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This module provides code to work with the BLAST XML output following the DTD available on the NCBI FTP ftp://ftp.ncbi.nlm.nih.gov/blast/documents/xml/NCBI_BlastOutput.dtd Classes: BlastParser Parses XML output from BLAST (direct use discouraged). This (now) returns a list of Blast records. Historically it returned a single Blast record. You are expected to use this via the parse or read functions. _XMLParser Generic SAX parser (private). Functions: parse Incremental parser, this is an iterator that returns Blast records. It uses the BlastParser internally. read Returns a single Blast record. Uses the BlastParser internally.
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_XMLparser Generic SAX Parser |
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BlastParser Parse XML BLAST data into a Record.Blast object |
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Returns a single Blast record (assumes just one query). This function is for use when there is one and only one BLAST result in your XML file. Use the Bio.Blast.NCBIXML.parse() function if you expect more than one BLAST record (i.e. if you have more than one query sequence). |
Returns an iterator a Blast record for each query. handle - file handle to and XML file to parse debug - integer, amount of debug information to print This is a generator function that returns multiple Blast records objects - one for each query sequence given to blast. The file is read incrementally, returning complete records as they are read in. Should cope with new BLAST 2.2.14+ which gives a single XML file for mutliple query records. Should also cope with XML output from older versions BLAST which gave multiple XML files concatenated together (giving a single file which strictly speaking wasn't valid XML). |
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