Web Service: MutalyzerService
Target Namespace:
http://mutalyzer.nl/2.0/services
Port Mutalyzer Port typeSource code
Location:
https://v2.mutalyzer.nl/services/
Protocol:
SOAP
Default style:
document
Transport protocol:
SOAP over HTTP
Operations:
- checkSyntaxDetailSource code
- chromAccessionDetailSource code
- chromosomeNameDetailSource code
- descriptionExtractDetailSource code
- getBatchJobDetailSource code
- getCacheDetailSource code
- getGeneAndTranscriptDetailSource code
- getGeneLocationDetailSource code
- getGeneNameDetailSource code
- getTranscriptsDetailSource code
- getTranscriptsAndInfoDetailSource code
- getTranscriptsByGeneNameDetailSource code
- getTranscriptsMappingDetailSource code
- getTranscriptsRangeDetailSource code
- getchromNameDetailSource code
- getdbSNPDescriptionsDetailSource code
- infoDetailSource code
- mapTranscriptToChromosomesDetailSource code
- mappingInfoDetailSource code
- monitorBatchJobDetailSource code
- numberConversionDetailSource code
- pingDetailSource code
- runMutalyzerDetailSource code
- runMutalyzerLightDetailSource code
- sliceChromosomeDetailSource code
- sliceChromosomeByGeneDetailSource code
- submitBatchJobDetailSource code
- transcriptInfoDetailSource code
- uploadGenBankLocalFileDetailSource code
- uploadGenBankRemoteFileDetailSource code
Operations
- checkSyntaxDescription:Checks the syntax of a variant. @arg variant: The variant to check. @type variant: string @return: Object with fields: - valid: A boolean indicating parse result (true for succes, false in case of a parse error). - messages: List of (error) messages as strings. @rtype: objectStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:checkSyntaxInput:checkSyntax (wsdlsoap11:body, use = literal)Source codecheckSyntax type checkSyntax
- variant type string
Output:checkSyntaxResponse (wsdlsoap11:body, use = literal)Source codecheckSyntaxResponse type checkSyntaxResponse- checkSyntaxResult - optional, nillable; type CheckSyntaxOutput
- messages - optional, nillable; type SoapMessageArray
- SoapMessage - optional, unbounded, nillable; type SoapMessage
- errorcode type string
- message type string
- SoapMessage - optional, unbounded, nillable; type SoapMessage
- valid type boolean
- messages - optional, nillable; type SoapMessageArray
- chromAccessionDescription:Get the accession number of a chromosome, given a name. @arg build: The genome build (hg19, hg18, mm10). @type build: string @arg name: The name of a chromosome (e.g. chr1). @type name: string @return: The accession number of a chromosome. @rtype: stringStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:chromAccessionInput:chromAccession (wsdlsoap11:body, use = literal)Source codechromAccession type chromAccession
- build type string
- name type string
Output:chromAccessionResponse (wsdlsoap11:body, use = literal)Source codechromAccessionResponse type chromAccessionResponse- chromAccessionResult type string
- chromosomeNameDescription:Get the name of a chromosome, given a chromosome accession number. @arg build: The genome build (hg19, hg18, mm10). @type build: string @arg accNo: The accession number of a chromosome (NC_...). @type accNo: string @return: The name of a chromosome. @rtype: stringStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:chromosomeNameInput:chromosomeName (wsdlsoap11:body, use = literal)Source codechromosomeName type chromosomeName
- build type string
- accNo type string
Output:chromosomeNameResponse (wsdlsoap11:body, use = literal)Source codechromosomeNameResponse type chromosomeNameResponse- chromosomeNameResult type string
- descriptionExtractDescription:Extract the HGVS variant description from a reference sequence and an observed sequence. Note that this only works on DNA sequences for now.Style:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:descriptionExtractInput:descriptionExtract (wsdlsoap11:body, use = literal)Source codedescriptionExtract type descriptionExtract
- reference type string
- observed type string
Output:descriptionExtractResponse (wsdlsoap11:body, use = literal)Source codedescriptionExtractResponse type descriptionExtractResponse- descriptionExtractResult - optional, nillable; type Allele
- description type string
- allele - optional, nillable; type RawVarArray
- RawVar - optional, unbounded, nillable; type RawVar
- sample_start type integer
- end type integer
- weight type integer
- sample_end type integer
- deleted type string
- type type string
- inserted type string
- start_offset type integer
- start type integer
- shift type integer
- sample_start_offset type integer
- end_offset type integer
- sample_end_offset type integer
- description type string
- RawVar - optional, unbounded, nillable; type RawVar
- getBatchJobDescription:Get the result of a batch job. Input and output file formats for batch jobs are explained on the websiteStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getBatchJobInput:getBatchJob (wsdlsoap11:body, use = literal)Source codegetBatchJob type getBatchJob
- job_id type string
Output:getBatchJobResponse (wsdlsoap11:body, use = literal)Source codegetBatchJobResponse type getBatchJobResponse- getBatchJobResult - optional, nillable; type base64Binary
- getCacheDescription:Get a list of entries from the local cache created since given date. This method is intended to be used by Mutalyzer itself to synchronize the cache between installations on different servers.Style:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getCacheInput:getCache (wsdlsoap11:body, use = literal)Source codegetCache type getCache
- created_since - optional, nillable; type dateTime
Output:getCacheResponse (wsdlsoap11:body, use = literal)Source codegetCacheResponse type getCacheResponse- getCacheResult - optional, nillable; type CacheEntryArray
- CacheEntry - optional, unbounded, nillable; type CacheEntry
- hash type string
- name type string
- chromosomeOrientation - optional, nillable; type integer
- url - optional, nillable; type string
- created type dateTime
- cached - optional, nillable; type string
- chromosomeStop - optional, nillable; type integer
- chromosomeName - optional, nillable; type string
- gi - optional, nillable; type string
- chromosomeStart - optional, nillable; type integer
- CacheEntry - optional, unbounded, nillable; type CacheEntry
- getGeneAndTranscriptDescription:Todo: documentation.Style:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getGeneAndTranscriptInput:getGeneAndTranscript (wsdlsoap11:body, use = literal)Source codegetGeneAndTranscript type getGeneAndTranscript
- genomicReference type string
- transcriptReference type string
Output:getGeneAndTranscriptResponse (wsdlsoap11:body, use = literal)Source codegetGeneAndTranscriptResponse type getGeneAndTranscriptResponse- getGeneAndTranscriptResult - optional, nillable; type TranscriptNameInfo
- transcriptName type string
- productName type string
- getGeneLocationDescription:Get the location of a gene on the given genome build (assembly), using the system's transcript mapping database. @arg gene: Gene symbol. @type gene: string @arg build: Genome build (assembly) by name or alias. If omited, the system's default assembly is used. @type build: string @return: Object with the following fields: - gene: Gene symbol. - start: Gene start position (one-based, inclusive, in chromosomal orientation). If multiple transcripts for the gene are known, this contains the lowest start position. - stop: Gene stop position (one-based, inclusive, in chromosomal orientation). If multiple transcripts for the gene are known, this contains the highest stop position. - orientation: Gene orientation, either 'forward' or 'reverse'. - chromosome_name: Gene chromosome by name (e.g., 'chrX'). - chromosome_accession: Gene chromosome by accession (e.g., 'NC_000023.10'). - assembly_name: Selected genome build (assembly) by name (e.g., 'GRCh37'). - assembly_alias: Selected genome build (assembly) by alias (e.g., 'hg19').Style:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getGeneLocationInput:getGeneLocation (wsdlsoap11:body, use = literal)Source codegetGeneLocation type getGeneLocation
- gene type string
- build - optional, nillable; type string
Output:getGeneLocationResponse (wsdlsoap11:body, use = literal)Source codegetGeneLocationResponse type getGeneLocationResponse- getGeneLocationResult - optional, nillable; type GeneLocation
- assembly_name type string
- orientation type string
- stop type integer
- start type integer
- chromosome_accession type string
- chromosome_name type string
- gene type string
- assembly_alias type string
