Package Bio :: Package Blast :: Module NCBIXML :: Class BlastParser
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Class BlastParser

ContentHandler --+    
                 |    
        _XMLparser --+
                     |
                    BlastParser


Parse XML BLAST data into a Record.Blast object

Methods:
parse           Parses BLAST XML data.
                Returns a list of Blast records

All XML 'action' methods are private methods and may be:
_start_TAG      called when the start tag is found
_end_TAG        called when the end tag is found

Method Summary
  __init__(self, debug)
Constructor
  parse(self, handler)
Parses the XML data
  reset(self)
Reset all the data allowing reuse of the BlastParser() object
  _end_BlastOutput_db(self)
the database(s) searched
  _end_BlastOutput_hits(self)
hits to the database sequences, one for every sequence
  _end_BlastOutput_program(self)
BLAST program, e.g., blastp, blastn, etc.
  _end_BlastOutput_query_def(self)
the definition line of the query
  _end_BlastOutput_query_ID(self)
the identifier of the query
  _end_BlastOutput_query_len(self)
the length of the query
  _end_BlastOutput_reference(self)
a reference to the article describing the algorithm
  _end_BlastOutput_version(self)
version number of the BLAST engine (e.g., 2.1.2)
  _end_Hit(self)
  _end_Hit_accession(self)
accession of the database sequence
  _end_Hit_def(self)
definition line of the database sequence
  _end_Hit_id(self)
identifier of the database sequence
  _end_Hit_len(self)
  _end_Hsp_align_len(self)
length of the alignment
  _end_Hsp_bit_score(self)
bit score of HSP
  _end_Hsp_evalue(self)
expect value value of the HSP
  _end_Hsp_gaps(self)
number of gaps in the alignment
  _end_Hsp_hit_frame(self)
frame of the database sequence if applicable
  _end_Hsp_hit_from(self)
offset of the database at the start of the alignment (one-offset)
  _end_Hsp_hit_to(self)
offset of the database at the end of the alignment (one-offset)
  _end_Hsp_hseq(self)
alignment string for the database
  _end_Hsp_identity(self)
number of identities in the alignment
  _end_Hsp_midline(self)
Formatting middle line as normally seen in BLAST report
  _end_Hsp_positive(self)
number of positive (conservative) substitutions in the alignment
  _end_Hsp_qseq(self)
alignment string for the query
  _end_Hsp_query_frame(self)
frame of the query if applicable
  _end_Hsp_query_from(self)
offset of query at the start of the alignment (one-offset)
  _end_Hsp_query_to(self)
offset of query at the end of the alignment (one-offset)
  _end_Hsp_score(self)
raw score of HSP
  _end_Iteration(self)
  _end_Iteration_query_def(self)
the definition line of the query
  _end_Iteration_query_ID(self)
the identifier of the query
  _end_Iteration_query_len(self)
the length of the query
  _end_Parameters_expect(self)
expect values cutoff (-e)
  _end_Parameters_filter(self)
filtering options (-F)
  _end_Parameters_gap_extend(self)
gap extension cose (-E)
  _end_Parameters_gap_open(self)
gap existence cost (-G)
  _end_Parameters_matrix(self)
matrix used (-M)
  _end_Parameters_sc_match(self)
match score for nucleotide-nucleotide comparaison (-r)
  _end_Parameters_sc_mismatch(self)
mismatch penalty for nucleotide-nucleotide comparaison (-r)
  _end_Statistics_db_len(self)
number of letters in the database
  _end_Statistics_db_num(self)
number of sequences in the database
  _end_Statistics_eff_space(self)
the effective search space
  _end_Statistics_entropy(self)
Karlin-Altschul parameter H
  _end_Statistics_hsp_len(self)
the effective HSP length
  _end_Statistics_kappa(self)
Karlin-Altschul parameter K
  _end_Statistics_lambda(self)
Karlin-Altschul parameter Lambda
  _start_Hit(self)
  _start_Hsp(self)
  _start_Iteration(self)
    Inherited from _XMLparser
  _secure_name(self, name)
Removes 'dangerous' from tag names
  characters(self, ch)
Found some text
  endElement(self, name)
Found XML end tag
  startElement(self, name, attr)
Found XML start tag
    Inherited from ContentHandler
  endDocument(self)
Receive notification of the end of a document.
  endElementNS(self, name, qname)
Signals the end of an element in namespace mode.
  endPrefixMapping(self, prefix)
End the scope of a prefix-URI mapping.
  ignorableWhitespace(self, whitespace)
Receive notification of ignorable whitespace in element content.
  processingInstruction(self, target, data)
Receive notification of a processing instruction.
  setDocumentLocator(self, locator)
Called by the parser to give the application a locator for locating the origin of document events.
  skippedEntity(self, name)
Receive notification of a skipped entity.
  startDocument(self)
Receive notification of the beginning of a document.
  startElementNS(self, name, qname, attrs)
Signals the start of an element in namespace mode.
  startPrefixMapping(self, prefix, uri)
Begin the scope of a prefix-URI Namespace mapping.

