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python-biopython  1.60
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Bio.Blast.Applications.NcbipsiblastCommandline 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

Private Member Functions

def _validate

Detailed Description

Wrapper for the NCBI BLAST+ program psiblast.

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI
replaced the old blastpgp tool with a similar tool psiblast. This wrapper
therefore replaces BlastpgpCommandline, the wrapper for blastpgp.

>>> from Bio.Blast.Applications import NcbipsiblastCommandline
>>> cline = NcbipsiblastCommandline(help=True)
>>> cline
NcbipsiblastCommandline(cmd='psiblast', help=True)
>>> print cline
psiblast -help

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

Definition at line 1130 of file Applications.py.


Constructor & Destructor Documentation

def Bio.Blast.Applications.NcbipsiblastCommandline.__init__ (   self,
  cmd = "psiblast",
  kwargs 
)
Create a new instance of a command line wrapper object.

Reimplemented from Bio.Blast.Applications._Ncbiblast2SeqCommandline.

Definition at line 1147 of file Applications.py.

01147 
01148     def __init__(self, cmd="psiblast", **kwargs):
01149         self.parameters = [
01150             #General search options:
01151             _Option(["-matrix", "matrix"],
01152                     "Scoring matrix name (default BLOSUM62).",
01153                     equate=False),
01154             _Option(["-threshold", "threshold"],
01155                     "Minimum word score such that the word is added to the "
01156                     "BLAST lookup table (float)",
01157                     equate=False),
01158             _Option(["-comp_based_stats", "comp_based_stats"],
01159                     """Use composition-based statistics (string, default 2, i.e. True).
01160 
01161                     0, F or f: no composition-based statistics
01162                     2, T or t, D or d : Composition-based score adjustment
01163                     as in Bioinformatics 21:902-911, 2005, conditioned on
01164                     sequence properties
01165 
01166                     Note that tblastn also supports values of 1 and 3.""",
01167                     checker_function=lambda value : value in "0Ft2TtDd",
01168                     equate=False),
01169             #Query filtering options:
01170             _Option(["-seg", "seg"],
01171                     """Filter query sequence with SEG (string).
01172 
01173                     Format: "yes", "window locut hicut", or "no" to disable.
01174                     Default is "12 2.2 2.5""",
01175                     equate=False),
01176             #Extension options:
01177             _Option(["-gap_trigger", "gap_trigger"],
01178                     "Number of bits to trigger gapping (float, default 22)",
01179                     equate=False),
01180             #Miscellaneous options:
01181             _Switch(["-use_sw_tback", "use_sw_tback"],
01182                     "Compute locally optimal Smith-Waterman alignments?"),
01183             #PSI-BLAST options:
01184             _Option(["-num_iterations", "num_iterations"],
01185                     """Number of iterations to perform, integer
01186 
01187                     Integer of at least one. Default is one.
01188                     Incompatible with: remote""",
01189                     equate=False),
01190             _Option(["-out_pssm", "out_pssm"],
01191                     "File name to store checkpoint file",
01192                     filename=True,
01193                     equate=False),
01194             _Option(["-out_ascii_pssm", "out_ascii_pssm"],
01195                     "File name to store ASCII version of PSSM",
01196                     filename=True,
01197                     equate=False),
01198             _Option(["-in_msa", "in_msa"],
01199                     """File name of multiple sequence alignment to restart
01200                     PSI-BLAST
01201 
01202                     Incompatible with: in_pssm, query""",
01203                     filename=True,
01204                     equate=False),
01205             _Option(["-msa_master_idx", "msa_master_idx"],
01206                     """Index of sequence to use as master in MSA.
01207 
01208                     Index (1-based) of sequence to use as the master in the
01209                     multiple sequence alignment. If not specified, the first
01210                     sequence is used.""",
01211                     equate=False),
01212             _Option(["-in_pssm", "in_pssm"],
01213                     """PSI-BLAST checkpoint file
01214 
01215                     Incompatible with: in_msa, query, phi_pattern""",
01216                     filename=True,
01217                     equate=False),
01218             #PSSM engine options:
01219             _Option(["-pseudocount", "pseudocount"],
01220                     """Pseudo-count value used when constructing PSSM
01221 
01222                     Integer. Default is zero.""",
01223                     equate=False),
01224             _Option(["-inclusion_ethresh", "inclusion_ethresh"],
01225                     """E-value inclusion threshold for pairwise alignments
01226 
01227                     Float. Default is 0.002.""",
01228                     equate=False),
01229             #PHI-BLAST options:
01230             _Option(["-phi_pattern", "phi_pattern"],
01231                     """File name containing pattern to search
01232 
01233                     Incompatible with: in_pssm""",
01234                     filename=True,
01235                     equate=False),
01236             ]
01237         _Ncbiblast2SeqCommandline.__init__(self, cmd, **kwargs)

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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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Make sure the required parameters have been set (PRIVATE).

No return value - it either works or raises a ValueError.

This is a separate method (called from __str__) so that subclasses may
override it.

Reimplemented from Bio.Blast.Applications._Ncbiblast2SeqCommandline.

Definition at line 1238 of file Applications.py.

01238 
01239     def _validate(self):
01240         incompatibles = {"num_iterations":["remote"],
01241                          "in_msa":["in_pssm", "query"],
01242                          "in_pssm":["in_msa","query","phi_pattern"]}
01243         self._validate_incompatibilities(incompatibles)
01244         _Ncbiblast2SeqCommandline._validate(self)
01245 

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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

Reimplemented from Bio.Blast.Applications._Ncbiblast2SeqCommandline.

Definition at line 1148 of file Applications.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: