Web Service: MutalyzerService

Target Namespace:
http://mutalyzer.nl/2.0/services

Port Mutalyzer Port typeSource code

Location:
https://mutalyzer.nl/services/
Protocol:
SOAP
Default style:
document
Transport protocol:
SOAP over HTTP
Operations:
  1. checkSyntaxDetailSource code
  2. chromAccessionDetailSource code
  3. chromosomeNameDetailSource code
  4. descriptionExtractDetailSource code
  5. getBatchJobDetailSource code
  6. getCacheDetailSource code
  7. getGeneAndTranscriptDetailSource code
  8. getGeneLocationDetailSource code
  9. getGeneNameDetailSource code
  10. getTranscriptsDetailSource code
  11. getTranscriptsAndInfoDetailSource code
  12. getTranscriptsByGeneNameDetailSource code
  13. getTranscriptsMappingDetailSource code
  14. getTranscriptsRangeDetailSource code
  15. getchromNameDetailSource code
  16. getdbSNPDescriptionsDetailSource code
  17. infoDetailSource code
  18. mapTranscriptToChromosomesDetailSource code
  19. mappingInfoDetailSource code
  20. monitorBatchJobDetailSource code
  21. numberConversionDetailSource code
  22. pingDetailSource code
  23. runMutalyzerDetailSource code
  24. runMutalyzerLightDetailSource code
  25. sliceChromosomeDetailSource code
  26. sliceChromosomeByGeneDetailSource code
  27. submitBatchJobDetailSource code
  28. transcriptInfoDetailSource code
  29. uploadGenBankLocalFileDetailSource code
  30. uploadGenBankRemoteFileDetailSource code