- getGeneNameDescription:Find the gene name associated with a transcript. @arg build: The genome build (hg19, hg18, mm10). @type build: string @arg accno: The identifier of a transcript, with optional version. @type accno: string @return: The name of the associated gene. @rtype: stringStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getGeneNameInput:getGeneName (wsdlsoap11:body, use = literal)Source codegetGeneName type getGeneName
- build type string
- accno type string
Output:getGeneNameResponse (wsdlsoap11:body, use = literal)Source codegetGeneNameResponse type getGeneNameResponse- getGeneNameResult type string
- getTranscriptsDescription:Get all the transcripts that overlap with a chromosomal position. On error an exception is raised: - detail ; Human readable description of the error. - faultstring: ; A code to indicate the type of error. - EARG ; The argument was not valid. - ERANGE ; An invalid range was given. @arg build: The genome build (hg19, hg18, mm10). @type build: string @arg chrom: A chromosome encoded as "chr1", ..., "chrY". @type chrom: string @arg pos: A position on the chromosome (one-based). @type pos: int @kwarg versions: If set to True, also include transcript versions. @type versions: bool @return: A list of transcripts. @rtype: listStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getTranscriptsInput:getTranscripts (wsdlsoap11:body, use = literal)Source codegetTranscripts type getTranscripts
- build type string
- chrom type string
- pos type integer
- versions - optional, nillable; type boolean
Output:getTranscriptsResponse (wsdlsoap11:body, use = literal)Source codegetTranscriptsResponse type getTranscriptsResponse- getTranscriptsResult - optional, nillable; type stringArray
- string - unbounded; type string
- getTranscriptsAndInfoDescription:Given a genomic reference, return all its transcripts with their transcription/cds start/end sites and exons. @arg genomicReference: Name of a reference sequence. @type genomicReference: string @arg geneName: Name of gene to restrict returned transcripts to. Default is to return all transcripts. @type geneName: string @return: Array of TranscriptInfo objects with fields: - name - id - product - cTransStart - gTransStart - chromTransStart - cTransEnd - gTransEnd - chromTransEnd - sortableTransEnd - cCDSStart - gCDSStart - chromCDSStart - cCDSStop - gCDSStop - chromCDSStop - locusTag - linkMethod - exons: Array of ExonInfo objects with fields: - cStart - gStart - chromStart - cStop - gStop - chromStop - proteinTranscript: ProteinTranscript object with fields: - name - id - productStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getTranscriptsAndInfoInput:getTranscriptsAndInfo (wsdlsoap11:body, use = literal)Source codegetTranscriptsAndInfo type getTranscriptsAndInfo
- genomicReference type string
- geneName - optional, nillable; type string
Output:getTranscriptsAndInfoResponse (wsdlsoap11:body, use = literal)Source codegetTranscriptsAndInfoResponse type getTranscriptsAndInfoResponse- getTranscriptsAndInfoResult - optional, nillable; type TranscriptInfoArray
- TranscriptInfo - optional, unbounded, nillable; type TranscriptInfo
- linkMethod type string
- exons - optional, nillable; type ExonInfoArray
- ExonInfo - optional, unbounded, nillable; type ExonInfo
- chromStop - optional, nillable; type integer
- gStop type integer
- cStart type string
- gStart type integer
- cStop type string
- chromStart - optional, nillable; type integer
- ExonInfo - optional, unbounded, nillable; type ExonInfo
- cCDSStop type string
- chromTransStart - optional, nillable; type integer
- locusTag type string
- chromCDSStart - optional, nillable; type integer
- gTransStart type integer
- id type string
- cTransEnd type string
- cCDSStart type string
- chromTransEnd - optional, nillable; type integer
- gTransEnd type integer
- product type string
- proteinTranscript - optional, nillable; type ProteinTranscript
- name type string
- product type string
- id type string
- sortableTransEnd type integer
- name type string
- chromCDSStop - optional, nillable; type integer
- gCDSStop type integer
- gCDSStart type integer
- cTransStart type string
- TranscriptInfo - optional, unbounded, nillable; type TranscriptInfo
- getTranscriptsByGeneNameDescription:Todo: documentation.Style:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getTranscriptsByGeneNameInput:getTranscriptsByGeneName (wsdlsoap11:body, use = literal)Source codegetTranscriptsByGeneName type getTranscriptsByGeneName
- build type string
- name type string
Output:getTranscriptsByGeneNameResponse (wsdlsoap11:body, use = literal)Source codegetTranscriptsByGeneNameResponse type getTranscriptsByGeneNameResponse- getTranscriptsByGeneNameResult - optional, nillable; type stringArray
- string - unbounded; type string
- getTranscriptsMappingDescription:Get all the transcripts and their info that overlap with a range on a chromosome. The range should be provided as one-based, inclusive positions. @arg build: The genome build (hg19, hg18, mm10). @type build: string @arg chrom: A chromosome encoded as "chr1", ..., "chrY". @type chrom: string @arg pos1: The first postion of the range. @type pos1: integer @arg pos2: The last postion of the range. @type pos2: integer @arg method: The method of determining overlap: - 0 ; Return only the transcripts that completely fall in the range [pos1, pos2]. - 1 ; Return all hit transcripts. @return: Array of TranscriptMappingInfo objects with fields: - transcript - name - version - gene - orientation - start - stop - cds_start - cds_stop All returned ranges are one-based, inclusive, and in gene orientation.Style:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getTranscriptsMappingInput:getTranscriptsMapping (wsdlsoap11:body, use = literal)Source codegetTranscriptsMapping type getTranscriptsMapping
- build type string
- chrom type string
- pos1 type integer
- pos2 type integer
- method type integer
Output:getTranscriptsMappingResponse (wsdlsoap11:body, use = literal)Source codegetTranscriptsMappingResponse type getTranscriptsMappingResponse- getTranscriptsMappingResult - optional, nillable; type TranscriptMappingInfoArray
- TranscriptMappingInfo - optional, unbounded, nillable; type TranscriptMappingInfo
- cds_start type integer
- cds_stop type integer
- name type string
- stop type integer
- start type integer
- version type integer
- gene type string
- transcript type string
- orientation type string
- TranscriptMappingInfo - optional, unbounded, nillable; type TranscriptMappingInfo
- getTranscriptsRangeDescription:Get all the transcripts that overlap with a range on a chromosome. The range should be provided as one-based, inclusive positions. @arg build: The genome build (hg19, hg18, mm10). @type build: string @arg chrom: A chromosome encoded as "chr1", ..., "chrY". @type chrom: string @arg pos1: The first postion of the range. @type pos1: integer @arg pos2: The last postion of the range. @type pos2: integer @arg method: The method of determining overlap: - 0 ; Return only the transcripts that completely fall in the range [pos1, pos2]. - 1 ; Return all hit transcripts. @kwarg versions: If set to True, also include transcript versions. @type versions: bool @return: A list of transcripts. @rtype: listStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getTranscriptsRangeInput:getTranscriptsRange (wsdlsoap11:body, use = literal)Source codegetTranscriptsRange type getTranscriptsRange
- build type string
- chrom type string
- pos1 type integer
- pos2 type integer
- method type integer
- versions - optional, nillable; type boolean
Output:getTranscriptsRangeResponse (wsdlsoap11:body, use = literal)Source codegetTranscriptsRangeResponse type getTranscriptsRangeResponse- getTranscriptsRangeResult - optional, nillable; type stringArray
- string - unbounded; type string
- getchromNameDescription:Get the chromosome name, given a transcript identifier (NM number). @arg build: The genome build (hg19, hg18, mm10). @type build: string @arg acc: The NM accession number (version NOT included) or LRG. @type acc: string @return: The name of a chromosome. @rtype: stringStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getchromNameInput:getchromName (wsdlsoap11:body, use = literal)Source codegetchromName type getchromName
- build type string
- acc type string
Output:getchromNameResponse (wsdlsoap11:body, use = literal)Source codegetchromNameResponse type getchromNameResponse- getchromNameResult type string
- getdbSNPDescriptionsDescription:Lookup HGVS descriptions for a dbSNP rs identifier. @arg rs_id: The dbSNP rs identifier, e.g. 'rs9919552'. @type rs_id: string @return: List of HGVS descriptions. @rtype: list(string)Style:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:getdbSNPDescriptionsInput:getdbSNPDescriptions (wsdlsoap11:body, use = literal)Source codegetdbSNPDescriptions type getdbSNPDescriptions
