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Package Bio :: Package Blast :: Module NCBIXML :: Class BlastParser |
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ContentHandler
--+ |_XMLparser
--+ | BlastParser
Parse XML BLAST data into a Record.Blast object
Methods: parse Parses BLAST XML data.
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 foundMethod Summary | |
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Constructor | |
Parses the XML data | |
the database(s) searched | |
hits to the database sequences, one for every sequence | |
BLAST program, e.g., blastp, blastn, etc. | |
the definition line of the query | |
the length of the query | |
a reference to the article describing the algorithm | |
version number of the BLAST engine (e.g., 2.1.2) | |
accession of the database sequence | |
definition line of the database sequence | |
identifier of the database sequence | |
_end_Hit_len(self)
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expect value value of the HSP | |
number of gaps in the alignment | |
frame of the database sequence if applicable | |
offset of the database at the start of the alignment (one-offset) | |
alignment string for the database | |
number of identities in the alignment | |
Formatting middle line as normally seen in BLAST report | |
number of positive (conservative) substitutions in the alignment | |
alignment string for the query | |
frame of the query if applicable | |
offset of query at the start of the alignment (one-offset) | |
score (in bits) of HSP | |
expect values cutoff (-e) | |
filtering options (-F) | |
gap extension cose (-E) | |
gap existence cost (-G) | |
matrix used (-M) | |
match score for nucleotide-nucleotide comparaison (-r) | |
mismatch penalty for nucleotide-nucleotide comparaison (-r) | |
number of letters in the database | |
number of sequences in the database | |
the effective search space | |
Karlin-Altschul parameter H | |
the effective HSP length | |
Karlin-Altschul parameter K | |
Karlin-Altschul parameter Lambda | |
_start_Hit(self)
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_start_Hsp(self)
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Inherited from _XMLparser | |
Removes 'dangerous' from tag names | |
Found some text | |
Found XML end tag | |
Found XML start tag | |
Inherited from ContentHandler | |
Receive notification of the end of a document. | |
Signals the end of an element in namespace mode. | |
End the scope of a prefix-URI mapping. | |
Receive notification of ignorable whitespace in element content. | |
Receive notification of a processing instruction. | |
Called by the parser to give the application a locator for locating the origin of document events. | |
Receive notification of a skipped entity. | |
Receive notification of the beginning of a document. | |
Signals the start of an element in namespace mode. | |
Begin the scope of a prefix-URI Namespace mapping. |
Method Details |
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__init__(self)
Constructor
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parse(self, handler)Parses the XML data handler -- file handler or StringIO |
_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_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_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_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_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_score(self)score (in bits) of HSP |
_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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