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python-biopython  1.60
Classes | Namespaces | Functions | Variables
NCBIXML.py File Reference

Go to the source code of this file.

Classes

class  Bio.Blast.NCBIXML._XMLparser
class  Bio.Blast.NCBIXML.BlastParser

Namespaces

namespace  Bio.Blast.NCBIXML

Functions

def Bio.Blast.NCBIXML._end_BlastOutput_hits
 def _end_BlastOutput_query_seq(self): """the query sequence """ pass # XXX Missing in Record.Blast ?
def Bio.Blast.NCBIXML._end_Parameters_matrix
 def _end_BlastOutput_message(self): """error messages """ pass # XXX What to do ?
def Bio.Blast.NCBIXML._end_Parameters_expect
def Bio.Blast.NCBIXML._end_Parameters_sc_match
 def _end_Parameters_include(self): """inclusion threshold for a psi-blast iteration (-h) """ pass # XXX TODO PSI
def Bio.Blast.NCBIXML._end_Parameters_sc_mismatch
def Bio.Blast.NCBIXML._end_Parameters_gap_open
def Bio.Blast.NCBIXML._end_Parameters_gap_extend
def Bio.Blast.NCBIXML._end_Parameters_filter
def Bio.Blast.NCBIXML._start_Hit
 def _end_Parameters_pattern(self): """pattern used for phi-blast search """ pass # XXX TODO PSI
def Bio.Blast.NCBIXML._end_Hit
def Bio.Blast.NCBIXML._end_Hit_id
def Bio.Blast.NCBIXML._end_Hit_def
def Bio.Blast.NCBIXML._end_Hit_accession
def Bio.Blast.NCBIXML._end_Hit_len
def Bio.Blast.NCBIXML._start_Hsp
def Bio.Blast.NCBIXML._end_Hsp_score
def Bio.Blast.NCBIXML._end_Hsp_bit_score
def Bio.Blast.NCBIXML._end_Hsp_evalue
def Bio.Blast.NCBIXML._end_Hsp_query_from
def Bio.Blast.NCBIXML._end_Hsp_query_to
def Bio.Blast.NCBIXML._end_Hsp_hit_from
def Bio.Blast.NCBIXML._end_Hsp_hit_to
def Bio.Blast.NCBIXML._end_Hsp_query_frame
 def _end_Hsp_pattern_from(self): """start of phi-blast pattern on the query (one-offset) """ pass # XXX TODO PSI
def Bio.Blast.NCBIXML._end_Hsp_hit_frame
def Bio.Blast.NCBIXML._end_Hsp_identity
def Bio.Blast.NCBIXML._end_Hsp_positive
def Bio.Blast.NCBIXML._end_Hsp_gaps
def Bio.Blast.NCBIXML._end_Hsp_align_len
def Bio.Blast.NCBIXML._end_Hsp_qseq
 def _en_Hsp_density(self): """score density """ pass # XXX ???
def Bio.Blast.NCBIXML._end_Hsp_hseq
def Bio.Blast.NCBIXML._end_Hsp_midline
def Bio.Blast.NCBIXML._end_Statistics_db_num
def Bio.Blast.NCBIXML._end_Statistics_db_len
def Bio.Blast.NCBIXML._end_Statistics_hsp_len
def Bio.Blast.NCBIXML._end_Statistics_eff_space
def Bio.Blast.NCBIXML._end_Statistics_kappa
def Bio.Blast.NCBIXML._end_Statistics_lambda
def Bio.Blast.NCBIXML._end_Statistics_entropy
def Bio.Blast.NCBIXML.read
def Bio.Blast.NCBIXML.parse

Variables

tuple Bio.Blast.NCBIXML.handle = open(sys.argv[1])
tuple Bio.Blast.NCBIXML.r_list = parse(handle)
float Bio.Blast.NCBIXML.E_VALUE_THRESH = 0.04
 Bio.Blast.NCBIXML._hit
 Bio.Blast.NCBIXML._descr
 Bio.Blast.NCBIXML._hsp
 Bio.Blast.NCBIXML._mult_al