- rs_id type string
Output:getdbSNPDescriptionsResponse (wsdlsoap11:body, use = literal)Source codegetdbSNPDescriptionsResponse type getdbSNPDescriptionsResponse- getdbSNPDescriptionsResult - optional, nillable; type stringArray
- string - unbounded; type string
- infoDescription:Gives some static application information, such as the current running version. @return: Object with fields: - version: A string of the current running version. - versionParts: The parts of the current running version as a list of strings. - releaseDate: The release date for the running version as a string, or the empty string in case of a development version. - nomenclatureVersion: Version of the HGVS nomenclature used. - nomenclatureVersionParts: The parts of the HGVS nomenclature version as a list of strings. - serverName: The name of the server that is being queried. - contactEmail: The email address to contact for more information. - announcement: Announcement body text. - announcementUrl: URL to go with the announcement for further information. @rtype: objectStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:infoInput:info (wsdlsoap11:body, use = literal)Source codeinfo type infoOutput:infoResponse (wsdlsoap11:body, use = literal)Source codeinfoResponse type infoResponse
- infoResult - optional, nillable; type InfoOutput
- contactEmail - optional, nillable; type string
- announcement - optional, nillable; type string
- serverName - optional, nillable; type string
- nomenclatureVersion - optional, nillable; type string
- announcementUrl - optional, nillable; type string
- releaseDate - optional, nillable; type string
- version - optional, nillable; type string
- versionParts - optional, nillable; type stringArray
- string - unbounded; type string
- nomenclatureVersionParts - optional, nillable; type stringArray
- string - unbounded; type string
- infoResult - optional, nillable; type InfoOutput
- mapTranscriptToChromosomesDescription:Searches for a transcript reference (NM) in the chromosomal database and returns the chromosome accession.version numbers list. Example: transcript input: NM_000267.3 output: [ { "transcript": "NM_000267.3", "chromosome": "NC_000017.10" }, { "transcript": "NM_000267.3", "chromosome": "NC_000017.11" } ] @arg transcript: The transcript 'accession[.version]'. @type transcript: string @return: Complex object: - transcript ; Transcription accesion.version. - chromosome ; Chromosome accesioin.version. @rtype: objectStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:mapTranscriptToChromosomesInput:mapTranscriptToChromosomes (wsdlsoap11:body, use = literal)Source codemapTranscriptToChromosomes type mapTranscriptToChromosomes
- transcript type string
Output:mapTranscriptToChromosomesResponse (wsdlsoap11:body, use = literal)Source codemapTranscriptToChromosomesResponse type mapTranscriptToChromosomesResponse- mapTranscriptToChromosomesResult - optional, nillable; type TranscriptInChromosomeArray
- TranscriptInChromosome - optional, unbounded, nillable; type TranscriptInChromosome
- transcript type string
- chromosome type string
- TranscriptInChromosome - optional, unbounded, nillable; type TranscriptInChromosome
- mappingInfoDescription: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 I{g.} notation if the variant is in I{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, an error is returned. - If the variant is not accepted by the nomenclature parser, a parse error will be printed. @arg LOVD_ver: The LOVD version. @type LOVD_ver: string @arg build: The genome build (hg19, hg18, mm10). @type build: string @arg accNo: The NM accession number and version or LRG. @type accNo: string @arg variant: The variant. @type variant: string @return: Complex object: - start_main ; The main coordinate of the start position in I{c.} (non-star) notation. - start_offset ; The offset coordinate of the start position in I{c.} notation (intronic position). - end_main ; The main coordinate of the end position in I{c.} (non-star) notation. - end_offset ; The offset coordinate of the end position in I{c.} notation (intronic position). - start_g ; The I{g.} notation of the start position. - end_g ; The I{g.} notation of the end position. - type ; The mutation type. @rtype: objectStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:mappingInfoInput:mappingInfo (wsdlsoap11:body, use = literal)Source codemappingInfo type mappingInfo
- LOVD_ver type string
- build type string
- accNo type string
- variant type string
Output:mappingInfoResponse (wsdlsoap11:body, use = literal)Source codemappingInfoResponse type mappingInfoResponse- mappingInfoResult - optional, nillable; type Mapping
- endoffset - optional, nillable; type integer
- start_g - optional, nillable; type integer
- messages - optional, nillable; type SoapMessageArray
- SoapMessage - optional, unbounded, nillable; type SoapMessage
- errorcode type string
- message type string
- SoapMessage - optional, unbounded, nillable; type SoapMessage
- errorcode - optional, nillable; type integer
- startoffset - optional, nillable; type integer
- mutationType - optional, nillable; type string
- end_g - optional, nillable; type integer
- startmain - optional, nillable; type integer
- endmain - optional, nillable; type integer
- monitorBatchJobDescription:Get the number of entries left for a batch job. Input and output file formats for batch jobs are explained on the websiteStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:monitorBatchJobInput:monitorBatchJob (wsdlsoap11:body, use = literal)Source codemonitorBatchJob type monitorBatchJob
- job_id type string
Output:monitorBatchJobResponse (wsdlsoap11:body, use = literal)Source codemonitorBatchJobResponse type monitorBatchJobResponse- monitorBatchJobResult - optional, nillable; type integer
- numberConversionDescription:Converts I{c.} to I{g.} notation or vice versa @arg build: The genome build (hg19, hg18, mm10). @type build: string @arg variant: The variant in either I{c.} or I{g.} notation, full HGVS notation, including NM_, NC_, or LRG_ accession number. @type variant: string @kwarg gene: Optional gene name. If given, return variant descriptions on all transcripts for this gene. @type gene: string @return: The variant(s) in either I{g.} or I{c.} notation. @rtype: listStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:numberConversionInput:numberConversion (wsdlsoap11:body, use = literal)Source codenumberConversion type numberConversion
- build type string
- variant type string
- gene - optional, nillable; type string
Output:numberConversionResponse (wsdlsoap11:body, use = literal)Source codenumberConversionResponse type numberConversionResponse- numberConversionResult - optional, nillable; type stringArray
- string - unbounded; type string
- pingDescription:Simple function to test the interface. @return: Always the value 'pong'. @rtype: stringStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:pingInput:ping (wsdlsoap11:body, use = literal)Source codeping type pingOutput:pingResponse (wsdlsoap11:body, use = literal)Source codepingResponse type pingResponse
- pingResult type string
- runMutalyzerDescription:Run the Mutalyzer name checker. @arg variant: The variant description to check. @type variant: string @return: Object with fields: - referenceId: Identifier of the reference sequence used. - sourceId: Identifier of the reference sequence source, e.g. the chromosomal accession number and version in case referenceId is a UD reference created as a chromosomal slice. - sourceAccession: Accession number of the reference sequence source (only for genbank references). - sourceVersion: Version number of the reference sequence source (only for genbank references). - molecule: Molecular type of the reference sequence. - original: Original sequence. - mutated: Mutated sequence. - origMRNA: Original transcript sequence. - mutatedMRNA: Mutated transcript sequence. - origCDS: Original CDS. - newCDS: Mutated CDS. - origProtein: Original protein sequence. - newProtein: Mutated protein sequence. - altProtein: Alternative mutated protein sequence. - errors: Number of errors. - warnings: Number of warnings. - summary: Summary of messages. - chromDescription: Chromosomal description. - genomicDescription: Genomic description. - transcriptDescriptions: List of transcript descriptions. - proteinDescriptions: List of protein descriptions. - rawVariants: List of raw variants where each raw variant is represented by an object with fields: - description: Description of the raw variant. - visualisation: ASCII visualisation of the raw variant. - exons: If a transcript is selected, array of ExonInfo objects for each exon in the selected transcript with fields: - cStart - gStart - cStop - gStop - legend: Array with name and information per transcript variant and protein isoform. Each entry is an array with the following fields: - name - id - locusTag - product - linkMethod - messages: List of (error) messages.Style:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:runMutalyzerInput:runMutalyzer (wsdlsoap11:body, use = literal)Source coderunMutalyzer type runMutalyzer
