script_info[ "script_description" ] = """A wrapper for the align_seqs.py PyNAST option, intended to make use of multicore/multiprocessor environments to perform analyses in parallel.""" script_info["script_usage"] = [] script_info["script_usage"].append( ( """Example""", """Align the input file (-i) against using PyNAST and write the output (-o) to $PWD/pynast_aligned_seqs/. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).""", """%prog -i $PWD/inseqs.fasta -o $PWD/pynast_aligned_seqs/""", ) ) script_info["output_description"] = """This results in a multiple sequence alignment (FASTA-formatted).""" script_info["required_options"] = [options_lookup["fasta_as_primary_input"], options_lookup["output_dir"]] pairwise_alignment_method_choices = pairwise_alignment_methods.keys() blast_db_default_help = ( qiime_config["pynast_template_alignment_blastdb"] or "created on-the-fly from template_alignment" ) script_info["optional_options"] = [ make_option( "-a", "--pairwise_alignment_method", type="choice", help="Method to use for pairwise alignments" + " [default: %default]", default="uclust", choices=pairwise_alignment_method_choices, ), make_option( "-d",
'brief_description'] = """Parallel sequence alignment using PyNAST""" script_info[ 'script_description'] = """A wrapper for the align_seqs.py PyNAST option, intended to make use of multicore/multiprocessor environments to perform analyses in parallel.""" script_info['script_usage'] = [] script_info['script_usage'].append(( """Example""", """Align the input file (-i) against using PyNAST and write the output (-o) to $PWD/pynast_aligned_seqs/. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).""", """%prog -i $PWD/inseqs.fasta -o $PWD/pynast_aligned_seqs/""")) script_info[ 'output_description'] = """This results in a multiple sequence alignment (FASTA-formatted).""" script_info['required_options'] = [ options_lookup['fasta_as_primary_input'], options_lookup['output_dir'] ] pairwise_alignment_method_choices = pairwise_alignment_methods.keys() blast_db_default_help =\ qiime_config['pynast_template_alignment_blastdb'] or \ 'created on-the-fly from template_alignment' script_info['optional_options'] = [ make_option('-a', '--pairwise_alignment_method', type='choice', help='Method to use for pairwise alignments' + ' [default: %default]', default='uclust', choices=pairwise_alignment_method_choices), make_option('-d', '--blast_db', type='blast_db',