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
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reset(self)
Reset all the data allowing reuse of the BlastParser() object |
source code
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_end_Iteration_query_ID(self)
the identifier of the query |
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_end_Iteration_query_def(self)
the definition line of the query |
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_end_Iteration_query_len(self)
the length of the query |
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_end_BlastOutput_hits(self)
hits to the database sequences, one for every sequence |
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_end_Parameters_matrix(self)
matrix used (-M) |
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_end_Parameters_expect(self)
expect values cutoff (-e) |
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_end_Parameters_sc_match(self)
match score for nucleotide-nucleotide comparaison (-r) |
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_end_Parameters_sc_mismatch(self)
mismatch penalty for nucleotide-nucleotide comparaison (-r) |
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_end_Parameters_gap_open(self)
gap existence cost (-G) |
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_end_Parameters_gap_extend(self)
gap extension cose (-E) |
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_end_Parameters_filter(self)
filtering options (-F) |
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_end_Hit_id(self)
identifier of the database sequence |
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_end_Hit_def(self)
definition line of the database sequence |
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_end_Hit_accession(self)
accession of the database sequence |
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_end_Hsp_evalue(self)
expect value value of the HSP |
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_end_Hsp_query_from(self)
offset of query at the start of the alignment (one-offset) |
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_end_Hsp_query_to(self)
offset of query at the end of the alignment (one-offset) |
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_end_Hsp_hit_from(self)
offset of the database at the start of the alignment (one-offset) |
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_end_Hsp_hit_to(self)
offset of the database at the end of the alignment (one-offset) |
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_end_Hsp_query_frame(self)
frame of the query if applicable |
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_end_Hsp_hit_frame(self)
frame of the database sequence if applicable |
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_end_Hsp_identity(self)
number of identities in the alignment |
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_end_Hsp_positive(self)
number of positive (conservative) substitutions in the alignment |
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_end_Hsp_gaps(self)
number of gaps in the alignment |
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_end_Hsp_align_len(self)
length of the alignment |
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_end_Hsp_qseq(self)
alignment string for the query |
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_end_Hsp_hseq(self)
alignment string for the database |
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_end_Hsp_midline(self)
Formatting middle line as normally seen in BLAST report |
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_end_Statistics_db_num(self)
number of sequences in the database |
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_end_Statistics_db_len(self)
number of letters in the database |
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_end_Statistics_hsp_len(self)
the effective HSP length |
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_end_Statistics_eff_space(self)
the effective search space |
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_end_Statistics_kappa(self)
Karlin-Altschul parameter K |
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_end_Statistics_lambda(self)
Karlin-Altschul parameter Lambda |
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_end_Statistics_entropy(self)
Karlin-Altschul parameter H |
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Inherited from _XMLparser :
characters ,
endElement ,
startElement
Inherited from xml.sax.handler.ContentHandler :
endDocument ,
endElementNS ,
endPrefixMapping ,
ignorableWhitespace ,
processingInstruction ,
setDocumentLocator ,
skippedEntity ,
startDocument ,
startElementNS ,
startPrefixMapping
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