ost.bindings.blast Namespace Reference

Data Structures
class	AlignedPatch
class	BlastHit
class	BlastError

Functions
def	ParseBlastOutput (string, seqid_thres=0, evalue_thres=float("infinity"))
def	CreateDB (infasta, dbout, mkdb_cmd=None)
def	BlastVersion (blast_location=None)
def	Blast (query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62', blast_location=None, outfmt=0, filter_low_complexity=True)

Function Documentation

Blast()

def ost.bindings.blast.Blast	(		query,
			database,
			gap_open = 11,
			gap_ext = 1,
			matrix = 'BLOSUM62',
			blast_location = None,
			outfmt = 0,
			filter_low_complexity = True
	)

Runs a protein vs. protein blast search. The results are returned
according to the value of the ``outfmt`` parameter.

:param query: the query sequence
:type query: :class:`seq.ConstSequenceHandle`

:param database: The filename of the sequence database. Make sure that
    formatdb has been run on the database and the <database>.pin file exists.
:param matrix: The substitution matrix to be used. Must be one of 'BLOSUM45',
   'BLOSUM62', 'BLOSUM80', 'PAM30', 'PAM70'.
:param gap_open: Gap opening penalty. Note that only a subset of gap opening
   penalties is supported for each substitutition matrix. Consult the blast
   docs for more information.
:param gap_ext: Gap extension penalty. Only a subset of gap extension
   penalties are supported for each of the substitution matrices. Consult the
   blast docs for more information.
:param outfmt: output format, where '0' corresponds to default output (parsed 
   blast output and 1 to raw string output).
:param filter_low_complexity: Mask off segments of the query sequence that 
   have low compositional complexity, as determined by the SEG program of 
   Wootton & Federhen (Computers and Chemistry, 1993)
:rtype: :class:`BlastHit` (with ``outfmt=0``) or :class:`str` 
   (with ``outfmt=1``)

Definition at line 208 of file blast.py.

BlastVersion()

def ost.bindings.blast.BlastVersion

(

blast_location = None

)

Returns the version of the BLAST executable, e.g. 2.2.24 as a string

Definition at line 174 of file blast.py.

CreateDB()

def ost.bindings.blast.CreateDB	(		infasta,
			dbout,
			mkdb_cmd = None
	)

Create a blast DB from a fasta file

:param infasta: the pdb fasta from which the database will be created
:type infasta: :class:`string`

:param dbout: output location for blastDB file
:type dbout: :class:`string`

Definition at line 137 of file blast.py.

ParseBlastOutput()

def ost.bindings.blast.ParseBlastOutput	(		string,
			seqid_thres = 0,
			evalue_thres = float("infinity")
	)

Parses the blast output and returns a list of BlastHits
setting no seqid_thres or evalue_thres, restores default behaviour without filtering

Definition at line 62 of file blast.py.