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 rna_dump(self, options):
"""Dump all 5S, 16S, and 23S sequences to files."""
check_file_exists(options.genomic_file)
make_sure_path_exists(options.output_dir)
rna_workflow = RNA_Workflow(1)
rna_workflow.dump(options.genomic_file, options.gtdb_taxonomy,
options.min_5S_len, options.min_16S_ar_len,
options.min_16S_bac_len, options.min_23S_len,
options.min_contig_len, options.include_user,
options.genome_list, options.output_dir)
self.logger.info('Results written to: %s' % options.output_dir)
def rna_tree(self, options):
"""Infer 16S + 23S tree spanning GTDB genomes."""
check_dependencies(['FastTreeMP'])
check_file_exists(options.ssu_msa)
check_file_exists(options.ssu_tree)
check_file_exists(options.lsu_msa)
check_file_exists(options.lsu_tree)
make_sure_path_exists(options.output_dir)
rna_workflow = RNA_Workflow(options.cpus)
rna_workflow.combine(options.ssu_msa, options.ssu_tree,
options.lsu_msa, options.lsu_tree,
options.output_dir)
self.logger.info('Results written to: %s' % options.output_dir)
def rna_dump(self, options):
"""Dump all 5S, 16S, and 23S sequences to files."""
check_file_exists(options.genomic_file)
make_sure_path_exists(options.output_dir)
rna_workflow = RNA_Workflow(1)
rna_workflow.dump(options.genomic_file,
options.gtdb_taxonomy,
options.min_5S_len,
options.min_16S_ar_len,
options.min_16S_bac_len,
options.min_23S_len,
options.min_contig_len,
options.include_user,
options.genome_list,
options.output_dir)
self.logger.info('Results written to: %s' % options.output_dir)
def rna_tree(self, options):
"""Infer 16S + 23S tree spanning GTDB genomes."""
check_dependencies(['FastTreeMP'])
check_file_exists(options.ssu_msa)
check_file_exists(options.ssu_tree)
check_file_exists(options.lsu_msa)
check_file_exists(options.lsu_tree)
make_sure_path_exists(options.output_dir)
rna_workflow = RNA_Workflow(options.cpus)
rna_workflow.combine(options.ssu_msa,
options.ssu_tree,
options.lsu_msa,
options.lsu_tree,
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)