- variant type string
Output:runMutalyzerResponse (wsdlsoap11:body, use = literal)Source coderunMutalyzerResponse type runMutalyzerResponse- runMutalyzerResult - optional, nillable; type MutalyzerOutput
- referenceId type string
- genomicDescription - optional, nillable; type string
- rawVariants - optional, nillable; type RawVariantArray
- RawVariant - optional, unbounded, nillable; type RawVariant
- description type string
- visualisation type string
- RawVariant - optional, unbounded, nillable; type RawVariant
- origMRNA - optional, nillable; type string
- altProtein - optional, nillable; type string
- errors - optional, nillable; type integer
- exons - optional, nillable; type ExonInfoArray
- ExonInfo - optional, unbounded, nillable; type ExonInfo
- chromStop - optional, nillable; type integer
- gStop type integer
- cStart type string
- gStart type integer
- cStop type string
- chromStart - optional, nillable; type integer
- ExonInfo - optional, unbounded, nillable; type ExonInfo
- sourceAccession - optional, nillable; type string
- sourceVersion - optional, nillable; type string
- mutated - optional, nillable; type string
- mutatedMRNA - optional, nillable; type string
- varDetails - optional, nillable; type VarDetails
- info - optional, nillable; type stringArray
- string - unbounded; type string
- operation - optional, nillable; type string
- stop - optional, nillable; type integer
- start - optional, nillable; type integer
- alt - optional, nillable; type string
- ref - optional, nillable; type string
- reference_file - optional, nillable; type string
- info - optional, nillable; type stringArray
- origCDS - optional, nillable; type string
- warnings - optional, nillable; type integer
- molecule type string
- newCDS - optional, nillable; type string
- legend - optional, nillable; type LegendRecordArray
- LegendRecord - optional, unbounded, nillable; type LegendRecord
- linkMethod - optional, nillable; type string
- name type string
- product - optional, nillable; type string
- locusTag - optional, nillable; type string
- id - optional, nillable; type string
- LegendRecord - optional, unbounded, nillable; type LegendRecord
- chromDescription - optional, nillable; type string
- newProtein - optional, nillable; type string
- sourceId type string
- proteinDescriptions - optional, nillable; type stringArray
- string - unbounded; type string
- messages - optional, nillable; type SoapMessageArray
- SoapMessage - optional, unbounded, nillable; type SoapMessage
- errorcode type string
- message type string
- SoapMessage - optional, unbounded, nillable; type SoapMessage
- summary - optional, nillable; type string
- transcriptDescriptions - optional, nillable; type stringArray
- string - unbounded; type string
- origProtein - optional, nillable; type string
- original - optional, nillable; type string
- runMutalyzerLightDescription:Run the Mutalyzer name checker. @arg variant: The variant description to check. @type variant: string @arg extras: Additional fields to be included in the response. @type extras: RequestExtras @return: Default response object contains the following fields: - referenceId: Identifier of the reference sequence used. - sourceId: Identifier of the reference sequence source, e.g. the chromosomal accession number and version in case referenceId is a UD reference created as a chromosomal slice. - sourceAccession: Accession number of the reference sequence source (only for genbank references). - sourceVersion: Version number of the reference sequence source (only for genbank references). - molecule: Molecular type of the reference sequence. - errors: Number of errors. - warnings: Number of warnings. - summary: Summary of messages. - chromDescription: Chromosomal description. - genomicDescription: Genomic description. - transcriptDescriptions: List of transcript descriptions. - proteinDescriptions: List of protein descriptions. - exons: If a transcript is selected, array of ExonInfo objects for each exon in the selected transcript with fields: - cStart - gStart - cStop - gStop - legend: Array with name and information per transcript variant and protein isoform. Each entry is an array with the following fields: - name - id - locusTag - product - linkMethod - messages: List of (error) messages. If extras is utilized the following fields are included, according to their selection: - original: Original sequence. - mutated: Mutated sequence. - varDetails: - reference_file: reference file - ref: reference bases ('.' for insertions) - alt: alternative bases ('.' for deletions) - start: start position - stop: stop position - info: information about the conversion process failureStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:runMutalyzerLightInput:runMutalyzerLight (wsdlsoap11:body, use = literal)Source coderunMutalyzerLight type runMutalyzerLight
- variant type string
- extras - optional, nillable; type RequestExtras
- original - optional, nillable; type boolean
- mutated - optional, nillable; type boolean
- varDetails - optional, nillable; type boolean
Output:runMutalyzerLightResponse (wsdlsoap11:body, use = literal)Source coderunMutalyzerLightResponse type runMutalyzerLightResponse- runMutalyzerLightResult - optional, nillable; type MutalyzerOutput
- referenceId type string
- genomicDescription - optional, nillable; type string
- rawVariants - optional, nillable; type RawVariantArray
- RawVariant - optional, unbounded, nillable; type RawVariant
- description type string
- visualisation type string
- RawVariant - optional, unbounded, nillable; type RawVariant
- origMRNA - optional, nillable; type string
- altProtein - optional, nillable; type string
- errors - optional, nillable; type integer
- exons - optional, nillable; type ExonInfoArray
- ExonInfo - optional, unbounded, nillable; type ExonInfo
- chromStop - optional, nillable; type integer
- gStop type integer
- cStart type string
- gStart type integer
- cStop type string
- chromStart - optional, nillable; type integer
- ExonInfo - optional, unbounded, nillable; type ExonInfo
- sourceAccession - optional, nillable; type string
- sourceVersion - optional, nillable; type string
- mutated - optional, nillable; type string
- mutatedMRNA - optional, nillable; type string
- varDetails - optional, nillable; type VarDetails
- info - optional, nillable; type stringArray
- string - unbounded; type string
- operation - optional, nillable; type string
- stop - optional, nillable; type integer
- start - optional, nillable; type integer
- alt - optional, nillable; type string
- ref - optional, nillable; type string
- reference_file - optional, nillable; type string
- info - optional, nillable; type stringArray
- origCDS - optional, nillable; type string
- warnings - optional, nillable; type integer
- molecule type string
- newCDS - optional, nillable; type string
- legend - optional, nillable; type LegendRecordArray
- LegendRecord - optional, unbounded, nillable; type LegendRecord
- linkMethod - optional, nillable; type string
- name type string
- product - optional, nillable; type string
- locusTag - optional, nillable; type string
- id - optional, nillable; type string
- LegendRecord - optional, unbounded, nillable; type LegendRecord
- chromDescription - optional, nillable; type string
- newProtein - optional, nillable; type string
- sourceId type string
- proteinDescriptions - optional, nillable; type stringArray
- string - unbounded; type string
- messages - optional, nillable; type SoapMessageArray
- SoapMessage - optional, unbounded, nillable; type SoapMessage
- errorcode type string
- message type string
- SoapMessage - optional, unbounded, nillable; type SoapMessage
- summary - optional, nillable; type string
- transcriptDescriptions - optional, nillable; type stringArray
- string - unbounded; type string
- origProtein - optional, nillable; type string
- original - optional, nillable; type string