Operations

    Port type MutalyzerSource code

    1. checkSyntax
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      checkSyntax
      Input:
      checkSyntax (soap:body, use = literal)Source code
      checkSyntax type checkSyntax
      • variant type string
      Output:
      checkSyntaxResponse (soap:body, use = literal)Source code
      checkSyntaxResponse type checkSyntaxResponse
      • checkSyntaxResult - optional, nillable; type CheckSyntaxOutput
        • messages - optional, nillable; type SoapMessageArray
          • SoapMessage - optional, unbounded, nillable; type SoapMessage
            • errorcode type string
            • message type string
        • valid type boolean
    2. chromAccession
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      chromAccession
      Input:
      chromAccession (soap:body, use = literal)Source code
      chromAccession type chromAccession
      • build type string
      • name type string
      Output:
      chromAccessionResponse (soap:body, use = literal)Source code
      chromAccessionResponse type chromAccessionResponse
      • chromAccessionResult type string
    3. chromosomeName
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      chromosomeName
      Input:
      chromosomeName (soap:body, use = literal)Source code
      chromosomeName type chromosomeName
      • build type string
      • accNo type string
      Output:
      chromosomeNameResponse (soap:body, use = literal)Source code
      chromosomeNameResponse type chromosomeNameResponse
      • chromosomeNameResult type string
    4. descriptionExtract
      Description:
      Extract the HGVS variant description from a reference sequence and an observed sequence. Note that this only works on DNA sequences for now.
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      descriptionExtract
      Input:
      descriptionExtract (soap:body, use = literal)Source code
      descriptionExtract type descriptionExtract
      • reference type string
      • observed type string
      Output:
      descriptionExtractResponse (soap:body, use = literal)Source code
      descriptionExtractResponse 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
    5. getBatchJob
      Description:
      Get the result of a batch job. Input and output file formats for batch jobs are explained on the website . 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).
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getBatchJob
      Input:
      getBatchJob (soap:body, use = literal)Source code
      getBatchJob type getBatchJob
      • job_id type string
      Output:
      getBatchJobResponse (soap:body, use = literal)Source code
      getBatchJobResponse type getBatchJobResponse
      • getBatchJobResult - optional, nillable; type base64Binary
    6. getCache
      Description:
      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:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getCache
      Input:
      getCache (soap:body, use = literal)Source code
      getCache type getCache
      • created_since - optional, nillable; type dateTime
      Output:
      getCacheResponse (soap:body, use = literal)Source code
      getCacheResponse 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
    7. getGeneAndTranscript
      Description:
      Todo: documentation.
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getGeneAndTranscript
      Input:
      getGeneAndTranscript (soap:body, use = literal)Source code
      getGeneAndTranscript type getGeneAndTranscript
      • genomicReference type string
      • transcriptReference type string
      Output:
      getGeneAndTranscriptResponse (soap:body, use = literal)Source code
      getGeneAndTranscriptResponse type getGeneAndTranscriptResponse
      • getGeneAndTranscriptResult - optional, nillable; type TranscriptNameInfo
        • transcriptName type string
        • productName type string
    8. getGeneLocation
      Description:
      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:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getGeneLocation
      Input:
      getGeneLocation (soap:body, use = literal)Source code
      getGeneLocation type getGeneLocation
      • gene type string
      • build - optional, nillable; type string
      Output:
      getGeneLocationResponse (soap:body, use = literal)Source code
      getGeneLocationResponse 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
    9. getGeneName
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getGeneName
      Input:
      getGeneName (soap:body, use = literal)Source code
      getGeneName type getGeneName
      • build type string
      • accno type string
      Output:
      getGeneNameResponse (soap:body, use = literal)Source code
      getGeneNameResponse type getGeneNameResponse
      • getGeneNameResult type string
    10. getTranscripts
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getTranscripts
      Input:
      getTranscripts (soap:body, use = literal)Source code
      getTranscripts type getTranscripts
      • build type string
      • chrom type string
      • pos type integer
      • versions - optional, nillable; type boolean
      Output:
      getTranscriptsResponse (soap:body, use = literal)Source code
      getTranscriptsResponse type getTranscriptsResponse
      • getTranscriptsResult - optional, nillable; type stringArray
        • string - unbounded; type string
    11. getTranscriptsAndInfo
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getTranscriptsAndInfo
      Input:
      getTranscriptsAndInfo (soap:body, use = literal)Source code
      getTranscriptsAndInfo type getTranscriptsAndInfo
      • genomicReference type string
      • geneName - optional, nillable; type string
      Output:
      getTranscriptsAndInfoResponse (soap:body, use = literal)Source code
      getTranscriptsAndInfoResponse 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
          • 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
    12. getTranscriptsByGeneName
      Description:
      Todo: documentation.
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getTranscriptsByGeneName
      Input:
      getTranscriptsByGeneName (soap:body, use = literal)Source code
