Bio.Blast.ParseBlastTable module

A parser for the NCBI blastpgp version 2.2.5 output format.

Currently only supports the ‘-m 9’ option, (table w/ annotations). Returns a BlastTableRec instance

class Bio.Blast.ParseBlastTable.BlastTableEntry(in_rec)

Bases: object

Container for Blast Table Entry, the field values from the table.

__init__(self, in_rec)

Initialize the class.

class Bio.Blast.ParseBlastTable.BlastTableRec

Bases: object

Container for Blast Table record, list of Blast Table Entries.

__init__(self)

Initialize the class.

add_entry(self, entry)

Add entry to Blast Table.

class Bio.Blast.ParseBlastTable.BlastTableReader(handle)

Bases: object

Reader for the output of blastpgp.

reader_keywords = {'BLASTP': 'version', 'Database': 'database', 'Fields': 'fields', 'Iteration': 'iteration', 'Query': 'query'}

__init__(self, handle)

Initialize the class.

__next__(self)

Return the next record when iterating over the file.