from __future__ import unicode_literals, absolute_import import sys from . import _option_parsers from ._version import TOMBO_VERSION import argparse class SubcommandHelpFormatter(argparse.RawDescriptionHelpFormatter): def _format_action(self, action): parts = super(SubcommandHelpFormatter, self)._format_action(action) if action.nargs == argparse.PARSER: parts = "\n".join(parts.split("\n")[1:]) return parts def main(args=None): """The main routine.""" if args is None: args = sys.argv[1:] # seperate re-squiggle command since all others are nested rsqgl_help = [ ('resquiggle', 'Re-annotate raw signal with genomic alignment from ' + 'existing basecalls.', _option_parsers.get_resquiggle_parser()),] nested_commands = [ ('preprocess', 'Pre-process nanopore reads for Tombo processing.', [ ('annotate_raw_with_fastqs','Add basecalled sequence ' + 'from FASTQs to raw FAST5s.', _option_parsers.get_add_fastqs_parser()), ]), ('filter', 'Apply filter to Tombo index file for specified criterion.', [ ('clear_filters', 'Clear filters to process all successfully re-squiggled reads.', _option_parsers.get_clear_filters_parser()), ('genome_locations', 'Filter reads based on mapping location.', _option_parsers.get_filter_genome_pos_parser()), ('raw_signal_matching', 'Filter reads with poor raw to expected signal matching.', _option_parsers.get_filter_signal_matching_parser()), ('q_score', 'Filter reads with poor mean basecalling quality.', _option_parsers.get_filter_qscore_parser()), ('level_coverage', 'Filter reads for more even coverage.', _option_parsers.get_filter_coverage_parser()), ('stuck', 'Filter reads with more "stuck" bases.', _option_parsers.get_filter_stuck_parser()), ]), ('detect_modifications', 'Perform statistical testing to detect ' + 'non-standard nucleotides.', [ ('de_novo', 'Test for shifts in raw signal against a ' + 'canonical base model.', _option_parsers.get_de_novo_test_signif_parser()), ('alternative_model', 'Test for shifts in raw signal which match ' + 'those of a specific known non-canonical base.', _option_parsers.get_alt_test_signif_parser()), ('model_sample_compare', 'Test for shifts in raw signal ' + 'against levels estimated from a canonical/control ' + 'sample (PCR/IVT) at each reference position.', _option_parsers.get_samp_comp_test_signif_parser()), ('level_sample_compare', 'Test for shifts in raw signal against ' + 'signal level distributions from a canonical/control sample ' + '(PCR/IVT) at each reference position.', _option_parsers.get_group_comp_test_signif_parser()), ('aggregate_per_read_stats', 'Aggregate Tombo per-read statistics ' + 'to produce a genomic base statistics file.', _option_parsers.get_aggregate_per_read_parser()), ]), ('text_output', 'Output Tombo results in text files.', [ ('browser_files', 'Write text outputs for genome browser ' + 'visualization and bioinformatic processing (wiggle or ' + 'bedGraph file format).', _option_parsers.get_browser_files_parser()), ('signif_sequence_context', 'Write genomic/transcriptomic sequence centered on most ' + 'modified genomic locations.', _option_parsers.get_write_signif_diff_parser()), ]), ('build_model', 'Create canonical and alternative base Tombo models.', [ ('estimate_reference', 'Estimate reference tombo model derived from the provided reads.', _option_parsers.get_est_ref_parser()), ('estimate_alt_reference', 'Estimate alternative tombo model from ' + 'a sample containing canonical bases spiked with a single ' + 'non-standard base.', _option_parsers.get_est_alt_ref_parser()), ('estimate_motif_alt_reference', 'Estimate alternative tombo ' + 'model from a sample containing modified bases within a known ' + 'sequence motif.', _option_parsers.get_est_motif_alt_ref_parser()), ('estimate_scale', 'Estimate a global scaling parameter from a ' + 'sub-set of reads.', _option_parsers.get_estimate_scale_parser()), ('event_resquiggle', 'Re-annotate raw signal with genomic ' + 'alignment from existing basecalls using event table.', _option_parsers.get_event_resquiggle_parser()), ]), ] plot_commands = ( 'plot', 'Save plots to visualize raw nanopore signal or ' + 'testing results.', [ ('Genome Location (Standard)', (('max_coverage', 'Plot raw signal in regions with maximal coverage.', _option_parsers.get_max_cov_parser()), ('genome_locations', 'Plot raw signal at defined genomic locations.', _option_parsers.get_genome_loc_parser()), ('motif_centered', 'Plot raw signal at a specific motif.', _option_parsers.get_motif_loc_parser()), ('max_difference', 'Plot raw signal where signal differs most between two ' + 'read groups.', _option_parsers.get_max_diff_parser()), ('most_significant', 'Plot raw signal at most modified locations.', _option_parsers.get_signif_diff_parser()), )), ('Genome Location (Other)', ( ('motif_with_stats', 'Plot example signal and statistic distributions around a ' + 'motif of interst.', _option_parsers.get_signif_motif_parser()), ('per_read', 'Plot per-read modified base probabilities.', _option_parsers.get_per_read_parser()), )), ('Ground Truth Performance Evaluation', (('roc','Plot ROC curve from known motif(s).', _option_parsers.get_roc_parser()), ('sample_compare_roc', 'Plot ROC curve comparing two samples at known