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python-biopython  1.60
Public Member Functions | Public Attributes
Bio.Sequencing.Applications._Novoalign.NovoalignCommandline Class Reference
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List of all members.

Public Member Functions

def __init__
def __str__
def __repr__
def set_parameter
def __setattr__
def __call__

Public Attributes

 parameters
 program_name

Detailed Description

Command line wrapper for novoalign by Novocraft.

See www.novocraft.com - novoalign is a short read alignment program.

Example:

>>> from Bio.Sequencing.Applications import NovoalignCommandline
>>> novoalign_cline = NovoalignCommandline(database='some_db',
...                                        readfile='some_seq.txt')
>>> print novoalign_cline
novoalign -d some_db -f some_seq.txt

As will all the Biopython application wrappers, you can also add or
change options after creating the object:

>>> novoalign_cline.format = 'PRBnSEQ'
>>> novoalign_cline.r_method='0.99' # limited valid values
>>> novoalign_cline.fragment = '250 20' # must be given as a string
>>> novoalign_cline.miRNA = 100
>>> print novoalign_cline
novoalign -d some_db -f some_seq.txt -F PRBnSEQ -r 0.99 -i 250 20 -m 100

You would typically run the command line with novoalign_cline() or via
the Python subprocess module, as described in the Biopython tutorial.

Last checked against version: 2.05.04

Definition at line 10 of file _Novoalign.py.


Constructor & Destructor Documentation

def Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__ (   self,
  cmd = "novoalign",
  kwargs 
)
Create a new instance of a command line wrapper object.

Reimplemented from Bio.Application.AbstractCommandline.

Definition at line 38 of file _Novoalign.py.

