Bio package¶
Subpackages¶
- Bio.Affy package
- Bio.Align package
- Bio.AlignIO package
- Bio.Alphabet package
- Bio.Application package
- Bio.Blast package
- Bio.CAPS package
- Bio.Cluster package
- Bio.Compass package
- Bio.Crystal package
- Bio.Data package
- Bio.Emboss package
- Bio.Entrez package
- Bio.ExPASy package
- Bio.FSSP package
- Bio.GenBank package
- Bio.Geo package
- Bio.Graphics package
- Bio.HMM package
- Bio.KEGG package
- Bio.Medline package
- Bio.NMR package
- Bio.Nexus package
- Bio.PDB package
- Subpackages
- Submodules
- Bio.PDB.AbstractPropertyMap module
- Bio.PDB.Atom module
- Bio.PDB.Chain module
- Bio.PDB.DSSP module
- Bio.PDB.Dice module
- Bio.PDB.Entity module
- Bio.PDB.FragmentMapper module
- Bio.PDB.HSExposure module
- Bio.PDB.MMCIF2Dict module
- Bio.PDB.MMCIFParser module
- Bio.PDB.Model module
- Bio.PDB.NACCESS module
- Bio.PDB.NeighborSearch module
- Bio.PDB.PDBExceptions module
- Bio.PDB.PDBIO module
- Bio.PDB.PDBList module
- Bio.PDB.PDBParser module
- Bio.PDB.PICIO module
- Bio.PDB.PSEA module
- Bio.PDB.Polypeptide module
- Bio.PDB.Residue module
- Bio.PDB.ResidueDepth module
- Bio.PDB.SCADIO module
- Bio.PDB.Selection module
- Bio.PDB.Structure module
- Bio.PDB.StructureAlignment module
- Bio.PDB.StructureBuilder module
- Bio.PDB.Superimposer module
- Bio.PDB.ic_data module
- Bio.PDB.ic_rebuild module
- Bio.PDB.internal_coords module
- Bio.PDB.mmcifio module
- Bio.PDB.parse_pdb_header module
- Bio.PDB.vectors module
- Module contents
- Bio.Pathway package
- Bio.Phylo package
- Subpackages
- Submodules
- Bio.Phylo.BaseTree module
- Bio.Phylo.CDAO module
- Bio.Phylo.CDAOIO module
- Bio.Phylo.Consensus module
- Bio.Phylo.NeXML module
- Bio.Phylo.NeXMLIO module
- Bio.Phylo.Newick module
- Bio.Phylo.NewickIO module
- Bio.Phylo.NexusIO module
- Bio.Phylo.PhyloXML module
- Bio.Phylo.PhyloXMLIO module
- Bio.Phylo.TreeConstruction module
- Module contents
- Bio.PopGen package
- Bio.Restriction package
- Bio.SCOP package
- Bio.SVDSuperimposer package
- Bio.SearchIO package
- Bio.SeqIO package
- Submodules
- Bio.SeqIO.AbiIO module
- Bio.SeqIO.AceIO module
- Bio.SeqIO.FastaIO module
- Bio.SeqIO.GckIO module
- Bio.SeqIO.IgIO module
- Bio.SeqIO.InsdcIO module
- Bio.SeqIO.Interfaces module
- Bio.SeqIO.NibIO module
- Bio.SeqIO.PdbIO module
- Bio.SeqIO.PhdIO module
- Bio.SeqIO.PirIO module
- Bio.SeqIO.QualityIO module
- Bio.SeqIO.SeqXmlIO module
- Bio.SeqIO.SffIO module
- Bio.SeqIO.SnapGeneIO module
- Bio.SeqIO.SwissIO module
- Bio.SeqIO.TabIO module
- Bio.SeqIO.UniprotIO module
- Bio.SeqIO.XdnaIO module
- Module contents
- Submodules
- Bio.SeqUtils package
- Bio.Sequencing package
- Bio.Statistics package
- Bio.SubsMat package
- Submodules
- Module contents
- General:
- Usage:
- Generating an Accepted Replacement Matrix:
- Generating the observed frequency matrix (OFM):
- Generating an expected frequency matrix (EFM):
- Generating a substitution frequency matrix (SFM):
- Generating a log-odds matrix (LOM):
- External:
- Methods for subtraction, addition and multiplication of matrices:
- Bio.SwissProt package
- Bio.TogoWS package
- Bio.UniGene package
- Bio.UniProt package
- Bio.Wise package
- Bio.codonalign package
- Bio.motifs package
- Bio.phenotype package
Submodules¶
Module contents¶
Collection of modules for dealing with biological data in Python.
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
-
exception
Bio.
MissingExternalDependencyError
¶ Bases:
Exception
Missing an external dependency.
Used for things like missing command line tools. Important for our unit tests to allow skipping tests with missing external dependencies.
-
exception
Bio.
MissingPythonDependencyError
¶ Bases:
Bio.MissingExternalDependencyError
,ImportError
Missing an external python dependency (subclass of ImportError).
Used for missing Python modules (rather than just a typical ImportError). Important for our unit tests to allow skipping tests with missing external python dependencies, while also allowing the exception to be caught as an ImportError.
-
exception
Bio.
StreamModeError
¶ Bases:
ValueError
Incorrect stream mode (text vs binary).
This error should be raised when a stream (file or file-like object) argument is in text mode while the receiving function expects binary mode, or vice versa.
-
exception
Bio.
BiopythonWarning
¶ Bases:
Warning
Biopython warning.
Biopython should use this warning (or subclasses of it), making it easy to silence all our warning messages should you wish to:
>>> import warnings >>> from Bio import BiopythonWarning >>> warnings.simplefilter('ignore', BiopythonWarning)
Consult the warnings module documentation for more details.
-
exception
Bio.
BiopythonParserWarning
¶ Bases:
Bio.BiopythonWarning
Biopython parser warning.
Some in-valid data files cannot be parsed and will trigger an exception. Where a reasonable interpretation is possible, Biopython will issue this warning to indicate a potential problem. To silence these warnings, use:
>>> import warnings >>> from Bio import BiopythonParserWarning >>> warnings.simplefilter('ignore', BiopythonParserWarning)
Consult the warnings module documentation for more details.
-
exception
Bio.
BiopythonDeprecationWarning
¶ Bases:
Bio.BiopythonWarning
Biopython deprecation warning.
Biopython uses this warning instead of the built in DeprecationWarning since those are ignored by default since Python 2.7.
To silence all our deprecation warning messages, use:
>>> import warnings >>> from Bio import BiopythonDeprecationWarning >>> warnings.simplefilter('ignore', BiopythonDeprecationWarning)
Code marked as deprecated is likely to be removed in a future version of Biopython. To avoid removal of this code, please contact the Biopython developers via the mailing list or GitHub.
-
exception
Bio.
BiopythonExperimentalWarning
¶ Bases:
Bio.BiopythonWarning
Biopython experimental code warning.
Biopython uses this warning for experimental code (‘alpha’ or ‘beta’ level code) which is released as part of the standard releases to mark sub-modules or functions for early adopters to test & give feedback.
Code issuing this warning is likely to change (or even be removed) in a subsequent release of Biopython. Such code should NOT be used for production/stable code. It should only be used if:
You are running the latest release of Biopython, or ideally the latest code from our repository.
You are subscribed to the biopython-dev mailing list to provide feedback on this code, and to be alerted of changes to it.
If all goes well, experimental code would be promoted to stable in a subsequent release, and this warning removed from it.