This file provides documentation for modules in Biopython that have been moved or deprecated in favor of other modules. This provides some quick and easy to find documentation about how to update your code to work again. Python releases go first, then code (modules, methods, functions).
First supported in release 1.79, although it was mostly working in 1.78. Support deprecated as of Release 1.84.
First supported in release 1.75. Support deprecated as of Release 1.83, and no longer supported as of Release 1.84.
No longer supported as of Release 1.82. First supported in release 1.73.
No longer supported as of Release 1.80, having triggered a deprecation warning as of release 1.79. First supported in release 1.69.
No longer supported as of Release 1.77. First supported in release 1.66.
No longer supported as of Release 1.75, having triggered a deprecation warning in release 1.74. First supported in release 1.64.
No longer supported as of Release 1.70, having triggered a warning with release 1.67 onwards.
Never officially supported, these triggered a warning in Release 1.62 recommending Python 3.3 or later. As of Biopython Release 1.63 onwards, installation simply aborts with a error message.
No longer supported as of Release 1.77 (2020, in line with end-of-life or sunset date for Python 2.7 itself), having triggered a warning in prior releases.
No longer supported as of Release 1.77 with the end of Python 2 support. Biopython was mostly working under Jython 2.7.0, but support for Jython was deprecated as of Release 1.70.
The SimpleFastaParser (which is used by Bio.SeqIO.parse if
format='fasta' or format='fasta-2line') interprets lines before the
first line starting with '>' as comments and skips them. To be consistent with
the most common interpretation of the FASTA file format, the use of such
comment lines at the beginning of the FASTA file was deprecated in Biopython
Release 1.85.
As an alternative, you can use format='fasta-pearson' to specify the FASTA
file format as defined by William Pearson's FASTA aligner program, allowing for
comment lines at the top of the FASTA file (lines anywhere in the file starting
by ';' are also regarded as comment lines and skipped).
Another option is to use format='fasta-blast'; this follows the FASTA file
format accepted by BLAST, treating any lines starting with '#', ';', or '!' as
comment lines and ignoring them.
The egquery function wrapping the NCBI EGQuery (Entrez Global Query)
API was deprecated in Release 1.84. The API has stopped working and the
NCBI said this API was no longer being maintained.
The search function was deprecated in Release 1.84. The CGI API this
wrapped is no longer available since SCOP moved to the EBI website.
The pos_specific_score_matrix method of the SummaryInfo class and the
PSSM class were deprecated in release 1.82. As an alternative, please use
the alignment property of a MultipleSeqAlignment object to obtains a
new-style Alignment object, and use it to create a Bio.motifs.Motif
object. For example,
>>> alignment = msa.alignment
>>> from Bio.motifs import Motif
>>> motif = Motif('ACGT', alignment)
>>> counts = motif.countsThe counts object contains the same information as the PSSM returned by
pos_specific_score_matrix, but note that the indices are reversed:
>>> counts[letter][i] == pssm[index][letter]
TrueThe information_content method and the ic_vector attribute of the
SummaryInfo class were deprecated in release 1.82. As an alternative,
please use the relative_entropy attribute of the motif instance (see
above); it contains the same values as the ic_vector attribute, while
sum(relative_entropy) is equal to the value returned by
information_content.
The replacement_dictionary method of the SummaryInfo class was
deprecated in release 1.82. As an alternative, please use the alignment
property of the MultipleSeqAlignment object to obtain a new-style
Alignment object, and use its substitutions attribute to obtain the
replacement dictionary:
>>> alignment = msa.alignment
>>> dictionary = alignment.substitutionsIf the multiple sequence alignment object msa was obtained using
Bio.AlignIO, then you can obtain a new-style Alignment object directly
by using Bio.Align.read instead of Bio.AlignIO.read, or
Bio.Align.parse instead of Bio.AlignIO.parse.
The dumb_consensus and gap_consensus methods of the SummaryInfo
class were deprecated in Release 1.82.
The print_info_content function in Bio.Align.AlignInfo was deprecated
in Release 1.82.
Deprecated in release 1.82, consider using scikit-learn instead.
Deprecated in release 1.82, consider using scikit-learn instead.
Deprecated in release 1.82, consider using skikit-learn instead.
Deprecated in release 1.82, consider using scikit-learn instead.
Deprecated in release 1.82, consider using hmmlearn (https://pypi.org/project/hmmlearn/) instead.
The Bio.HMM.DynamicProgramming, Bio.HMM.Trainer, Bio.HMM.MarkovModel, and Bio.HMM.Utilities modules were deprecated in release 1.82. Consider using hmmlearn (https://pypi.org/project/hmmlearn/) instead.
Deprecated in release 1.80, and removed in release 1.82. Please use Bio.Data.PDBData instead.
Declared obsolete in release 1.79, and deprecated in release 1.82. Please use the standard library subprocess module directly instead.
Deprecated in release 1.75, removed in release 1.77. Was not used anywhere in Biopython.
Declared obsolete in release 1.75, deprecated in release 1.76, removed in release 1.79. PDB NDB files can be opened with Bio.PDB.
Bio.motifs.mast plain-text parsing deprecated in favor of XML parsing as of
release 1.74. Also affects Bio.motifs.read and Bio.motifs.parse for the
mast format.
The format method of the Motif class in Bio.motifs was deprecated
in release 1.77, in favor of a __format__ method that can be used from the
format built-in function. This decision was reversed in release 1.79.
