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',