00038 
00039     def __init__(self, cmd="novoalign", **kwargs):
00040         
00041         READ_FORMAT = ['FA', 'SLXFQ', 'STDFQ', 'ILMFQ', 'PRB', 'PRBnSEQ']
00042         REPORT_FORMAT = ['Native', 'Pairwise', 'SAM']
00043         REPEAT_METHOD = ['None', 'Random', 'All', 'Exhaustive', '0.99']
00044         
00045         self.parameters = \
00046            [
00047             _Option(["-d", "database"],
00048                     "database filename",
00049                     filename=True,
00050                     equate=False),
00051             _Option(["-f", "readfile"],
00052                     "read file",
00053                     filename=True,
00054                     equate=False),
00055             _Option(["-F", "format"],
00056                     "Format of read files.\n\nAllowed values: %s" \
00057                     % ", ".join(READ_FORMAT),
00058                     checker_function=lambda x: x in READ_FORMAT,
00059                     equate=False),
00060             
00061             # Alignment scoring options
00062             _Option(["-t", "threshold"],
00063                     "Threshold for alignment score",
00064                     checker_function=lambda x: isinstance(x, types.IntType),
00065                     equate=False),
00066             _Option(["-g", "gap_open"],
00067                     "Gap opening penalty [default: 40]",
00068                     checker_function=lambda x: isinstance(x, types.IntType),
00069                     equate=False),
00070             _Option(["-x", "gap_extend"],
00071                     "Gap extend penalty [default: 15]",
00072                     checker_function=lambda x: isinstance(x, types.IntType),
00073                     equate=False),
00074             _Option(["-u", "unconverted"],
00075                     "Experimental: unconverted cytosines penalty in bisulfite mode\n\n"
00076                     "Default: no penalty",
00077                     checker_function=lambda x: isinstance(x, types.IntType),
00078                     equate=False),
00079             
00080             # Quality control and read filtering
00081             _Option(["-l", "good_bases"],
00082                     "Minimum number of good quality bases [default: log(N_g, 4) + 5]",
00083                     checker_function=lambda x: isinstance(x, types.IntType),
00084                     equate=False),
00085             _Option(["-h", "homopolymer"],
00086                     "Homopolymer read filter [default: 20; disable: negative value]",
00087                     checker_function=lambda x: isinstance(x, types.IntType),
00088                     equate=False),
00089             
00090             # Read preprocessing options
00091             _Option(["-a", "adapter3"],
00092                     "Strips a 3' adapter sequence prior to alignment.\n\n"
00093                     "With paired ends two adapters can be specified",
00094                     checker_function=lambda x: isinstance(x, types.StringType),
00095                     equate=False),
00096             _Option(["-n", "truncate"],
00097                     "Truncate to specific length before alignment",
00098                     checker_function=lambda x: isinstance(x, types.IntType),
00099                     equate=False),
00100             _Option(["-s", "trimming"],
00101                     "If fail to align, trim by s bases until they map or become shorter than l.\n\n"
00102                     "Ddefault: 2",
00103                     checker_function=lambda x: isinstance(x, types.IntType),
00104                     equate=False),
00105             _Option(["-5", "adapter5"],
00106                     "Strips a 5' adapter sequence.\n\n"
00107                     "Similar to -a (adaptor3), but on the 5' end.",
00108                     checker_function=lambda x: isinstance(x, types.StringType),
00109                     equate=False),
00110             # Reporting options
00111             _Option(["-o", "report"],
00112                     "Specifies the report format.\n\nAllowed values: %s\nDefault: Native" \
00113                     % ", ".join(REPORT_FORMAT),
00114                     checker_function=lambda x: x in REPORT_FORMAT,
00115                     equate=False),
00116             _Option(["-Q", "quality"],
00117                     "Lower threshold for an alignment to be reported [default: 0]",
00118                     checker_function=lambda x: isinstance(x, types.IntType),
00119                     equate=False),
00120             _Option(["-R", "repeats"],
00121                     "If score difference is higher, report repeats.\n\n"
00122                     "Otherwise -r read method applies [default: 5]",
00123                     checker_function=lambda x: isinstance(x, types.IntType),
00124                     equate=False),
00125             _Option(["-r", "r_method"],
00126                     "Methods to report reads with multiple matches.\n\n"
00127                     "Allowed values: %s\n"
00128                     "'All' and 'Exhaustive' accept limits." \
00129                     % ", ".join(REPEAT_METHOD),
00130                     checker_function=lambda x: x.split()[0] in REPEAT_METHOD,
00131                     equate=False),
00132             _Option(["-e", "recorded"],
00133                     "Alignments recorded with score equal to the best.\n\n"
00134                     "Default: 1000 in default read method, otherwise no limit.",
00135                     checker_function=lambda x: isinstance(x, types.IntType),
00136                     equate=False),
00137             _Option(["-q", "qual_digits"],
00138                     "Decimal digits for quality scores [default: 0]",
00139                     checker_function=lambda x: isinstance(x, types.IntType),
00140                     equate=False),
00141 
00142             # Paired end options
00143             _Option(["-i", "fragment"],
00144                     "Fragment length (2 reads + insert) and standard deviation [default: 250 30]",
00145                     checker_function=lambda x: len(x.split()) == 2,
00146                     equate=False),
00147             _Option(["-v", "variation"],
00148                     "Structural variation penalty [default: 70]",
00149                     checker_function=lambda x: isinstance(x, types.IntType),
00150                     equate=False),
00151             
00152             # miRNA mode
00153             _Option(["-m", "miRNA"],
00154                     "Sets miRNA mode and optionally sets a value for the region scanned [default: off]",
00155                     checker_function=lambda x: isinstance(x, types.IntType),
00156                     equate=False),
00157             
00158             # Multithreading
00159             _Option(["-c", "cores"],
00160                     "Number of threads, disabled on free versions [default: number of cores]",
00161                     checker_function=lambda x: isinstance(x, types.IntType),
00162                     equate=False),
00163             
00164             # Quality calibrations
00165             _Option(["-k", "read_cal"],
00166                     "Read quality calibration from file (mismatch counts)",
00167                     checker_function=lambda x: isinstance(x, types.StringType),
00168                     equate=False),
00169             _Option(["-K", "write_cal"],
00170                     "Accumulate mismatch counts and write to file",
00171                     checker_function=lambda x: isinstance(x, types.StringType),
00172                     equate=False),
00173             ]
00174         AbstractCommandline.__init__(self, cmd, **kwargs)


Member Function Documentation

def Bio.Application.AbstractCommandline.__call__ (   self,
  stdin = None,
  stdout = True,
  stderr = True,
  cwd = None,
  env = None 
) [inherited]
Executes the command, waits for it to finish, and returns output.

