biopython v1.71.0 Bio.Blast.NCBIXML.BlastParser
Parse XML BLAST data into a Record.Blast object.
Parses XML output from BLAST (direct use discouraged). This (now) returns a list of Blast records. Historically it returned a single Blast record. You are expected to use this via the parse or read functions.
All XML ‘action’ methods are private methods and may be:
_start_TAGcalled when the start tag is found_end_TAGcalled when the end tag is found
Link to this section Summary
Functions
Constructor
The database(s) searched (PRIVATE)
Hits to the database sequences, one for every sequence (PRIVATE)
BLAST program, e.g., blastp, blastn, etc
The identifier of the query (PRIVATE)
The definition line of the query (PRIVATE)
The length of the query (PRIVATE)
A reference to the article describing the algorithm (PRIVATE)
Version number and date of the BLAST engine
Accession of the database sequence (PRIVATE)
Definition line of the database sequence (PRIVATE)
Identifier of the database sequence (PRIVATE)
Length of the alignment (PRIVATE)
Bit score of HSP (PRIVATE)
Expect value of the HSP (PRIVATE)
Number of gaps in the alignment (PRIVATE)
Frame of the database sequence if applicable (PRIVATE)
Offset of the database at the start of the alignment (one-offset) (PRIVATE)
Offset of the database at the end of the alignment (one-offset) (PRIVATE)
Alignment string for the database (PRIVATE)
Number of identities in the alignment (PRIVATE)
Formatting middle line as normally seen in BLAST report (PRIVATE)
Number of positive (conservative) substitutions in the alignment (PRIVATE)
Alignment string for the query (PRIVATE)
Frame of the query if applicable (PRIVATE)
Offset of query at the start of the alignment (one-offset) (PRIVATE)
Offset of query at the end of the alignment (one-offset) (PRIVATE)
Raw score of HSP (PRIVATE)
The identifier of the query (PRIVATE)
The definition line of the query (PRIVATE)
The length of the query (PRIVATE)
Expect values cutoff (PRIVATE)
Filtering options (-F) (PRIVATE)
Gap extension cose (-E) (PRIVATE)
Gap existence cost (-G) (PRIVATE)
Matrix used (-M on legacy BLAST) (PRIVATE)
Match score for nucleotide-nucleotide comparison (-r) (PRIVATE)
Mismatch penalty for nucleotide-nucleotide comparison (-r) (PRIVATE)
Number of letters in the database (PRIVATE)
Number of sequences in the database (PRIVATE)
The effective search space (PRIVATE)
Karlin-Altschul parameter H (PRIVATE)
The effective HSP length (PRIVATE)
Karlin-Altschul parameter K (PRIVATE)
Karlin-Altschul parameter Lambda (PRIVATE)
Reset all the data allowing reuse of the BlastParser() object
Link to this section Functions
Constructor.
Arguments:
- debug - integer, amount of debug information to print
The database(s) searched (PRIVATE).
Save this to put on each blast record object
Hits to the database sequences, one for every sequence (PRIVATE).
BLAST program, e.g., blastp, blastn, etc.
Save this to put on each blast record object
The identifier of the query (PRIVATE).
Important in old pre 2.2.14 BLAST, for recent versions
The definition line of the query (PRIVATE).
Important in old pre 2.2.14 BLAST, for recent versions
The length of the query (PRIVATE).
Important in old pre 2.2.14 BLAST, for recent versions
A reference to the article describing the algorithm (PRIVATE).
Save this to put on each blast record object
Version number and date of the BLAST engine.
e.g. “BLASTX 2.2.12 [Aug-07-2005]” but there can also be variants like “BLASTP 2.2.18+” without the date.
Save this to put on each blast record object
Accession of the database sequence (PRIVATE).
Definition line of the database sequence (PRIVATE).
Identifier of the database sequence (PRIVATE).
Length of the alignment (PRIVATE).
Bit score of HSP (PRIVATE).
Expect value of the HSP (PRIVATE).
Number of gaps in the alignment (PRIVATE).
Frame of the database sequence if applicable (PRIVATE).
Offset of the database at the start of the alignment (one-offset) (PRIVATE).
Offset of the database at the end of the alignment (one-offset) (PRIVATE).
Alignment string for the database (PRIVATE).
Number of identities in the alignment (PRIVATE).
Formatting middle line as normally seen in BLAST report (PRIVATE).
Number of positive (conservative) substitutions in the alignment (PRIVATE).
Alignment string for the query (PRIVATE).
Frame of the query if applicable (PRIVATE).
Offset of query at the start of the alignment (one-offset) (PRIVATE).
Offset of query at the end of the alignment (one-offset) (PRIVATE).
Raw score of HSP (PRIVATE).
The identifier of the query (PRIVATE).
The definition line of the query (PRIVATE).
The length of the query (PRIVATE).
Expect values cutoff (PRIVATE).
Filtering options (-F) (PRIVATE).
Gap extension cose (-E) (PRIVATE).
Gap existence cost (-G) (PRIVATE).
Matrix used (-M on legacy BLAST) (PRIVATE).
Match score for nucleotide-nucleotide comparison (-r) (PRIVATE).
Mismatch penalty for nucleotide-nucleotide comparison (-r) (PRIVATE).
Number of letters in the database (PRIVATE).
Number of sequences in the database (PRIVATE).
The effective search space (PRIVATE).
Karlin-Altschul parameter H (PRIVATE).
The effective HSP length (PRIVATE).
Karlin-Altschul parameter K (PRIVATE).
Karlin-Altschul parameter Lambda (PRIVATE).
Reset all the data allowing reuse of the BlastParser() object.