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- soaplib.wsgi_soap.SimpleWSGISoapApp(soaplib.wsgi_soap.WSGISoapApp, soaplib.service.SoapServiceBase)
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- MutalyzerService
class MutalyzerService(soaplib.wsgi_soap.SimpleWSGISoapApp) |
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Mutalyzer webservices.
These methods are made public via a SOAP interface.
Public methods:
getTranscripts(v1, v2) ; Get all transcripts that
overlap with a chromosomal
position.
getTranscriptsRange(v1, v2, v3, v4) ; Get all transcripts that
overlap with a range on a
chromosome.
getGeneName(v1) ; Find the gene name associated
with a transcript.
varInfo(v1, v2, v3, v4) ; Convert g. to c. and vice
versa.
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- Method resolution order:
- MutalyzerService
- soaplib.wsgi_soap.SimpleWSGISoapApp
- soaplib.wsgi_soap.WSGISoapApp
- soaplib.service.SoapServiceBase
- __builtin__.object
Methods defined here:
- getGeneName(*args, **kwargs)
- Find the gene name associated with a transcript.
Arguments:
string v1 ; The identifier of a transcript.
Returns:
string ; The name of the associated gene.
- getTranscripts(*args, **kwargs)
- Get all the transcripts that overlap with a chromosomal position.
Arguments:
string v1 ; A chromosome encoded as "chr1", ..., "chrY".
int v2 ; A postion on the chromosome.
Returns:
string ; A list of transcripts.
- getTranscriptsRange(*args, **kwargs)
- Get all the transcripts that overlap with a range on a chromosome.
Arguments:
string v1 ; A chromosome encoded as "chr1", ..., "chrY".
int v2 ; The first postion of the range.
int v3 ; The last postion of the range.
int v4 ; The method of determining overlap:
0 ; Return all hit transcripts.
1 ; Return only the transcripts that completely fall
in the range [v2, v3].
Returns:
string ; A list of transcripts.
- varInfo(*args, **kwargs)
- Search for an NM number in the MySQL database, if the version
number matches, get the start and end positions in a variant and
translate these positions to g. notation if the variant is in c.
notation and vice versa.
- If no end position is present, the start position is assumed to
be the end position.
- If the version number is not found in the database, an error
message is generated and a suggestion for an other version is
given.
- If the reference sequence is not found at all, an error is
returned.
- If no variant is present, the transcription start and end and CDS
end in c. notation is returned.
- If the variant is not accepted by the nomenclature parser, a
parse error will be printed.
Arguments:
v1 ; The LOVD version.
v2 ; The human genome build (ignored for now, hg19 assumed).
v3 ; The NM accession number and version.
v4 ; The variant, or empty.
Returns:
string:
start_main ; The main coordinate of the start position
in c. (non-star) notation.
start_offset ; The offset coordinate of the start position
in c. notation (intronic position).
end_main ; The main coordinate of the end position in
c. (non-star) notation.
end_offset ; The offset coordinate of the end position in
c. notation (intronic position).
start_g ; The g. notation of the start position.
end_g ; The g. notation of the end position.
type ; The mutation type.
Returns (alternative):
string:
trans_start ; Transcription start in c. notation.
trans_stop ; Transcription stop in c. notation.
CDS_stop ; CDS stop in c. notation.
Methods inherited from soaplib.wsgi_soap.SimpleWSGISoapApp:
- __init__(self)
- getHandler(self, environ)
Methods inherited from soaplib.wsgi_soap.WSGISoapApp:
- __call__(self, environ, start_response, address_url=None)
- This method conforms to the WSGI spec for callable wsgi applications (PEP 333).
This method looks in environ['wsgi.input'] for a fully formed soap request envelope,
will deserialize the request parameters and call the method on the object returned
by the getHandler() method.
@param the http environment
@param a callable that begins the response message
@returns the string representation of the soap call
- onCall(self, environ)
- This is the first method called when this WSGI app is invoked
@param the wsgi environment
- onException(self, environ, exc, resp)
- Called when an error occurs durring execution
@param the wsgi environment
@param the exception
@param the response string
- onMethodExec(self, environ, body, py_params, soap_params)
- Called BEFORE the service implementing the functionality is called
@param the wsgi environment
@param the body element of the soap request
@param the tuple of python params being passed to the method
@param the soap elements for each params
- onResults(self, environ, py_results, soap_results)
- Called AFTER the service implementing the functionality is called
@param the wsgi environment
@param the python results from the method
@param the xml serialized results of the method
- onReturn(self, environ, returnString)
- Called before the application returns
@param the wsgi environment
@param return string of the soap request
- onWsdl(self, environ, wsdl)
- This is called when a wsdl is requested
@param the wsgi environment
@param the wsdl string
- onWsdlException(self, environ, exc, resp)
- Called when an exception occurs durring wsdl generation
@param the wsgi environment
@param exc the exception
@param the fault response string
Data descriptors inherited from soaplib.wsgi_soap.WSGISoapApp:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
Methods inherited from soaplib.service.SoapServiceBase:
- getServiceNames(self)
- Returns the service name(s) for this service. If this
object has callbacks, then a second service is declared in
the wsdl for those callbacks
- header_objects(self)
- methods(self)
- returns the soap methods for this object
@return method descriptor list
- wsdl(self, url)
- This method generates and caches the wsdl for this object based
on the soap methods designated by the soapmethod or soapdocument
descriptors
@param url the url that this service can be found at. This must be
passed in by the caller because this object has no notion of the
server environment in which it runs.
@returns the string of the wsdl
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