from skbio.app.util import which except ImportError as e: raise ImportError("%s\n%s" % (e, core_dependency_missing_msg)) try: from matplotlib import __version__ as matplotlib_lib_version except ImportError: matplotlib_lib_version = "Not installed." try: from emperor import __version__ as emperor_lib_version except ImportError: emperor_lib_version = "Not installed." pynast_lib_version = get_pynast_version() if pynast_lib_version is None: pynast_lib_version = "Not installed." script_info = {} script_info['brief_description'] = """Print out the qiime config settings.""" script_info[ 'script_description'] = """A simple scripts that prints out the qiime config settings and does some sanity checks.""" script_info['script_usage'] = [] script_info['script_usage'].append( ("Example 1", """Print qiime config settings:""", """print_qiime_config.py""")) script_info['script_usage'].append( ("Example 2", """Print and check qiime config settings for sanity:""", """print_qiime_config.py -t""")) script_info[
1. \"..._aligned.fasta\" - This is a FASTA file containing all aligned sequences. 2. \"..._failures.fasta\" - This is a FASTA file containing all sequences which did not meet all the criteria specified. (PyNAST only) 3. \"..._log.txt\" - This is a log file containing information pertaining to the results obtained from a particular method (e.g. BLAST percent identity, etc.).""" script_info['required_options'] = [ options_lookup['fasta_as_primary_input'] ] script_info['optional_options'] = [] # Check if PyNAST is installed - if get_pynast_version() returns None, # PyNAST is not installed. pynast_installed = get_pynast_version() is not None if pynast_installed: script_info['optional_options'].append( make_option('-m', '--alignment_method', type='choice', help='Method for aligning' + ' sequences. Valid choices are: ' + ', '.join(alignment_method_choices) + ' [default: %default]', choices=alignment_method_choices, default='pynast')) script_info['optional_options'].append( make_option('-a', '--pairwise_alignment_method', type='choice', help='method for performing pairwise ' + 'alignment in PyNAST. Valid choices are ' + ', '.join(pairwise_alignment_method_choices) +
from qcli import __version__ as qcli_lib_version except ImportError: qcli_lib_version = "ERROR: Not installed - this is required!" try: from matplotlib import __version__ as matplotlib_lib_version except ImportError: matplotlib_lib_version = "Not installed." try: from emperor import __version__ as emperor_lib_version except ImportError: emperor_lib_version = "Not installed." pynast_lib_version = get_pynast_version() if pynast_lib_version == None: pynast_lib_version = "Not installed." script_info = {} script_info['brief_description']= """Print out the qiime config settings.""" script_info['script_description'] = """A simple scripts that prints out the qiime config settings and does some sanity checks.""" script_info['script_usage']=[] script_info['script_usage'].append( ("Example 1","""Print qiime config settings:""","""print_qiime_config.py""")) script_info['script_usage'].append( ("Example 2","""Print and check qiime config settings for sanity:""", """print_qiime_config.py -t"""))
script_info[ 'output_description'] = """All aligners will output a fasta file containing the alignment and log file in the directory specified by --output_dir (default <alignment_method>_aligned). PyNAST additionally outputs a failures file, containing the sequences which failed to align. So the result of %prog will be up to three files, where the prefix of each file depends on the user supplied FASTA file: 1. \"..._aligned.fasta\" - This is a FASTA file containing all aligned sequences. 2. \"..._failures.fasta\" - This is a FASTA file containing all sequences which did not meet all the criteria specified. (PyNAST only) 3. \"..._log.txt\" - This is a log file containing information pertaining to the results obtained from a particular method (e.g. BLAST percent identity, etc.).""" script_info['required_options'] = [options_lookup['fasta_as_primary_input']] script_info['optional_options'] = [] # Check if PyNAST is installed - if get_pynast_version() returns None, # PyNAST is not installed. pynast_installed = get_pynast_version() is not None if pynast_installed: script_info['optional_options'].append( make_option( '-m', '--alignment_method', type='choice', help='Method for aligning' + ' sequences. Valid choices are: ' + ', '.join(alignment_method_choices) + ' [default: %default]', choices=alignment_method_choices, default='pynast')) script_info['optional_options'].append( make_option('-a', '--pairwise_alignment_method', type='choice',
1. \"..._aligned.fasta\" - This is a FASTA file containing all aligned sequences. 2. \"..._failures.fasta\" - This is a FASTA file containing all sequences which did not meet all the criteria specified. (PyNAST only) 3. \"..._log.txt\" - This is a log file containing information pertaining to the results obtained from a particular method (e.g. BLAST percent identity, etc.).""" script_info['required_options']=[\ options_lookup['fasta_as_primary_input'] ] script_info['optional_options'] = [] # Check if PyNAST is installed - if get_pynast_version() returns None, # PyNAST is not installed. pynast_installed = get_pynast_version() != None if pynast_installed: script_info['optional_options'].append( make_option('-m','--alignment_method',\ type='choice',help='Method for aligning'+\ ' sequences. Valid choices are: ' +\ ', '.join(alignment_method_choices) + ' [default: %default]', choices=alignment_method_choices,\ default='pynast')) script_info['optional_options'].append( make_option('-a','--pairwise_alignment_method',\ type='choice',help='method for performing pairwise ' +\ 'alignment in PyNAST. Valid choices are '+\ ', '.join(pairwise_alignment_method_choices) +\ ' [default: %default]',\