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Data Structures | Functions
ost.bindings.blast Namespace Reference

Data Structures

class  AlignedPatch
 
class  BlastHit
 
class  BlastError
 

Functions

def ParseBlastOutput
 
def CreateDB
 
def BlastVersion
 
def Blast
 

Function Documentation

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 209 of file blast.py.

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.

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.

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.