Exemplo n.º 1
0
    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[
Exemplo n.º 2
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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) +
Exemplo n.º 3
0
    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"""))
Exemplo n.º 4
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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',
Exemplo n.º 5
0
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]',\
Exemplo n.º 6
0
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]',\