssu_finder_parser.add_argument('seq_file', help="sequences used to generate bins (fasta format)")
574     ssu_finder_parser.add_argument('bin_dir', help="directory containing bins (fasta format)")
575     ssu_finder_parser.add_argument('output_dir', help="directory to write output files")
577 …ssu_finder_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (other …
578 …ssu_finder_parser.add_argument('-e', '--evalue', help='e-value threshold for identifying hits', ty…
579 …ssu_finder_parser.add_argument('-c', '--concatenate', help='concatenate hits that are within the s…
580     ssu_finder_parser.add_argument('-t', '--threads', help='number of threads', type=int, default=1)
581 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
588 … bin_compare_parser.add_argument('seq_file', help="sequences used to generate bins (fasta format)")
589     bin_compare_parser.add_argument('bin_dir1', help="directory containing bins (fasta format)")
590     bin_compare_parser.add_argument('bin_dir2', help="directory containing bins (fasta format)")
591     bin_compare_parser.add_argument('output_file', help="output file showing overlap between bins")
593 …bin_compare_parser.add_argument('-x', '--extension1', default='fna', help="extension of bins in di…
594 …bin_compare_parser.add_argument('-y', '--extension2', default='fna', help="extension of bins in di…
595 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
608     bin_union_parser.add_argument('output_dir', help="directory for outputting")
609 …bin_union_parser.add_argument('bin_or_checkm_qa_table', nargs='+', help="bin directories and check…
610 …bin_union_parser.add_argument('-x', '--extension', default='fna', help="extension of bins in bin d…
611 …bin_union_parser.add_argument('--min_completeness', help="ignore bins with less completeness than …
612 …bin_union_parser.add_argument('--max_contamination', help="ignore bins with more contamination tha…
613 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
620 …merge_parser.add_argument('marker_file', help="marker file to use for assessing potential bin merg…
621     merge_parser.add_argument('bin_dir', help="directory containing bins (fasta format)")
622     merge_parser.add_argument('output_dir', help="directory to write output files")
623 …'-g', '--genes', dest='bCalledGenes', action="store_true", default=False, help="bins contain genes…
624 …merge_parser.add_argument('--delta_comp', help="minimum increase in completeness to report pair", …
625 …merge_parser.add_argument('--delta_cont', help="maximum increase in contamination to report pair",…
626 …merge_parser.add_argument('--merged_comp', help="minimum merged completeness to report pair", type…
627 …merge_parser.add_argument('--merged_cont', help="maximum merged contamination to report pair", typ…
628 …merge_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (other files…
629     merge_parser.add_argument('-t', '--threads', type=int, default=1, help="number of threads")
630 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
638     outlier_parser.add_argument('bin_dir', help="directory containing bins (fasta format)")
639 …outlier_parser.add_argument('tetra_profile', help='tetranucleotide profiles for each sequence (see…
640     outlier_parser.add_argument('output_file', help="print results to file")
641 …outlier_parser.add_argument('-d', '--distributions', help='reference distribution used to identify…
642 …outlier_parser.add_argument('-r', '--report_type', help="report sequences that are outliers in 'al…
643 …outlier_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (other fil…
644 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
651     modify_parser.add_argument('seq_file', help="sequences used to generate bins (fasta format)")
652     modify_parser.add_argument('bin_file', help="bin to be modified")
653     modify_parser.add_argument('output_file', help="modified bin")
654 …modify_parser.add_argument('-a', '--add', action='append', help="ID of sequence to add to bin (may…
655 …modify_parser.add_argument('-r', '--remove', action='append', help="ID of sequence to remove from …
656 …modify_parser.add_argument('-o', '--outlier_file', help="remove all sequences marked as outliers i…
657 …ument('-q', '--quiet', dest='bQuiet', action="store_true", default=False, help="suppress console o…
664     unique_parser.add_argument('bin_dir', help="directory containing bins (fasta format)")
665 …unique_parser.add_argument('-x', '--extension', default='fna', help="extension of bins (all other …
672     test_parser.add_argument('output_dir', help="output directory for test data")
673 …test_parser.add_argument('--tmpdir', action=ChangeTempAction, help="specify an alternative directo…
680         debug_parser.add_argument('data', help="some data")