def main(): parser = argparse.ArgumentParser() sub = parser.add_subparsers(help='Assembly stages') predict_haplo.stageparser(sub.add_parser('predict_haplo')) args = parser.parse_args() args.func(**sysutils.args_params(args))
def console(): parser = argparse.ArgumentParser( formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) sub = parser.add_subparsers(help='''Insert descirption about phylo''') multiple_align.stageparser(sub.add_parser('multiple_align')) #build_tree.stageparser(sub.add_parser('build_tree')) args = parser.parse_args() args.func(**sysutils.args_params(args))
def console(): parser = argparse.ArgumentParser( description='Determine best-fit evolutionary model with ModelTest-NG.', formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) stageparser(parser) args = parser.parse_args() try: args.func(**sysutils.args_params(args)) except MissingRequiredArgument as e: parser.print_usage() print('error: %s' % e, file=sys.stderr)
def console(): parser = argparse.ArgumentParser( description='Haplotype reconstruction with CliqueSNV.', formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) stageparser(parser) args = parser.parse_args() try: args.func(**sysutils.args_params(args)) except MissingRequiredArgument as e: parser.print_usage() print('error: %s' % e, file=sys.stderr)
def console(): parser = argparse.ArgumentParser( description='Generate summary statistics. Required input: dir_list and/or ph_list and ref_gtf if amplicons used.', formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) stageparser(parser) args = parser.parse_args() try: args.func(**sysutils.args_params(args)) except MissingRequiredArgument as e: parser.print_usage() print('error: %s' % e, file=sys.stderr)
def main(): parser = argparse.ArgumentParser( formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) sub = parser.add_subparsers( help='''setup demo directory and test data. ''' ) demo.stageparser(sub.add_parser('demo')) args = parser.parse_args() args.func(**sysutils.args_params(args))
def console(): parser = argparse.ArgumentParser( description='Build Phylogenetic Tree with RAxML-NG', formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) stageparser(parser) args = parser.parse_args() try: args.func(**sysutils.args_params(args)) except MissingRequiredArgument as e: parser.print_usage() print('error: %s' % e, file=sys.stderr)
def console(): parser = argparse.ArgumentParser( formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) sub = parser.add_subparsers( help='''Manipulate reads. Input is reads in fastq format, output is modified reads in fastq format.''') sample_reads.stageparser(sub.add_parser('sample_reads')) trim_reads.stageparser(sub.add_parser('trim_reads')) join_reads.stageparser(sub.add_parser('join_reads')) ec_reads.stageparser(sub.add_parser('ec_reads')) args = parser.parse_args() args.func(**sysutils.args_params(args))
def console(): parser = argparse.ArgumentParser( description= 'Align sequences using MAFFT. Required input: --seqs AND/OR --dir_list AND --ref_gtf (unless --alignall option included).', formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) stageparser(parser) args = parser.parse_args() try: args.func(**sysutils.args_params(args)) except MissingRequiredArgument as e: parser.print_usage() print('error: %s' % e, file=sys.stderr)
def console(): """ Entry point Returns: None """ parser = argparse.ArgumentParser( description='Annotate consensus from reference annotation.', formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) stageparser(parser) args = parser.parse_args() args.func(**sysutils.args_params(args))
def console(): """ Entry point Returns: None """ parser = argparse.ArgumentParser( description='Parse output from PredictHaplo.', formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) stageparser(parser) args = parser.parse_args() args.func(**sysutils.args_params(args))
def console(): """ Entry point Returns: None """ parser = argparse.ArgumentParser( description='Join reads using FLASh.', formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) stageparser(parser) args = parser.parse_args() args.func(**sysutils.args_params(args))
def console(): """ Entry point Returns: None """ parser = argparse.ArgumentParser( description='Extract sequence regions from pairwise alignment.', formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) stageparser(parser) args = parser.parse_args() args.func(**sysutils.args_params(args))
def console(): parser = argparse.ArgumentParser( formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) sub = parser.add_subparsers( help='''Phylogenomic stages. Includes multiple alignment, evolutionary model testing using ModelTest-ng, and building phylogenetic trees with RAxML. ''') multiple_align.stageparser(sub.add_parser('multiple_align')) model_test.stageparser(sub.add_parser('model_test')) build_tree_NG.stageparser(sub.add_parser('build_tree')) args = parser.parse_args() args.func(**sysutils.args_params(args))