Runs the command line tool and waits for it to finish. If it returns
a non-zero error level, an exception is raised. Otherwise two strings
are returned containing stdout and stderr.

The optional stdin argument should be a string of data which will be
passed to the tool as standard input.

The optional stdout and stderr argument are treated as a booleans, and
control if the output should be captured (True, default), or ignored
by sending it to /dev/null to avoid wasting memory (False). In the
later case empty string(s) are returned.

The optional cwd argument is a string giving the working directory to
to run the command from. See Python's subprocess module documentation
for more details.

The optional env argument is a dictionary setting the environment
variables to be used in the new process. By default the current
process' environment variables are used. See Python's subprocess
module documentation for more details.

Default example usage:

from Bio.Emboss.Applications import WaterCommandline
water_cmd = WaterCommandline(gapopen=10, gapextend=0.5,
                     stdout=True, auto=True,
                     asequence="a.fasta", bsequence="b.fasta")
print "About to run:\n%s" % water_cmd
std_output, err_output = water_cmd()

This functionality is similar to subprocess.check_output() added in
Python 2.7. In general if you require more control over running the
command, use subprocess directly.

As of Biopython 1.56, when the program called returns a non-zero error
level, a custom ApplicationError exception is raised. This includes
any stdout and stderr strings captured as attributes of the exception
object, since they may be useful for diagnosing what went wrong.

Definition at line 368 of file __init__.py.

00368 
00369                  cwd=None, env=None):
00370         """Executes the command, waits for it to finish, and returns output.
00371         
00372         Runs the command line tool and waits for it to finish. If it returns
00373         a non-zero error level, an exception is raised. Otherwise two strings
00374         are returned containing stdout and stderr.
00375         
00376         The optional stdin argument should be a string of data which will be
00377         passed to the tool as standard input.
00378 
00379         The optional stdout and stderr argument are treated as a booleans, and
00380         control if the output should be captured (True, default), or ignored
00381         by sending it to /dev/null to avoid wasting memory (False). In the
00382         later case empty string(s) are returned.
00383 
00384         The optional cwd argument is a string giving the working directory to
00385         to run the command from. See Python's subprocess module documentation
00386         for more details.
00387 
00388         The optional env argument is a dictionary setting the environment
00389         variables to be used in the new process. By default the current
00390         process' environment variables are used. See Python's subprocess
00391         module documentation for more details.
00392 
00393         Default example usage:
00394 
00395         from Bio.Emboss.Applications import WaterCommandline
00396         water_cmd = WaterCommandline(gapopen=10, gapextend=0.5,
00397                                      stdout=True, auto=True,
00398                                      asequence="a.fasta", bsequence="b.fasta")
00399         print "About to run:\n%s" % water_cmd
00400         std_output, err_output = water_cmd()
00401 
00402         This functionality is similar to subprocess.check_output() added in
00403         Python 2.7. In general if you require more control over running the
00404         command, use subprocess directly.
00405         
00406         As of Biopython 1.56, when the program called returns a non-zero error
00407         level, a custom ApplicationError exception is raised. This includes
00408         any stdout and stderr strings captured as attributes of the exception
00409         object, since they may be useful for diagnosing what went wrong.
00410         """
00411         if stdout:
00412             stdout_arg = subprocess.PIPE
00413         else:
00414             stdout_arg = open(os.devnull)
00415         if stderr:
00416             stderr_arg = subprocess.PIPE
00417         else:
00418             stderr_arg = open(os.devnull)
00419         #We may not need to supply any piped input, but we setup the
00420         #standard input pipe anyway as a work around for a python
00421         #bug if this is called from a Windows GUI program.  For
00422         #details, see http://bugs.python.org/issue1124861
00423         #
00424         #Using universal newlines is important on Python 3, this
00425         #gives unicode handles rather than bytes handles.
00426         child_process = subprocess.Popen(str(self), stdin=subprocess.PIPE,
00427                                          stdout=stdout_arg, stderr=stderr_arg,
00428                                          universal_newlines=True,
00429                                          cwd=cwd, env=env,
00430                                          shell=(sys.platform!="win32"))
00431         #Use .communicate as can get deadlocks with .wait(), see Bug 2804
00432         stdout_str, stderr_str = child_process.communicate(stdin)
00433         if not stdout: assert not stdout_str
00434         if not stderr: assert not stderr_str
00435         return_code = child_process.returncode
00436         if return_code:
00437             raise ApplicationError(return_code, str(self),
00438                                    stdout_str, stderr_str)
00439         return stdout_str, stderr_str
00440 