Method Details

__init__(self, debug=0)
(Constructor)

Constructor

debug - integer, amount of debug information to print
Overrides:
Bio.Blast.NCBIXML._XMLparser.__init__

parse(self, handler)

Parses the XML data

handler -- file handler or StringIO

This method returns a list of Blast record objects.

reset(self)

Reset all the data allowing reuse of the BlastParser() object

_end_BlastOutput_db(self)

the database(s) searched

Save this to put on each blast record object

_end_BlastOutput_hits(self)

hits to the database sequences, one for every sequence

_end_BlastOutput_program(self)

BLAST program, e.g., blastp, blastn, etc.

Save this to put on each blast record object

_end_BlastOutput_query_def(self)

the definition line of the query

Important in old pre 2.2.14 BLAST, for recent versions <Iteration_query-def> is enough

_end_BlastOutput_query_ID(self)

the identifier of the query

Important in old pre 2.2.14 BLAST, for recent versions <Iteration_query-ID> is enough

_end_BlastOutput_query_len(self)

the length of the query

Important in old pre 2.2.14 BLAST, for recent versions <Iteration_query-len> is enough

_end_BlastOutput_reference(self)

a reference to the article describing the algorithm

Save this to put on each blast record object

_end_BlastOutput_version(self)

version number of the BLAST engine (e.g., 2.1.2)

Save this to put on each blast record object

_end_Hit_accession(self)

accession of the database sequence

_end_Hit_def(self)

definition line of the database sequence

_end_Hit_id(self)

identifier of the database sequence

_end_Hsp_align_len(self)

length of the alignment

_end_Hsp_bit_score(self)

bit score of HSP

_end_Hsp_evalue(self)

expect value value of the HSP

_end_Hsp_gaps(self)

number of gaps in the alignment

_end_Hsp_hit_frame(self)

frame of the database sequence if applicable

_end_Hsp_hit_from(self)

offset of the database at the start of the alignment (one-offset)

_end_Hsp_hit_to(self)

offset of the database at the end of the alignment (one-offset)

_end_Hsp_hseq(self)

alignment string for the database

_end_Hsp_identity(self)

number of identities in the alignment

_end_Hsp_midline(self)

Formatting middle line as normally seen in BLAST report

_end_Hsp_positive(self)

number of positive (conservative) substitutions in the alignment

_end_Hsp_qseq(self)

alignment string for the query

_end_Hsp_query_frame(self)

frame of the query if applicable

_end_Hsp_query_from(self)

offset of query at the start of the alignment (one-offset)

_end_Hsp_query_to(self)

offset of query at the end of the alignment (one-offset)

_end_Hsp_score(self)

raw score of HSP

_end_Iteration_query_def(self)

the definition line of the query

_end_Iteration_query_ID(self)

the identifier of the query

_end_Iteration_query_len(self)

the length of the query

_end_Parameters_expect(self)

expect values cutoff (-e)

_end_Parameters_filter(self)

filtering options (-F)

_end_Parameters_gap_extend(self)

gap extension cose (-E)

_end_Parameters_gap_open(self)

gap existence cost (-G)

_end_Parameters_matrix(self)

matrix used (-M)

_end_Parameters_sc_match(self)

match score for nucleotide-nucleotide comparaison (-r)

_end_Parameters_sc_mismatch(self)

mismatch penalty for nucleotide-nucleotide comparaison (-r)

_end_Statistics_db_len(self)

number of letters in the database

_end_Statistics_db_num(self)

number of sequences in the database

_end_Statistics_eff_space(self)

the effective search space

_end_Statistics_entropy(self)

Karlin-Altschul parameter H

_end_Statistics_hsp_len(self)

the effective HSP length

_end_Statistics_kappa(self)

Karlin-Altschul parameter K

_end_Statistics_lambda(self)

Karlin-Altschul parameter Lambda

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