def console(): """ Entry point Returns: None """ parser = argparse.ArgumentParser( description='Assemble contigs to amplicon regions.', formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) stageparser(parser) args = parser.parse_args() args.func(**sysutils.args_params(args))
def main(): parser = argparse.ArgumentParser( formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) sub = parser.add_subparsers( help='''Annotate consensus sequence(s). An assembled consensus sequence can be amino acid aligned to a reference (i.e. HXB2) so the same coordinate system can be used. Sequences can then be extracted based on the shared coordinate systems. ''') pairwise_align.stageparser(sub.add_parser('pairwise_align')) extract_pairwise.stageparser(sub.add_parser('extract_pairwise')) post_assembly.stageparser(sub.add_parser('post_assembly')) annotate_from_ref.stageparser(sub.add_parser('annotate_from_ref')) args = parser.parse_args() args.func(**sysutils.args_params(args))
def console(): """ Entry point Returns: None """ parser = argparse.ArgumentParser( description='''Align reads to reference.''', formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) stageparser(parser) args = parser.parse_args() try: args.func(**sysutils.args_params(args)) except MissingRequiredArgument as e: parser.print_usage() print('error: %s' % e, file=sys.stderr)
def main(): parser = argparse.ArgumentParser( formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, ) sub = parser.add_subparsers( help='''Assemble consensus sequence(s). Input reads (in fastq format) are assembled using either denovo assembly or reference-based alignment. Resulting consensus can be further refined or annotated. ''') # Denovo assemble_denovo.stageparser(sub.add_parser('assemble_denovo')) assemble_amplicons.stageparser(sub.add_parser('assemble_amplicons')) assemble_scaffold.stageparser(sub.add_parser('assemble_scaffold')) # Reference-based align_reads.stageparser(sub.add_parser('align_reads')) call_variants.stageparser(sub.add_parser('call_variants')) vcf_to_consensus.stageparser(sub.add_parser('vcf_to_consensus')) refine_assembly.stageparser(sub.add_parser('refine_assembly')) finalize_assembly.stageparser(sub.add_parser('finalize_assembly')) args = parser.parse_args() args.func(**sysutils.args_params(args))
def console(): parser = argparse.ArgumentParser(formatter_class=HF, add_help=False) parser.add_argument('-h', '--help', action=_BaseHelpAction) # Exit with help if no args were given if len(sys.argv) == 1: parser.parse_args(['-h']) # Subparsers sub = parser.add_subparsers() # Reads stages sample_reads.stageparser(sub.add_parser('sample_reads', formatter_class=HF)) trim_reads.stageparser(sub.add_parser('trim_reads', formatter_class=HF)) join_reads.stageparser(sub.add_parser('join_reads', formatter_class=HF)) ec_reads.stageparser(sub.add_parser('ec_reads', formatter_class=HF)) # Assemble stages assemble_denovo.stageparser( sub.add_parser('assemble_denovo', formatter_class=HF)) assemble_amplicons.stageparser( sub.add_parser('assemble_amplicons', formatter_class=HF)) assemble_scaffold.stageparser( sub.add_parser('assemble_scaffold', formatter_class=HF)) align_reads.stageparser(sub.add_parser('align_reads', formatter_class=HF)) call_variants.stageparser( sub.add_parser('call_variants', formatter_class=HF)) vcf_to_consensus.stageparser( sub.add_parser('vcf_to_consensus', formatter_class=HF)) refine_assembly.stageparser( sub.add_parser('refine_assembly', formatter_class=HF)) finalize_assembly.stageparser( sub.add_parser('finalize_assembly', formatter_class=HF)) # Haplotype predict_haplo.stageparser( sub.add_parser('predict_haplo', formatter_class=HF)) ph_parser.stageparser(sub.add_parser('ph_parser', formatter_class=HF)) cliquesnv.stageparser(sub.add_parser('cliquesnv', formatter_class=HF)) # Annotate/Description stages pairwise_align.stageparser( sub.add_parser('pairwise_align', formatter_class=HF)) extract_pairwise.stageparser( sub.add_parser('extract_pairwise', formatter_class=HF)) annotate_from_ref.stageparser( sub.add_parser('annotate_from_ref', formatter_class=HF)) summary_stats.stageparser( sub.add_parser('summary_stats', formatter_class=HF)) # post_assembly.stageparser( # sub.add_parser('post_assembly', formatter_class=HF) # ) # Phylo multiple_align.stageparser( sub.add_parser('multiple_align', formatter_class=HF)) model_test.stageparser(sub.add_parser('model_test', formatter_class=HF)) build_tree_NG.stageparser( sub.add_parser('build_tree_NG', formatter_class=HF)) # Miscellaneous demo.stageparser(sub.add_parser('demo', formatter_class=HF)) args = parser.parse_args() try: args.func(**sysutils.args_params(args)) except MissingRequiredArgument as e: sub._name_parser_map[sys.argv[1]].print_usage() print('error: %s' % e, file=sys.stderr)