- sliceChromosomeDescription:Retrieve a range of a chromosome by accession number. @arg chromAccNo: Chromosome or contig by accession number. @type chromAccNo: string @arg start: Start position (one-based, inclusive, in reference orientation). @type start: integer @arg end: End position (one-based, inclusive, in reference orientation). @type end: integer @arg orientation: Orientation of the slice. 1 for forward, 2 for reverse complement. @type orientation: integerStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:sliceChromosomeInput:sliceChromosome (wsdlsoap11:body, use = literal)Source codesliceChromosome type sliceChromosome
- chromAccNo type string
- start type integer
- end type integer
- orientation type integer
Output:sliceChromosomeResponse (wsdlsoap11:body, use = literal)Source codesliceChromosomeResponse type sliceChromosomeResponse- sliceChromosomeResult type string
- sliceChromosomeByGeneDescription:Retrieve part of the reference genome for a (HGNC) gene symbol. @arg geneSymbol: Gene symbol. @type geneSymbol: string @arg organism: Organism name without spaces. @type organism: string @arg upStream: Number of 5' flanking bases to include. @type upStream: integer @arg downStream: Number of 3' flanking bases to include. @type upStream: integer This uses the NCBI Entrez search engine and is therefore based on the current Entrez assembly for the given organism. @return: UD accession number for created slice.Style:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:sliceChromosomeByGeneInput:sliceChromosomeByGene (wsdlsoap11:body, use = literal)Source codesliceChromosomeByGene type sliceChromosomeByGene
- geneSymbol type string
- organism type string
- upStream type integer
- downStream type integer
Output:sliceChromosomeByGeneResponse (wsdlsoap11:body, use = literal)Source codesliceChromosomeByGeneResponse type sliceChromosomeByGeneResponse- sliceChromosomeByGeneResult type string
- submitBatchJobDescription:Submit a batch job. Input and output file formats for batch jobs are explained on the websiteStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:submitBatchJobInput:submitBatchJob (wsdlsoap11:body, use = literal)Source codesubmitBatchJob type submitBatchJob
- data type base64Binary
- process - optional, nillable; type string
- argument - optional, nillable; type string
- email - optional, nillable; type string
Output:submitBatchJobResponse (wsdlsoap11:body, use = literal)Source codesubmitBatchJobResponse type submitBatchJobResponse- submitBatchJobResult - optional, nillable; type string
- transcriptInfoDescription:Search for an NM number in the MySQL database, if the version number matches, the transcription start and end and CDS end in I{c.} notation is returned. @arg LOVD_ver: The LOVD version. @type LOVD_ver: string @arg build: The genome build (hg19, hg18, mm10). @type build: string @arg accNo: The NM accession number and version or LRG. @type accNo: string @return: Complex object: - trans_start ; Transcription start in I{c.} notation. - trans_stop ; Transcription stop in I{c.} notation. - CDS_stop ; CDS stop in I{c.} notation. @rtype: objectStyle:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:transcriptInfoInput:transcriptInfo (wsdlsoap11:body, use = literal)Source codetranscriptInfo type transcriptInfo
- LOVD_ver type string
- build type string
- accNo type string
Output:transcriptInfoResponse (wsdlsoap11:body, use = literal)Source codetranscriptInfoResponse type transcriptInfoResponse- transcriptInfoResult - optional, nillable; type Transcript
- trans_start - optional, nillable; type integer
- trans_stop - optional, nillable; type integer
- CDS_stop - optional, nillable; type integer
- uploadGenBankLocalFileDescription:Upload a genbank file. @arg data: Genbank file (UTF-8, base64 encoded). @return: UD accession number for the uploaded genbank file.Style:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:uploadGenBankLocalFileInput:uploadGenBankLocalFile (wsdlsoap11:body, use = literal)Source codeuploadGenBankLocalFile type uploadGenBankLocalFile
- data type base64Binary
Output:uploadGenBankLocalFileResponse (wsdlsoap11:body, use = literal)Source codeuploadGenBankLocalFileResponse type uploadGenBankLocalFileResponse- uploadGenBankLocalFileResult type string
- uploadGenBankRemoteFileDescription:Not implemented yet.Style:documentOperation type:Request-response. The endpoint receives a message, and sends a correlated message.SOAP action:uploadGenBankRemoteFileInput:uploadGenBankRemoteFile (wsdlsoap11:body, use = literal)Source codeuploadGenBankRemoteFile type uploadGenBankRemoteFile
- url type string
Output:uploadGenBankRemoteFileResponse (wsdlsoap11:body, use = literal)Source codeuploadGenBankRemoteFileResponse type uploadGenBankRemoteFileResponse- uploadGenBankRemoteFileResult type string
Port type MutalyzerSource code
WSDL source code
<?xml version="1.0"?>
<wsdl:definitions targetNamespace="http://mutalyzer.nl/2.0/services" name="Mutalyzer"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:xop="http://www.w3.org/2004/08/xop/include"
xmlns:wsdlsoap12="http://schemas.xmlsoap.org/wsdl/soap12/"
xmlns:wsdlsoap11="http://schemas.xmlsoap.org/wsdl/soap/"
xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/"
xmlns:wsa="http://schemas.xmlsoap.org/ws/2003/03/addressing"
xmlns:tns="http://mutalyzer.nl/2.0/services"
xmlns:soap12env="http://www.w3.org/2003/05/soap-envelope"
xmlns:soap12enc="http://www.w3.org/2003/05/soap-encoding"
xmlns:soap11env="http://schemas.xmlsoap.org/soap/envelope/"
xmlns:soap11enc="http://schemas.xmlsoap.org/soap/encoding/"
xmlns:s0="mutalyzer.models"
xmlns:plink="http://schemas.xmlsoap.org/ws/2003/05/partner-link/"
xmlns:http="http://schemas.xmlsoap.org/wsdl/http/"
><wsdl:types>
<xs:schema targetNamespace="mutalyzer.models" elementFormDefault="qualified">
<xs:complexType name="LegendRecord">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="RequestExtras"></xs:complexType>
<xs:complexType name="VarDetails">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="LegendRecordArray"></xs:complexType>
</xs:schema><xs:schema targetNamespace="http://mutalyzer.nl/2.0/services" elementFormDefault="qualified">
</wsdl:types><xs:complexType name="SoapMessage"></xs:complexType>
<xs:complexType name="SoapMessageArray"></xs:complexType>
<xs:complexType name="stringArray"></xs:complexType>
<xs:complexType name="ExonInfo">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="ExonInfoArray"></xs:complexType>
<xs:complexType name="CacheEntry">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="CheckSyntaxOutput"></xs:complexType>
<xs:complexType name="GeneLocation">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="InfoOutput">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="ProteinTranscript"></xs:complexType>
<xs:complexType name="RawVar">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="RawVariant"></xs:complexType>
<xs:complexType name="Transcript"></xs:complexType>
<xs:complexType name="TranscriptInChromosome"></xs:complexType>
<xs:complexType name="TranscriptMappingInfo">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="TranscriptNameInfo"></xs:complexType>
<xs:complexType name="checkSyntax"></xs:complexType>
<xs:complexType name="chromAccession"></xs:complexType>
<xs:complexType name="chromAccessionResponse"></xs:complexType>
<xs:complexType name="chromosomeName"></xs:complexType>
<xs:complexType name="chromosomeNameResponse"></xs:complexType>
<xs:complexType name="descriptionExtract"></xs:complexType>
<xs:complexType name="getBatchJob"></xs:complexType>
<xs:complexType name="getBatchJobResponse"></xs:complexType>
<xs:complexType name="getCache"></xs:complexType>
<xs:complexType name="getGeneAndTranscript"></xs:complexType>
<xs:complexType name="getGeneLocation"></xs:complexType>
<xs:complexType name="getGeneName"></xs:complexType>
<xs:complexType name="getGeneNameResponse"></xs:complexType>
<xs:complexType name="getTranscripts"></xs:complexType>
<xs:complexType name="getTranscriptsAndInfo"></xs:complexType>
<xs:complexType name="getTranscriptsByGeneName"></xs:complexType>
<xs:complexType name="getTranscriptsByGeneNameResponse"></xs:complexType>
<xs:complexType name="getTranscriptsMapping"></xs:complexType>
<xs:complexType name="getTranscriptsRange">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="getTranscriptsRangeResponse"></xs:complexType>
<xs:complexType name="getTranscriptsResponse"></xs:complexType>
<xs:complexType name="getchromName"></xs:complexType>
<xs:complexType name="getchromNameResponse"></xs:complexType>
<xs:complexType name="getdbSNPDescriptions"></xs:complexType>
<xs:complexType name="getdbSNPDescriptionsResponse"></xs:complexType>
<xs:complexType name="mapTranscriptToChromosomes"></xs:complexType>
<xs:complexType name="mappingInfo"></xs:complexType>
<xs:complexType name="monitorBatchJob"></xs:complexType>