      getTranscriptsByGeneName type getTranscriptsByGeneName
      • build type string
      • name type string
      Output:
      getTranscriptsByGeneNameResponse (soap:body, use = literal)Source code
      getTranscriptsByGeneNameResponse type getTranscriptsByGeneNameResponse
      • getTranscriptsByGeneNameResult - optional, nillable; type stringArray
        • string - unbounded; type string
    13. getTranscriptsMapping
      Description:
      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:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getTranscriptsMapping
      Input:
      getTranscriptsMapping (soap:body, use = literal)Source code
      getTranscriptsMapping type getTranscriptsMapping
      • build type string
      • chrom type string
      • pos1 type integer
      • pos2 type integer
      • method type integer
      Output:
      getTranscriptsMappingResponse (soap:body, use = literal)Source code
      getTranscriptsMappingResponse 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
    14. getTranscriptsRange
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getTranscriptsRange
      Input:
      getTranscriptsRange (soap:body, use = literal)Source code
      getTranscriptsRange type getTranscriptsRange
      • build type string
      • chrom type string
      • pos1 type integer
      • pos2 type integer
      • method type integer
      • versions - optional, nillable; type boolean
      Output:
      getTranscriptsRangeResponse (soap:body, use = literal)Source code
      getTranscriptsRangeResponse type getTranscriptsRangeResponse
      • getTranscriptsRangeResult - optional, nillable; type stringArray
        • string - unbounded; type string
    15. getchromName
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getchromName
      Input:
      getchromName (soap:body, use = literal)Source code
      getchromName type getchromName
      • build type string
      • acc type string
      Output:
      getchromNameResponse (soap:body, use = literal)Source code
      getchromNameResponse type getchromNameResponse
      • getchromNameResult type string
    16. getdbSNPDescriptions
      Description:
      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:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      getdbSNPDescriptions
      Input:
      getdbSNPDescriptions (soap:body, use = literal)Source code
      getdbSNPDescriptions type getdbSNPDescriptions
      • rs_id type string
      Output:
      getdbSNPDescriptionsResponse (soap:body, use = literal)Source code
      getdbSNPDescriptionsResponse type getdbSNPDescriptionsResponse
      • getdbSNPDescriptionsResult - optional, nillable; type stringArray
        • string - unbounded; type string
    17. info
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      info
      Input:
      info (soap:body, use = literal)Source code
      info type info
      Output:
      infoResponse (soap:body, use = literal)Source code
      infoResponse 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
    18. mapTranscriptToChromosomes
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      mapTranscriptToChromosomes
      Input:
      mapTranscriptToChromosomes (soap:body, use = literal)Source code
      mapTranscriptToChromosomes type mapTranscriptToChromosomes
      • transcript type string
      Output:
      mapTranscriptToChromosomesResponse (soap:body, use = literal)Source code
      mapTranscriptToChromosomesResponse type mapTranscriptToChromosomesResponse
      • mapTranscriptToChromosomesResult - optional, nillable; type TranscriptInChromosomeArray
        • TranscriptInChromosome - optional, unbounded, nillable; type TranscriptInChromosome
          • transcript type string
          • chromosome type string
    19. mappingInfo
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      mappingInfo
      Input:
      mappingInfo (soap:body, use = literal)Source code
      mappingInfo type mappingInfo
      • LOVD_ver type string
      • build type string
      • accNo type string
      • variant type string
      Output:
      mappingInfoResponse (soap:body, use = literal)Source code
      mappingInfoResponse 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
        • 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
    20. monitorBatchJob
      Description:
      Get the number of entries left for a batch job. Input and output file formats for batch jobs are explained on the website . @arg job_id: Batch job identifier. @return: Number of entries left.
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      monitorBatchJob
      Input:
      monitorBatchJob (soap:body, use = literal)Source code
      monitorBatchJob type monitorBatchJob
      • job_id type string
      Output:
      monitorBatchJobResponse (soap:body, use = literal)Source code
      monitorBatchJobResponse type monitorBatchJobResponse
      • monitorBatchJobResult - optional, nillable; type integer
    21. numberConversion
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      numberConversion
      Input:
      numberConversion (soap:body, use = literal)Source code
      numberConversion type numberConversion
      • build type string
      • variant type string
      • gene - optional, nillable; type string
      Output:
      numberConversionResponse (soap:body, use = literal)Source code
      numberConversionResponse type numberConversionResponse
      • numberConversionResult - optional, nillable; type stringArray
        • string - unbounded; type string
    22. ping
      Description:
      Simple function to test the interface. @return: Always the value 'pong'. @rtype: string
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      ping
      Input:
      ping (soap:body, use = literal)Source code
      ping type ping
      Output:
      pingResponse (soap:body, use = literal)Source code
      pingResponse type pingResponse
      • pingResult type string
    23. runMutalyzer
      Description:
      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:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      runMutalyzer
      Input:
      runMutalyzer (soap:body, use = literal)Source code
      runMutalyzer type runMutalyzer
      • variant type string
      Output:
