Back to index

python-biopython  1.60
Classes | Namespaces | Functions
NCBIStandalone.py File Reference

Go to the source code of this file.

Classes

class  Bio.Blast.NCBIStandalone.LowQualityBlastError
class  Bio.Blast.NCBIStandalone.ShortQueryBlastError
class  Bio.Blast.NCBIStandalone._Scanner
class  Bio.Blast.NCBIStandalone.BlastParser
class  Bio.Blast.NCBIStandalone.PSIBlastParser
class  Bio.Blast.NCBIStandalone._HeaderConsumer
class  Bio.Blast.NCBIStandalone._DescriptionConsumer
class  Bio.Blast.NCBIStandalone._AlignmentConsumer
class  Bio.Blast.NCBIStandalone._HSPConsumer
class  Bio.Blast.NCBIStandalone._DatabaseReportConsumer
class  Bio.Blast.NCBIStandalone._ParametersConsumer
class  Bio.Blast.NCBIStandalone._BlastConsumer
class  Bio.Blast.NCBIStandalone._PSIBlastConsumer
class  Bio.Blast.NCBIStandalone.Iterator
class  Bio.Blast.NCBIStandalone._BlastErrorConsumer
class  Bio.Blast.NCBIStandalone.BlastErrorParser

Namespaces

namespace  Bio.Blast.NCBIStandalone

Functions

def Bio.Blast.NCBIStandalone.blastall
def Bio.Blast.NCBIStandalone.blastpgp
def Bio.Blast.NCBIStandalone.rpsblast
def Bio.Blast.NCBIStandalone._re_search
def Bio.Blast.NCBIStandalone._get_cols
def Bio.Blast.NCBIStandalone._safe_int
def Bio.Blast.NCBIStandalone._safe_float
def Bio.Blast.NCBIStandalone._invoke_blast
def Bio.Blast.NCBIStandalone._security_check_parameters

Class Documentation

class Bio::Blast::NCBIStandalone::LowQualityBlastError
Error caused by running a low quality sequence through BLAST.

When low quality sequences (like GenBank entries containing only
stretches of a single nucleotide) are BLASTed, they will result in
BLAST generating an error and not being able to perform the BLAST.
search. This error should be raised for the BLAST reports produced
in this case.

Definition at line 64 of file NCBIStandalone.py.

class Bio::Blast::NCBIStandalone::ShortQueryBlastError
Error caused by running a short query sequence through BLAST.

If the query sequence is too short, BLAST outputs warnings and errors:
Searching[blastall] WARNING:  [000.000]  AT1G08320: SetUpBlastSearch failed.
[blastall] ERROR:  [000.000]  AT1G08320: Blast: 
[blastall] ERROR:  [000.000]  AT1G08320: Blast: Query must be at least wordsize
done

This exception is raised when that condition is detected.

Definition at line 75 of file NCBIStandalone.py.