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Return a representation of the command line object for debugging.

e.g.
>>> from Bio.Emboss.Applications import WaterCommandline
>>> cline = WaterCommandline(gapopen=10, gapextend=0.5)
>>> cline.asequence = "asis:ACCCGGGCGCGGT"
>>> cline.bsequence = "asis:ACCCGAGCGCGGT"
>>> cline.outfile = "temp_water.txt"
>>> print cline
water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5
>>> cline
WaterCommandline(cmd='water', outfile='temp_water.txt', asequence='asis:ACCCGGGCGCGGT', bsequence='asis:ACCCGAGCGCGGT', gapopen=10, gapextend=0.5)

Definition at line 251 of file __init__.py.

00251 
00252     def __repr__(self):
00253         """Return a representation of the command line object for debugging.
00254 
00255         e.g.
00256         >>> from Bio.Emboss.Applications import WaterCommandline
00257         >>> cline = WaterCommandline(gapopen=10, gapextend=0.5)
00258         >>> cline.asequence = "asis:ACCCGGGCGCGGT"
00259         >>> cline.bsequence = "asis:ACCCGAGCGCGGT"
00260         >>> cline.outfile = "temp_water.txt"
00261         >>> print cline
00262         water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5
00263         >>> cline
00264         WaterCommandline(cmd='water', outfile='temp_water.txt', asequence='asis:ACCCGGGCGCGGT', bsequence='asis:ACCCGAGCGCGGT', gapopen=10, gapextend=0.5)
00265         """
00266         answer = "%s(cmd=%s" % (self.__class__.__name__, repr(self.program_name))
00267         for parameter in self.parameters:
00268             if parameter.is_set:
00269                 if isinstance(parameter, _Switch):
00270                     answer += ", %s=True" % parameter.names[-1]
00271                 else:
00272                     answer += ", %s=%s" \
00273                               % (parameter.names[-1], repr(parameter.value))
00274         answer += ")"
00275         return answer

def Bio.Application.AbstractCommandline.__setattr__ (   self,
  name,
  value 
) [inherited]
Set attribute name to value (PRIVATE).

This code implements a workaround for a user interface issue.
Without this __setattr__ attribute-based assignment of parameters
will silently accept invalid parameters, leading to known instances
of the user assuming that parameters for the application are set,
when they are not.

>>> from Bio.Emboss.Applications import WaterCommandline
>>> cline = WaterCommandline(gapopen=10, gapextend=0.5, stdout=True)
>>> cline.asequence = "a.fasta"
>>> cline.bsequence = "b.fasta"
>>> cline.csequence = "c.fasta"
Traceback (most recent call last):
...
ValueError: Option name csequence was not found.
>>> print cline
water -stdout -asequence=a.fasta -bsequence=b.fasta -gapopen=10 -gapextend=0.5

This workaround uses a whitelist of object attributes, and sets the
object attribute list as normal, for these.  Other attributes are
assumed to be parameters, and passed to the self.set_parameter method
for validation and assignment.

Definition at line 337 of file __init__.py.