motif(s).', _option_parsers.get_control_roc_parser()), ('per_read_roc','Plot per-read ROC curve from known motif(s).', _option_parsers.get_per_read_roc_parser()), ('sample_compare_per_read_roc', 'Plot per-read ROC curve comparing two samples at known motif(s).', _option_parsers.get_control_per_read_roc_parser()), )), ('Other', (('kmer','Plot signal distributions acorss kmers.', _option_parsers.get_kmer_dist_parser()), ('cluster_most_significant', 'Clustering traces at bases with most significant stats.', _option_parsers.get_cluster_signif_diff_parser())) )]) desc = ('Tombo command groups (additional help available ' + 'within each command group):\n' + '\n'.join([ '\t{0: <25}{1}'.format(grp_name, grp_help) for grp_name, grp_help, _ in rsqgl_help + nested_commands + [plot_commands,]])) parser = argparse.ArgumentParser( prog='tombo', description='********** Tombo *********\n\nTombo is a suite of tools ' + 'primarily for the identification of modified nucleotides from ' + 'nanopore sequencing data.\n\nTombo also provides tools for the ' + 'analysis and visualization of raw nanopore signal.\n\n' + desc, formatter_class=SubcommandHelpFormatter) parser.add_argument( '-v', '--version', action='version', version='Tombo version: {}'.format(TOMBO_VERSION), help='show Tombo version and exit.') # Tombo command groups service_subparsers = parser.add_subparsers(dest="service_command") # seperate re-squiggle command since all others are nested rsqgl_parser = service_subparsers.add_parser( rsqgl_help[0][0], parents=[rsqgl_help[0][2],], add_help=False) # resquiggle is both the service parser and action parser rsqgl_parser.set_defaults(action_command=rsqgl_help[0][0]) for grp_name, grp_help, grp_sub_cmds in nested_commands: grp_desc = '\n'.join([ '\t{0: <30}{1}'.format(cmd_name, cmd_help) for cmd_name, cmd_help, _ in grp_sub_cmds]) grp_parser = service_subparsers.add_parser( grp_name, formatter_class=SubcommandHelpFormatter, description=grp_desc) grp_subparser = grp_parser.add_subparsers( title=grp_name, dest="action_command") for cmd_name, cmd_help, cmd_parser in grp_sub_cmds: subparser_cmd = grp_subparser.add_parser( cmd_name, parents=[cmd_parser,], add_help=False) # add plot commands in groups for easier command determination plot_desc = '\n\n'.join([ grp + '\n' + '\n'.join([ '\t{0: <30}{1}'.format(cmd, cmd_help) for cmd, cmd_help, _ in cmds]) for grp, cmds in plot_commands[2]]) plot_parser = service_subparsers.add_parser( 'plot', formatter_class=SubcommandHelpFormatter, description=plot_desc) plot_subparser = plot_parser.add_subparsers( title='plot', dest="action_command") for grp, cmds in plot_commands[2]: for cmd_name, cmd_help, cmd_parser in cmds: subparser_cmd = plot_subparser.add_parser( cmd_name, parents=[cmd_parser,], add_help=False) try: save_args = args args = parser.parse_args(args) except: # catch for re-squiggle advanced args printing import re if any(re.match(rsqgl_help[0][0], val) for val in args) and any( re.match(_option_parsers.printadv_opt[0], val) for val in args): args.extend(['foo', 'foo']) args = parser.parse_args(args) else: raise if args.service_command is None: parser.print_help() sys.stderr.write('\nTombo error: Must provide a tombo command group.\n') sys.exit(2) # if no second level parser is provided print that command groups help if args.action_command is None: save_args.append('-h') parser.parse_args(save_args) if args.action_command == 'resquiggle': from . import resquiggle resquiggle._resquiggle_main(args) elif args.action_command == 'annotate_raw_with_fastqs': from . import _preprocess _preprocess.annotate_reads_with_fastq_main(args) elif args.service_command == 'detect_modifications': from . import tombo_stats if args.action_command == 'aggregate_per_read_stats': tombo_stats._aggregate_per_read_main(args) else: tombo_stats._test_shifts_main(args) elif args.action_command == 'event_resquiggle': from . import _event_resquiggle _event_resquiggle._event_resquiggle_main(args) elif args.service_command == 'build_model': from . import tombo_stats if args.action_command == 'estimate_reference': tombo_stats._est_ref_main(args) elif args.action_command == 'estimate_alt_reference': tombo_stats._est_alt_ref_main(args) elif args.action_command == 'estimate_motif_alt_reference': tombo_stats._est_motif_alt_ref_main(args) elif args.action_command == 'estimate_scale': tombo_stats._estimate_scale_main(args) else: from . import tombo_helper tombo_helper._error_message_and_exit( 'Invalid Tombo build_model command.') elif args.service_command == 'filter': from . import _filter_reads _filter_reads.filter_main(args) elif args.service_command == 'text_output': from . import _text_output_commands if args.action_command == 'browser_files': _text_output_commands._browser_files_main(args) elif args.action_command == 'signif_sequence_context': _text_output_commands._write_signif_diff_main(args) else: from . import tombo_helper tombo_helper._error_message_and_exit( 'Invalid Tombo text_output command.') elif args.service_command == 'plot': from . import _plot_commands _plot_commands.plot_main(args) else: from . import tombo_helper tombo_helper._error_message_and_exit('Invalid Tombo command.') return if __name__ == "__main__": main()