<xs:complexType name="monitorBatchJobResponse"></xs:complexType>
<xs:complexType name="numberConversion"></xs:complexType>
<xs:complexType name="pingResponse"></xs:complexType>
<xs:complexType name="runMutalyzer"></xs:complexType>
<xs:complexType name="sliceChromosome"></xs:complexType>
<xs:complexType name="sliceChromosomeByGene"></xs:complexType>
<xs:complexType name="sliceChromosomeByGeneResponse"></xs:complexType>
<xs:complexType name="sliceChromosomeResponse"></xs:complexType>
<xs:complexType name="submitBatchJob">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="submitBatchJobResponse"></xs:complexType>
<xs:complexType name="transcriptInfo"></xs:complexType>
<xs:complexType name="uploadGenBankLocalFile"></xs:complexType>
<xs:complexType name="uploadGenBankLocalFileResponse"></xs:complexType>
<xs:complexType name="uploadGenBankRemoteFile">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="uploadGenBankRemoteFileResponse"></xs:complexType>
<xs:complexType name="TranscriptInChromosomeArray"></xs:complexType>
<xs:complexType name="RawVarArray"></xs:complexType>
<xs:complexType name="CacheEntryArray"></xs:complexType>
<xs:complexType name="RawVariantArray"></xs:complexType>
<xs:complexType name="TranscriptMappingInfoArray"></xs:complexType>
<xs:complexType name="checkSyntaxResponse"></xs:complexType>
<xs:complexType name="getGeneAndTranscriptResponse"></xs:complexType>
<xs:complexType name="getGeneLocationResponse"></xs:complexType>
<xs:complexType name="infoResponse"></xs:complexType>
<xs:complexType name="numberConversionResponse"></xs:complexType>
<xs:complexType name="runMutalyzerLight"></xs:complexType>
<xs:complexType name="transcriptInfoResponse"></xs:complexType>
<xs:complexType name="Allele"></xs:complexType>
<xs:complexType name="Mapping">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="MutalyzerOutput">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="TranscriptInfo">
<xs:sequence></xs:sequence>
</xs:complexType><xs:complexType name="getCacheResponse"></xs:complexType>
<xs:complexType name="getTranscriptsMappingResponse"></xs:complexType>
<xs:complexType name="mapTranscriptToChromosomesResponse"></xs:complexType>
<xs:complexType name="TranscriptInfoArray"></xs:complexType>
<xs:complexType name="descriptionExtractResponse"></xs:complexType>
<xs:complexType name="mappingInfoResponse"></xs:complexType>
<xs:complexType name="runMutalyzerLightResponse"></xs:complexType>
<xs:complexType name="runMutalyzerResponse"></xs:complexType>
<xs:complexType name="getTranscriptsAndInfoResponse"></xs:complexType>
</xs:schema><wsdl:message name="mappingInfo"></wsdl:message>
<wsdl:message name="mappingInfoResponse"></wsdl:message>
<wsdl:message name="getGeneAndTranscript"></wsdl:message>
<wsdl:message name="getGeneAndTranscriptResponse"></wsdl:message>
<wsdl:message name="getTranscriptsAndInfo"></wsdl:message>
<wsdl:message name="getTranscriptsAndInfoResponse"></wsdl:message>
<wsdl:message name="numberConversion"></wsdl:message>
<wsdl:message name="numberConversionResponse"></wsdl:message>
<wsdl:message name="getTranscriptsByGeneName"></wsdl:message>
<wsdl:message name="getTranscriptsByGeneNameResponse"></wsdl:message>
<wsdl:message name="uploadGenBankRemoteFile"></wsdl:message>
<wsdl:message name="uploadGenBankRemoteFileResponse"></wsdl:message>
<wsdl:message name="pingResponse"></wsdl:message>
<wsdl:message name="sliceChromosome"></wsdl:message>
<wsdl:message name="sliceChromosomeResponse"></wsdl:message>
<wsdl:message name="submitBatchJob"></wsdl:message>
<wsdl:message name="submitBatchJobResponse"></wsdl:message>
<wsdl:message name="uploadGenBankLocalFile"></wsdl:message>
<wsdl:message name="uploadGenBankLocalFileResponse"></wsdl:message>
<wsdl:message name="chromAccession"></wsdl:message>
<wsdl:message name="chromAccessionResponse"></wsdl:message>
<wsdl:message name="checkSyntax"></wsdl:message>
<wsdl:message name="checkSyntaxResponse"></wsdl:message>
<wsdl:message name="getGeneName"></wsdl:message>
<wsdl:message name="getGeneNameResponse"></wsdl:message>
<wsdl:message name="transcriptInfo"></wsdl:message>
<wsdl:message name="transcriptInfoResponse"></wsdl:message>
<wsdl:message name="getdbSNPDescriptions"></wsdl:message>
<wsdl:message name="getdbSNPDescriptionsResponse"></wsdl:message>
<wsdl:message name="descriptionExtract"></wsdl:message>
<wsdl:message name="descriptionExtractResponse"></wsdl:message>
<wsdl:message name="getchromName"></wsdl:message>
<wsdl:message name="getchromNameResponse"></wsdl:message>
<wsdl:message name="runMutalyzerLight"></wsdl:message>
<wsdl:message name="runMutalyzerLightResponse"></wsdl:message>
<wsdl:message name="mapTranscriptToChromosomes"></wsdl:message>
<wsdl:message name="mapTranscriptToChromosomesResponse"></wsdl:message>
<wsdl:message name="runMutalyzer"></wsdl:message>
<wsdl:message name="runMutalyzerResponse"></wsdl:message>
<wsdl:message name="getTranscriptsMapping"></wsdl:message>
<wsdl:message name="getTranscriptsMappingResponse"></wsdl:message>
<wsdl:message name="getBatchJob"></wsdl:message>
<wsdl:message name="getBatchJobResponse"></wsdl:message>
<wsdl:message name="getCacheResponse"></wsdl:message>
<wsdl:message name="getTranscripts"></wsdl:message>
<wsdl:message name="getTranscriptsResponse"></wsdl:message>
<wsdl:message name="infoResponse"></wsdl:message>
<wsdl:message name="sliceChromosomeByGene"></wsdl:message>
<wsdl:message name="sliceChromosomeByGeneResponse"></wsdl:message>
<wsdl:message name="getTranscriptsRange"></wsdl:message>
<wsdl:message name="getTranscriptsRangeResponse"></wsdl:message>
<wsdl:message name="chromosomeName"></wsdl:message>
<wsdl:message name="chromosomeNameResponse"></wsdl:message>
<wsdl:message name="monitorBatchJob"></wsdl:message>
<wsdl:message name="monitorBatchJobResponse"></wsdl:message>
<wsdl:message name="getGeneLocation"></wsdl:message>
<wsdl:message name="getGeneLocationResponse"></wsdl:message>
<wsdl:service name="MutalyzerService"></wsdl:service>
<wsdl:portType name="Mutalyzer">
<wsdl:operation name="mappingInfo" parameterOrder="mappingInfo">
<wsdl:documentation>
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 I{g.} notation if the variant is in I{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, an error is returned.
- If the variant is not accepted by the nomenclature parser, a parse
error will be printed.
@arg LOVD_ver: The LOVD version.
@type LOVD_ver: string
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
@arg accNo: The NM accession number and version or LRG.
@type accNo: string
@arg variant: The variant.
@type variant: string
@return: Complex object:
- start_main ; The main coordinate of the start position
in I{c.} (non-star) notation.
- start_offset ; The offset coordinate of the start position
in I{c.} notation (intronic position).
- end_main ; The main coordinate of the end position in
I{c.} (non-star) notation.
- end_offset ; The offset coordinate of the end position in
I{c.} notation (intronic position).
- start_g ; The I{g.} notation of the start position.
- end_g ; The I{g.} notation of the end position.
- type ; The mutation type.
@rtype: object
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getGeneAndTranscript" parameterOrder="getGeneAndTranscript">
<wsdl:documentation>
Todo: documentation.
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getTranscriptsAndInfo" parameterOrder="getTranscriptsAndInfo">
<wsdl:documentation>
Given a genomic reference, return all its transcripts with their
transcription/cds start/end sites and exons.
@arg genomicReference: Name of a reference sequence.
@type genomicReference: string
@arg geneName: Name of gene to restrict returned transcripts to.
Default is to return all transcripts.
@type geneName: string
@return: Array of TranscriptInfo objects with fields:
- name
- id
- product
- cTransStart
- gTransStart
- chromTransStart
- cTransEnd
- gTransEnd
- chromTransEnd
- sortableTransEnd
- cCDSStart
- gCDSStart
- chromCDSStart
- cCDSStop
- gCDSStop
- chromCDSStop
- locusTag
- linkMethod
- exons: Array of ExonInfo objects with fields:
- cStart
- gStart
- chromStart
- cStop
- gStop
- chromStop
- proteinTranscript: ProteinTranscript object with fields:
- name
- id
- product
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="numberConversion" parameterOrder="numberConversion">
<wsdl:documentation>
Converts I{c.} to I{g.} notation or vice versa
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
@arg variant: The variant in either I{c.} or I{g.} notation, full HGVS
notation, including NM_, NC_, or LRG_ accession number.
@type variant: string
@kwarg gene: Optional gene name. If given, return variant descriptions
on all transcripts for this gene.