00337 
00338     def __setattr__(self, name, value):
00339         """Set attribute name to value (PRIVATE).
00340 
00341         This code implements a workaround for a user interface issue.
00342         Without this __setattr__ attribute-based assignment of parameters
00343         will silently accept invalid parameters, leading to known instances
00344         of the user assuming that parameters for the application are set,
00345         when they are not.
00346         
00347         >>> from Bio.Emboss.Applications import WaterCommandline
00348         >>> cline = WaterCommandline(gapopen=10, gapextend=0.5, stdout=True)
00349         >>> cline.asequence = "a.fasta"
00350         >>> cline.bsequence = "b.fasta"
00351         >>> cline.csequence = "c.fasta"
00352         Traceback (most recent call last):
00353         ...
00354         ValueError: Option name csequence was not found.
00355         >>> print cline
00356         water -stdout -asequence=a.fasta -bsequence=b.fasta -gapopen=10 -gapextend=0.5
00357 
00358         This workaround uses a whitelist of object attributes, and sets the
00359         object attribute list as normal, for these.  Other attributes are
00360         assumed to be parameters, and passed to the self.set_parameter method
00361         for validation and assignment.
00362         """
00363         if name in ['parameters', 'program_name']: # Allowed attributes
00364             self.__dict__[name] = value
00365         else:
00366             self.set_parameter(name, value)  # treat as a parameter
    

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def Bio.Application.AbstractCommandline.__str__ (   self) [inherited]
Make the commandline string with the currently set options.

e.g.
>>> from Bio.Emboss.Applications import WaterCommandline
>>> cline = WaterCommandline(gapopen=10, gapextend=0.5)
>>> cline.asequence = "asis:ACCCGGGCGCGGT"
>>> cline.bsequence = "asis:ACCCGAGCGCGGT"
>>> cline.outfile = "temp_water.txt"
>>> print cline
water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5
>>> str(cline)
'water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5'

Definition at line 229 of file __init__.py.

00229 
00230     def __str__(self):
00231         """Make the commandline string with the currently set options.
00232 
00233         e.g.
00234         >>> from Bio.Emboss.Applications import WaterCommandline
00235         >>> cline = WaterCommandline(gapopen=10, gapextend=0.5)
00236         >>> cline.asequence = "asis:ACCCGGGCGCGGT"
00237         >>> cline.bsequence = "asis:ACCCGAGCGCGGT"
00238         >>> cline.outfile = "temp_water.txt"
00239         >>> print cline
00240         water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5
00241         >>> str(cline)
00242         'water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5'
00243         """
00244         self._validate()
00245         commandline = "%s " % self.program_name
00246         for parameter in self.parameters:
00247             if parameter.is_set:
00248                 #This will include a trailing space:
00249                 commandline += str(parameter)
00250         return commandline.strip() # remove trailing space

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def Bio.Application.AbstractCommandline.set_parameter (   self,
  name,
  value = None 
) [inherited]
Set a commandline option for a program.

Definition at line 297 of file __init__.py.

00297 
00298     def set_parameter(self, name, value = None):
00299         """Set a commandline option for a program.
00300         """
00301         set_option = False
00302         for parameter in self.parameters:
00303             if name in parameter.names:
00304                 if isinstance(parameter, _Switch):
00305                     if value is None:
00306                         import warnings
00307                         warnings.warn("For a switch type argument like %s, "
00308                                       "we expect a boolean.  None is treated "
00309                                       "as FALSE!" % parameter.names[-1])
00310                     parameter.is_set = bool(value)
00311                     set_option = True
00312                 else:
00313                     if value is not None:
00314                         self._check_value(value, name, parameter.checker_function)
00315                         parameter.value = value
00316                     parameter.is_set = True
00317                     set_option = True
00318         if not set_option:
00319             raise ValueError("Option name %s was not found." % name)

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Member Data Documentation

Definition at line 44 of file _Novoalign.py.

Reimplemented in Bio.Align.Applications._Dialign.DialignCommandline.

Definition at line 167 of file __init__.py.


The documentation for this class was generated from the following file: