def lsu_tree(self, options): """Infer 23S tree spanning GTDB genomes.""" check_dependencies([ 'esl-sfetch', 'cmsearch', 'cmalign', 'esl-alimask', 'FastTreeMP', 'blastn' ]) check_file_exists(options.gtdb_metadata_file) check_file_exists(options.gtdb_lsu_file) make_sure_path_exists(options.output_dir) rna_workflow = RNA_Workflow(options.cpus) rna_workflow.run( 'lsu', options.gtdb_metadata_file, options.gtdb_lsu_file, options.min_lsu_length, options.min_scaffold_length, options.min_quality, options.max_contigs, options.min_N50, not options.disable_tax_filter, # options.reps_only, # options.user_genomes, options.genome_list, options.output_dir) self.logger.info('Results written to: %s' % options.output_dir)
def lsu_tree(self, options): """Infer 23S tree spanning GTDB genomes.""" check_dependencies(['esl-sfetch', 'cmsearch', 'cmalign', 'esl-alimask', 'FastTreeMP', 'blastn']) check_file_exists(options.gtdb_metadata_file) check_file_exists(options.gtdb_lsu_file) make_sure_path_exists(options.output_dir) rna_workflow = RNA_Workflow(options.cpus) rna_workflow.run('lsu', options.gtdb_metadata_file, options.gtdb_lsu_file, options.min_lsu_length, options.min_scaffold_length, options.min_quality, options.max_contigs, options.min_N50, not options.disable_tax_filter, #options.reps_only, #options.user_genomes, options.genome_list, options.output_dir) self.logger.info('Results written to: %s' % options.output_dir)
def ssu_tree(self, options): """Infer 16S tree spanning GTDB genomes.""" check_dependencies( ['mothur', 'ssu-align', 'ssu-mask', 'FastTreeMP', 'blastn']) check_file_exists(options.gtdb_metadata_file) check_file_exists(options.gtdb_ssu_file) make_sure_path_exists(options.output_dir) rna_workflow = RNA_Workflow(options.cpus) rna_workflow.run('ssu', options.gtdb_metadata_file, options.gtdb_ssu_file, options.min_ssu_length, options.min_scaffold_length, options.min_quality, options.max_contigs, options.min_N50, not options.disable_tax_filter, options.genome_list, options.output_dir, options.align_method) self.logger.info('Results written to: %s' % options.output_dir)
def ssu_tree(self, options): """Infer 16S tree spanning GTDB genomes.""" check_dependencies(['mothur', 'ssu-align', 'ssu-mask', 'FastTreeMP', 'blastn']) check_file_exists(options.gtdb_metadata_file) check_file_exists(options.gtdb_ssu_file) make_sure_path_exists(options.output_dir) rna_workflow = RNA_Workflow(options.cpus) rna_workflow.run('ssu', options.gtdb_metadata_file, options.gtdb_ssu_file, options.min_ssu_length, options.min_scaffold_length, options.min_quality, options.max_contigs, options.min_N50, not options.disable_tax_filter, options.genome_list, options.output_dir, options.align_method) self.logger.info('Results written to: %s' % options.output_dir)