@type gene: string
@return: The variant(s) in either I{g.} or I{c.} notation.
@rtype: list
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getTranscriptsByGeneName" parameterOrder="getTranscriptsByGeneName">
<wsdl:documentation>
Todo: documentation.
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="uploadGenBankRemoteFile" parameterOrder="uploadGenBankRemoteFile">
<wsdl:documentation>
Not implemented yet.
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="ping" parameterOrder="ping">
<wsdl:documentation>
Simple function to test the interface.
@return: Always the value 'pong'.
@rtype: string
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="sliceChromosome" parameterOrder="sliceChromosome">
<wsdl:documentation>
Retrieve a range of a chromosome by accession number.
@arg chromAccNo: Chromosome or contig by accession number.
@type chromAccNo: string
@arg start: Start position (one-based, inclusive, in reference
orientation).
@type start: integer
@arg end: End position (one-based, inclusive, in reference
orientation).
@type end: integer
@arg orientation: Orientation of the slice. 1 for forward, 2 for
reverse complement.
@type orientation: integer
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="submitBatchJob" parameterOrder="submitBatchJob">
<wsdl:documentation>
Submit a batch job.
Input and output file formats for batch jobs are explained on the
website <https://mutalyzer.nl/batch-jobs>.
Batch jobs are processed using round-robin scheduling grouped by email
address (or client IP address if no email address is specified). Per
email address, jobs are processed sequentially in order of submission.
This means you will not see any progress on this job until all your
earlier jobs have finished.
On error an exception is raised:
- detail: Human readable description of the error.
- faultstring: A code to indicate the type of error.
- EPARSE: The batch input could not be parsed.
- EMAXSIZE: Input file exceeds maximum size.
@arg data: Input file (base64 encoded).
@arg process: Optional type of the batch job, choose from: NameChecker
(default), SyntaxChecker, PositionConverter, SnpConverter.
@arg argument: Additional argument. Currently only used if batch_type
is PositionConverter, denoting the human genome build.
@arg email: Optional email address. Notification of job completion
will be sent to this address.
@return: Batch job identifier.
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="uploadGenBankLocalFile" parameterOrder="uploadGenBankLocalFile">
<wsdl:documentation>
Upload a genbank file.
@arg data: Genbank file (UTF-8, base64 encoded).
@return: UD accession number for the uploaded genbank file.
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="chromAccession" parameterOrder="chromAccession">
<wsdl:documentation>
Get the accession number of a chromosome, given a name.
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
@arg name: The name of a chromosome (e.g. chr1).
@type name: string
@return: The accession number of a chromosome.
@rtype: string
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="checkSyntax" parameterOrder="checkSyntax">
<wsdl:documentation>
Checks the syntax of a variant.
@arg variant: The variant to check.
@type variant: string
@return: Object with fields:
- valid: A boolean indicating parse result (true for
succes, false in case of a parse error).
- messages: List of (error) messages as strings.
@rtype: object
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getGeneName" parameterOrder="getGeneName">
<wsdl:documentation>
Find the gene name associated with a transcript.
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
@arg accno: The identifier of a transcript, with optional version.
@type accno: string
@return: The name of the associated gene.
@rtype: string
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="transcriptInfo" parameterOrder="transcriptInfo">
<wsdl:documentation>
Search for an NM number in the MySQL database, if the version
number matches, the transcription start and end and CDS end
in I{c.} notation is returned.
@arg LOVD_ver: The LOVD version.
@type LOVD_ver: string
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
@arg accNo: The NM accession number and version or LRG.
@type accNo: string
@return: Complex object:
- trans_start ; Transcription start in I{c.} notation.
- trans_stop ; Transcription stop in I{c.} notation.
- CDS_stop ; CDS stop in I{c.} notation.
@rtype: object
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getdbSNPDescriptions" parameterOrder="getdbSNPDescriptions">
<wsdl:documentation>
Lookup HGVS descriptions for a dbSNP rs identifier.
@arg rs_id: The dbSNP rs identifier, e.g. 'rs9919552'.
@type rs_id: string
@return: List of HGVS descriptions.
@rtype: list(string)
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="descriptionExtract" parameterOrder="descriptionExtract">
<wsdl:documentation>
Extract the HGVS variant description from a reference sequence and an
observed sequence.
Note that this only works on DNA sequences for now.
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getchromName" parameterOrder="getchromName">
<wsdl:documentation>
Get the chromosome name, given a transcript identifier (NM number).
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
@arg acc: The NM accession number (version NOT included) or LRG.
@type acc: string
@return: The name of a chromosome.
@rtype: string
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="runMutalyzerLight" parameterOrder="runMutalyzerLight">
<wsdl:documentation>
Run the Mutalyzer name checker.
@arg variant: The variant description to check.
@type variant: string
@arg extras: Additional fields to be included in the response.
@type extras: RequestExtras
@return: Default response object contains the following fields:
- referenceId: Identifier of the reference sequence used.
- sourceId: Identifier of the reference sequence source, e.g. the
chromosomal accession number and version in case referenceId
is a UD reference created as a chromosomal slice.
- sourceAccession: Accession number of the reference sequence
source (only for genbank references).
- sourceVersion: Version number of the reference sequence source
(only for genbank references).
- molecule: Molecular type of the reference sequence.
- errors: Number of errors.
- warnings: Number of warnings.
- summary: Summary of messages.
- chromDescription: Chromosomal description.
- genomicDescription: Genomic description.
- transcriptDescriptions: List of transcript descriptions.
- proteinDescriptions: List of protein descriptions.
- exons: If a transcript is selected, array of ExonInfo objects
for each exon in the selected transcript with fields:
- cStart
- gStart
- cStop
- gStop
- legend: Array with name and information per transcript variant
and protein isoform. Each entry is an array with the following
fields:
- name
- id
- locusTag
- product
- linkMethod
- messages: List of (error) messages.
If extras is utilized the following fields are included, according
to their selection:
- original: Original sequence.
- mutated: Mutated sequence.
- varDetails:
- reference_file: reference file
- ref: reference bases ('.' for insertions)
- alt: alternative bases ('.' for deletions)
- start: start position
- stop: stop position
- info: information about the conversion process failure
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="mapTranscriptToChromosomes" parameterOrder="mapTranscriptToChromosomes">
<wsdl:documentation>
Searches for a transcript reference (NM) in the chromosomal database
and returns the chromosome accession.version numbers list. Example:
transcript input:
NM_000267.3
output:
[
{
"transcript": "NM_000267.3",
"chromosome": "NC_000017.10"
},
{
"transcript": "NM_000267.3",
"chromosome": "NC_000017.11"
}
]
@arg transcript: The transcript 'accession[.version]'.
@type transcript: string
@return: Complex object:
- transcript ; Transcription accesion.version.
- chromosome ; Chromosome accesioin.version.
@rtype: object
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="runMutalyzer" parameterOrder="runMutalyzer">
<wsdl:documentation>
Run the Mutalyzer name checker.
@arg variant: The variant description to check.
@type variant: string
@return: Object with fields:
- referenceId: Identifier of the reference sequence used.
- sourceId: Identifier of the reference sequence source, e.g. the
chromosomal accession number and version in case referenceId
is a UD reference created as a chromosomal slice.
- sourceAccession: Accession number of the reference sequence
source (only for genbank references).
- sourceVersion: Version number of the reference sequence source
(only for genbank references).
- molecule: Molecular type of the reference sequence.
- original: Original sequence.
- mutated: Mutated sequence.
- origMRNA: Original transcript sequence.
- mutatedMRNA: Mutated transcript sequence.
- origCDS: Original CDS.
- newCDS: Mutated CDS.
- origProtein: Original protein sequence.
- newProtein: Mutated protein sequence.
- altProtein: Alternative mutated protein sequence.
- errors: Number of errors.
- warnings: Number of warnings.
- summary: Summary of messages.
- chromDescription: Chromosomal description.
- genomicDescription: Genomic description.
- transcriptDescriptions: List of transcript descriptions.
- proteinDescriptions: List of protein descriptions.
- rawVariants: List of raw variants where each raw variant is
represented by an object with fields:
- description: Description of the raw variant.
- visualisation: ASCII visualisation of the raw variant.