      runMutalyzerResponse (soap:body, use = literal)Source code
      runMutalyzerResponse 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
        • 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
        • 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
        • 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
        • 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
        • summary - optional, nillable; type string
        • transcriptDescriptions - optional, nillable; type stringArray
          • string - unbounded; type string
        • origProtein - optional, nillable; type string
        • original - optional, nillable; type string
    24. runMutalyzerLight
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      runMutalyzerLight
      Input:
      runMutalyzerLight (soap:body, use = literal)Source code
      runMutalyzerLight 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 (soap:body, use = literal)Source code
      runMutalyzerLightResponse 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
        • 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
        • 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
        • 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
        • 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
        • summary - optional, nillable; type string
        • transcriptDescriptions - optional, nillable; type stringArray
          • string - unbounded; type string
        • origProtein - optional, nillable; type string
        • original - optional, nillable; type string
    25. sliceChromosome
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      sliceChromosome
      Input:
      sliceChromosome (soap:body, use = literal)Source code
      sliceChromosome type sliceChromosome
      • chromAccNo type string
      • start type integer
      • end type integer
      • orientation type integer
      Output:
      sliceChromosomeResponse (soap:body, use = literal)Source code
      sliceChromosomeResponse type sliceChromosomeResponse
      • sliceChromosomeResult type string
    26. sliceChromosomeByGene
      Description:
      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:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      sliceChromosomeByGene
      Input:
      sliceChromosomeByGene (soap:body, use = literal)Source code
      sliceChromosomeByGene type sliceChromosomeByGene
      • geneSymbol type string
      • organism type string
      • upStream type integer
      • downStream type integer
      Output:
      sliceChromosomeByGeneResponse (soap:body, use = literal)Source code
      sliceChromosomeByGeneResponse type sliceChromosomeByGeneResponse
      • sliceChromosomeByGeneResult type string
    27. submitBatchJob
      Description:
      Submit a batch job. Input and output file formats for batch jobs are explained on the website . 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.
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      submitBatchJob
      Input:
      submitBatchJob (soap:body, use = literal)Source code
      submitBatchJob type submitBatchJob
      • data type base64Binary
      • process - optional, nillable; type string
      • argument - optional, nillable; type string
      • email - optional, nillable; type string
      Output:
      submitBatchJobResponse (soap:body, use = literal)Source code
      submitBatchJobResponse type submitBatchJobResponse
      • submitBatchJobResult - optional, nillable; type string
    28. transcriptInfo
      Description:
      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
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      transcriptInfo
      Input:
      transcriptInfo (soap:body, use = literal)Source code
      transcriptInfo type transcriptInfo
      • LOVD_ver type string
      • build type string
      • accNo type string
      Output:
      transcriptInfoResponse (soap:body, use = literal)Source code
      transcriptInfoResponse 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
    29. uploadGenBankLocalFile
      Description:
      Upload a genbank file. @arg data: Genbank file (UTF-8, base64 encoded). @return: UD accession number for the uploaded genbank file.
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      uploadGenBankLocalFile
      Input:
      uploadGenBankLocalFile (soap:body, use = literal)Source code
      uploadGenBankLocalFile type uploadGenBankLocalFile
      • data type base64Binary
      Output:
      uploadGenBankLocalFileResponse (soap:body, use = literal)Source code
      uploadGenBankLocalFileResponse type uploadGenBankLocalFileResponse
      • uploadGenBankLocalFileResult type string
    30. uploadGenBankRemoteFile
      Description:
      Not implemented yet.
      Style:
      document
      Operation type:
      Request-response. The endpoint receives a message, and sends a correlated message.
      SOAP action:
      uploadGenBankRemoteFile
      Input:
      uploadGenBankRemoteFile (soap:body, use = literal)Source code
      uploadGenBankRemoteFile type uploadGenBankRemoteFile
      • url type string
      Output:
      uploadGenBankRemoteFileResponse (soap:body, use = literal)Source code
      uploadGenBankRemoteFileResponse type uploadGenBankRemoteFileResponse
      • uploadGenBankRemoteFileResult type string

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: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:soap="http://schemas.xmlsoap.org/wsdl/soap/"
xmlns:s0="mutalyzer.models"
xmlns:plink="http://schemas.xmlsoap.org/ws/2003/05/partner-link/"
>
<wsdl:types>
<xs:schema targetNamespace="mutalyzer.models" elementFormDefault="qualified"></xs:schema>
<xs:schema targetNamespace="http://mutalyzer.nl/2.0/services" elementFormDefault="qualified">
<xs:complexType name="MutalyzerOutput">
<xs:sequence></xs:sequence>
</xs:complexType>
</xs:schema>
</wsdl:types>
<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="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="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="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: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:portType>
<wsdl:binding name="Mutalyzer" type="tns:Mutalyzer"></wsdl:binding>
</wsdl:definitions>