Package Bio :: Package SearchIO :: Package BlastIO :: Module blast_xml
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Module blast_xml

source code

Bio.SearchIO parser for BLAST+ XML output formats.
Classes [hide private]
  BlastXmlParser
Parser for the BLAST XML format
  BlastXmlIndexer
Indexer class for BLAST XML output.
  _BlastXmlGenerator
Event-based XML Generator.
  BlastXmlWriter
Stream-based BLAST+ XML Writer.
Variables [hide private]
  _empty_bytes_string = ''
  _ELEM_QRESULT_OPT = {'Statistics_db-len': ('stat_db_len', <typ...
  _ELEM_HIT = {'Hit_accession': ('accession', <type 'str'>), 'Hi...
  _ELEM_HSP = {'Hsp_bit-score': ('bitscore', <type 'float'>), 'H...
  _ELEM_FRAG = {'Hsp_align-len': ('aln_span', <type 'int'>), 'Hs...
  _ELEM_META = {'BlastOutput_db': ('target', <type 'str'>), 'Bla...
  _ELEM_QRESULT_FALLBACK = {'BlastOutput_query-ID': ('id', <type...
  _WRITE_MAPS = {'hit': (('id', 'id'), ('def', 'description'), (...
  _DTD_OPT = ('BlastOutput_query-seq', 'BlastOutput_mbstat', 'It...
  _RE_VERSION = re.compile(r'\d+\.\d+\.\d+\+?')
  __package__ = 'Bio.SearchIO.BlastIO'
Variables Details [hide private]

_ELEM_QRESULT_OPT

Value:
{'Statistics_db-len': ('stat_db_len', <type 'int'>),
 'Statistics_db-num': ('stat_db_num', <type 'int'>),
 'Statistics_eff-space': ('stat_eff_space', <type 'float'>),
 'Statistics_entropy': ('stat_entropy', <type 'float'>),
 'Statistics_hsp-len': ('stat_hsp_len', <type 'int'>),
 'Statistics_kappa': ('stat_kappa', <type 'float'>),
 'Statistics_lambda': ('stat_lambda', <type 'float'>)}

_ELEM_HIT

Value:
{'Hit_accession': ('accession', <type 'str'>),
 'Hit_len': ('seq_len', <type 'int'>)}

_ELEM_HSP

Value:
{'Hsp_bit-score': ('bitscore', <type 'float'>),
 'Hsp_density': ('density', <type 'float'>),
 'Hsp_evalue': ('evalue', <type 'float'>),
 'Hsp_gaps': ('gap_num', <type 'int'>),
 'Hsp_identity': ('ident_num', <type 'int'>),
 'Hsp_positive': ('pos_num', <type 'int'>),
 'Hsp_score': ('bitscore_raw', <type 'int'>)}

_ELEM_FRAG

Value:
{'Hsp_align-len': ('aln_span', <type 'int'>),
 'Hsp_hit-frame': ('hit_frame', <type 'int'>),
 'Hsp_hit-from': ('hit_start', <type 'int'>),
 'Hsp_hit-to': ('hit_end', <type 'int'>),
 'Hsp_hseq': ('hit', <type 'str'>),
 'Hsp_pattern-from': ('pattern_start', <type 'int'>),
 'Hsp_pattern-to': ('pattern_end', <type 'int'>),
 'Hsp_qseq': ('query', <type 'str'>),
...

_ELEM_META

Value:
{'BlastOutput_db': ('target', <type 'str'>),
 'BlastOutput_program': ('program', <type 'str'>),
 'BlastOutput_reference': ('reference', <type 'str'>),
 'BlastOutput_version': ('version', <type 'str'>),
 'Parameters_entrez-query': ('param_entrez_query', <type 'str'>),
 'Parameters_expect': ('param_evalue_threshold', <type 'float'>),
 'Parameters_filter': ('param_filter', <type 'str'>),
 'Parameters_gap-extend': ('param_gap_extend', <type 'int'>),
...

_ELEM_QRESULT_FALLBACK

Value:
{'BlastOutput_query-ID': ('id', <type 'str'>),
 'BlastOutput_query-def': ('description', <type 'str'>),
 'BlastOutput_query-len': ('len', <type 'str'>)}

_WRITE_MAPS

Value:
{'hit': (('id', 'id'),
         ('def', 'description'),
         ('accession', 'accession'),
         ('len', 'seq_len')),
 'hsp': (('bit-score', 'bitscore'),
         ('score', 'bitscore_raw'),
         ('evalue', 'evalue'),
         ('query-from', 'query_start'),
...

_DTD_OPT

Value:
('BlastOutput_query-seq',
 'BlastOutput_mbstat',
 'Iteration_query-def',
 'Iteration_query-len',
 'Iteration-hits',
 'Iteration_stat',
 'Iteration_message',
 'Parameters_matrix',
...