- exons: If a transcript is selected, array of ExonInfo objects
for each exon in the selected transcript with fields:
- cStart
- gStart
- cStop
- gStop
- legend: Array with name and information per transcript variant
and protein isoform. Each entry is an array with the following
fields:
- name
- id
- locusTag
- product
- linkMethod
- messages: List of (error) messages.
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getTranscriptsMapping" parameterOrder="getTranscriptsMapping">
<wsdl:documentation>
Get all the transcripts and their info that overlap with a range on a
chromosome.
The range should be provided as one-based, inclusive positions.
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
@arg chrom: A chromosome encoded as "chr1", ..., "chrY".
@type chrom: string
@arg pos1: The first postion of the range.
@type pos1: integer
@arg pos2: The last postion of the range.
@type pos2: integer
@arg method: The method of determining overlap:
- 0 ; Return only the transcripts that completely fall in the range
[pos1, pos2].
- 1 ; Return all hit transcripts.
@return: Array of TranscriptMappingInfo objects with fields:
- transcript
- name
- version
- gene
- orientation
- start
- stop
- cds_start
- cds_stop
All returned ranges are one-based, inclusive, and in gene
orientation.
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getBatchJob" parameterOrder="getBatchJob">
<wsdl:documentation>
Get the result of a batch job.
Input and output file formats for batch jobs are explained on the
website <https://mutalyzer.nl/batch-jobs>.
On error an exception is raised:
- detail: Human readable description of the error.
- faultstring: A code to indicate the type of error.
- EBATCHNOTREADY: The batch job result is not yet ready.
@arg job_id: Batch job identifier.
@return: Batch job result file (UTF-8, base64 encoded).
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getCache" parameterOrder="getCache">
<wsdl:documentation>
Get a list of entries from the local cache created since given date.
This method is intended to be used by Mutalyzer itself to synchronize
the cache between installations on different servers.
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getTranscripts" parameterOrder="getTranscripts">
<wsdl:documentation>
Get all the transcripts that overlap with a chromosomal position.
On error an exception is raised:
- detail ; Human readable description of the error.
- faultstring: ; A code to indicate the type of error.
- EARG ; The argument was not valid.
- ERANGE ; An invalid range was given.
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
@arg chrom: A chromosome encoded as "chr1", ..., "chrY".
@type chrom: string
@arg pos: A position on the chromosome (one-based).
@type pos: int
@kwarg versions: If set to True, also include transcript versions.
@type versions: bool
@return: A list of transcripts.
@rtype: list
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="info" parameterOrder="info">
<wsdl:documentation>
Gives some static application information, such as the current running
version.
@return: Object with fields:
- version: A string of the current running version.
- versionParts: The parts of the current running version as a list
of strings.
- releaseDate: The release date for the running version as a
string, or the empty string in case of a development version.
- nomenclatureVersion: Version of the HGVS nomenclature used.
- nomenclatureVersionParts: The parts of the HGVS nomenclature
version as a list of strings.
- serverName: The name of the server that is being queried.
- contactEmail: The email address to contact for more information.
- announcement: Announcement body text.
- announcementUrl: URL to go with the announcement for further
information.
@rtype: object
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="sliceChromosomeByGene" parameterOrder="sliceChromosomeByGene">
<wsdl:documentation>
Retrieve part of the reference genome for a (HGNC) gene symbol.
@arg geneSymbol: Gene symbol.
@type geneSymbol: string
@arg organism: Organism name without spaces.
@type organism: string
@arg upStream: Number of 5' flanking bases to include.
@type upStream: integer
@arg downStream: Number of 3' flanking bases to include.
@type upStream: integer
This uses the NCBI Entrez search engine and is therefore based on the
current Entrez assembly for the given organism.
@return: UD accession number for created slice.
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getTranscriptsRange" parameterOrder="getTranscriptsRange">
<wsdl:documentation>
Get all the transcripts that overlap with a range on a chromosome.
The range should be provided as one-based, inclusive positions.
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
@arg chrom: A chromosome encoded as "chr1", ..., "chrY".
@type chrom: string
@arg pos1: The first postion of the range.
@type pos1: integer
@arg pos2: The last postion of the range.
@type pos2: integer
@arg method: The method of determining overlap:
- 0 ; Return only the transcripts that completely fall in the range
[pos1, pos2].
- 1 ; Return all hit transcripts.
@kwarg versions: If set to True, also include transcript versions.
@type versions: bool
@return: A list of transcripts.
@rtype: list
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="chromosomeName" parameterOrder="chromosomeName">
<wsdl:documentation>
Get the name of a chromosome, given a chromosome accession number.
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
@arg accNo: The accession number of a chromosome (NC_...).
@type accNo: string
@return: The name of a chromosome.
@rtype: string
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="monitorBatchJob" parameterOrder="monitorBatchJob">
<wsdl:documentation>
Get the number of entries left for a batch job.
Input and output file formats for batch jobs are explained on the
website <https://mutalyzer.nl/batch-jobs>.
@arg job_id: Batch job identifier.
@return: Number of entries left.
</wsdl:documentation>
</wsdl:operation><wsdl:operation name="getGeneLocation" parameterOrder="getGeneLocation">
</wsdl:portType><wsdl:documentation>
Get the location of a gene on the given genome build (assembly), using
the system's transcript mapping database.
@arg gene: Gene symbol.
@type gene: string
@arg build: Genome build (assembly) by name or alias. If omited,
the system's default assembly is used.
@type build: string
@return: Object with the following fields:
- gene: Gene symbol.
- start: Gene start position (one-based, inclusive, in chromosomal
orientation). If multiple transcripts for the gene are known,
this contains the lowest start position.
- stop: Gene stop position (one-based, inclusive, in chromosomal
orientation). If multiple transcripts for the gene are known,
this contains the highest stop position.
- orientation: Gene orientation, either 'forward' or 'reverse'.
- chromosome_name: Gene chromosome by name (e.g., 'chrX').
- chromosome_accession: Gene chromosome by accession (e.g.,
'NC_000023.10').
- assembly_name: Selected genome build (assembly) by name (e.g.,
'GRCh37').
- assembly_alias: Selected genome build (assembly) by alias (e.g.,
'hg19').
</wsdl:documentation>
</wsdl:operation><wsdl:binding name="Mutalyzer" type="tns:Mutalyzer">
</wsdl:definitions><wsdl:operation name="mappingInfo"></wsdl:operation>
<wsdl:operation name="getGeneAndTranscript"></wsdl:operation>
<wsdl:operation name="getTranscriptsAndInfo"></wsdl:operation>
<wsdl:operation name="numberConversion"></wsdl:operation>
<wsdl:operation name="getTranscriptsByGeneName"></wsdl:operation>
<wsdl:operation name="uploadGenBankRemoteFile"></wsdl:operation>
<wsdl:operation name="ping"></wsdl:operation>
<wsdl:operation name="sliceChromosome"></wsdl:operation>
<wsdl:operation name="submitBatchJob"></wsdl:operation>
<wsdl:operation name="uploadGenBankLocalFile"></wsdl:operation>
<wsdl:operation name="chromAccession"></wsdl:operation>
<wsdl:operation name="checkSyntax"></wsdl:operation>
<wsdl:operation name="getGeneName"></wsdl:operation>
<wsdl:operation name="transcriptInfo"></wsdl:operation>
<wsdl:operation name="getdbSNPDescriptions"></wsdl:operation>
<wsdl:operation name="descriptionExtract"></wsdl:operation>
<wsdl:operation name="getchromName"></wsdl:operation>
<wsdl:operation name="runMutalyzerLight"></wsdl:operation>
<wsdl:operation name="mapTranscriptToChromosomes"></wsdl:operation>
<wsdl:operation name="runMutalyzer"></wsdl:operation>
<wsdl:operation name="getTranscriptsMapping"></wsdl:operation>
<wsdl:operation name="getBatchJob"></wsdl:operation>
<wsdl:operation name="getCache"></wsdl:operation>
<wsdl:operation name="getTranscripts"></wsdl:operation>
<wsdl:operation name="info"></wsdl:operation>
<wsdl:operation name="sliceChromosomeByGene"></wsdl:operation>
<wsdl:operation name="getTranscriptsRange"></wsdl:operation>
<wsdl:operation name="chromosomeName"></wsdl:operation>
<wsdl:operation name="monitorBatchJob"></wsdl:operation>
</wsdl:binding>