The search method of the Instances class in Bio.motifs was
deprecated in release 1.82. Instead of instances.search(sequence),
sequence.search(instances) can be used, where sequence is a Seq object.
This allows instances to have different lengths.
The version parameter of the weblogo method of the Motif class in
Bio.motifs was deprecated in release 1.83. Using the parameter has no
effect.
The Instances class and the instances argument of the Motif class
initializer in Bio.motifs were deprecated in release 1.82. Instead of
>>> from Bio.motifs import Instances
>>> instances = Instances([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')])
>>> motif = Motif(alphabet='ACGT', instances=instances)please use
>>> from Bio.Align import Alignment
>>> alignment = Alignment([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')])
>>> motif = Motif(alphabet='ACGT', alignment=alignment)The instances attribute of the Motif class in Bio.motifs was
deprecated in release 1.82. Instead of mymotif.instances, please use
mymotif.alignment.sequences.
The Instance class in Bio.motifs.meme was deprecated in release 1.85.
This class is a subclass from Seq, but does not provide any additional
capabilities. Please use a Seq object instead.
Removed in Biopython 1.74 without explicit deprecation period. RanaConfig was a configuration file containing some constants for Bio.Restriction.PrintFormat and ranacompiler.py, a script to update Bio.Restriction.Restriction_Dictionary, and which is not part of the Biopython installation. The constants were implemented in the respective modules.
Declared obsolete in Biopython release 1.74, and removed from Biopython in
release 1.78. This module defined an Alphabet class and various subclasses,
which were used as attributes to Seq and objects to describe how the
individual characters in the sequence string should be interpreted. For
example, a string "AGTACACTGGT" could be a DNA sequence or a protein sequence
that happens to be rich in Alanines, Glycines, Cysteines and Threonines.
However, as the exact definition of the alphabet and its purpose remained
unclear, this class was removed from Biopython.
Starting with Biopython 1.78, the molecule type, if specified in the input
file, is stored by the SeqIO parser as molecule_type in the annotations
of each SeqRecord. We urge users to use this attribute with caution, as the
molecule type means different things in different sequence file formats, and in
a sense the interpretation of molecule_type can still be ambiguous.
These two functions were labelled as broken in Release 1.70, and removed in Release 1.73, since the underlying web-server API no longer exists.
This was deprecated in Biopython 1.70, and removed in Release 1.73. Please consider using a dedicated genetic algorithm library like DEAP instead.
This was deprecated in Biopython 1.70, and removed in Release 1.73. Please consider using a dedicated machine learning library like scikit-learn or TensorFlow instead.
This exception was deprecated as of Release 1.70 as it was no longer used within Biopython, and removed in Release 1.75.
This was deprecated in Biopython 1.69, and removed in Release 1.71.
This new experimental module included in Biopython 1.64 was renamed to Bio.codonalign in Biopython 1.65 to follow PEP8 module naming rules.
As of Release 1.67, the SeqRecord objects (and their subclasses) no longer use the default Python object comparison. Instead they will raise an exception if you try to compare them.
For backward compatibility and/or to explicitly use object comparison, please use id(record1) == id(record2) instead.
Otherwise please test whichever specific attributes you are interested in explicitly, for example record1.id == record2.id or record1.seq == record.seq (see also the note below about sequence equality).
As of Release 1.65, the Seq and MutableSeq objects (and their subclasses) use string-like equality testing and hashing (ignoring any difference in alphabet except to issue warnings).
Prior releases used Python's object comparison. Warnings of this change were first added in Release 1.54 (May 2010), with hash warnings present from Release 1.62 (August 2013) to Release 1.76 (December 2019).
For backward compatibility and/or to silence warnings about this, please use explicit string comparison, str(seq1) == str(seq2), or object comparison, id(seq1) == id(seq2), as required.
Deprecated in release 1.64, and removed in release 1.73. You should now use str(Bio.Seq.Seq) or str(Bio.Seq.MutableSeq) instead of the tostring() methods.
Deprecated in release 1.79, removed in release 1.81. Instead of myseq.tomutable() or mymutableseq.toseq(), you should now use Bio.Seq.MutableSeq(myseq) or Bio.Seq.Seq(mymutableseq), respectively.
Declared obsolete in release 1.79, deprecated in release 1.80, and removed in release 1.82. Instead of myseq.ungap(), please use myseq.replace("-", "").
Deprecated in release 1.79, and removed in release 1.81.
Instead of UnknownSeq(length), please use Seq(None, length=length).
Note that the sequence contents of a Seq object constructed in this way
is considered to be unknown, and any attempt to access the sequence contents
(for example, by calling print on the object) will result in an
UndefinedSequenceError.
Starting from release 1.82, the inplace argument of complement and
reverse_complement in Bio.Seq always default to False both for
Seq and MutableSeq objects.
To modify a MutableSeq in-place, use inplace=True.
The .next() method defined for any Biopython iterator is deprecated as of Biopython 1.63 under Python 2 (and not present on Python 3). Please replace my_iterator.next() with next(my_iterator) using the new built-in function next() instead. Python 2 support and the remaining next methods were removed in release 1.77.
As of Release 1.63, the main class (confusingly also called) SVDSuperimposer is best imported as follows:
>>> from Bio.SVDSuperimposer import SVDSuperimposer
>>> super_imposer = SVDSuperimposer()This short form also works on older releases. The longer even more confusing historical alternatives dependent on the double module name no longer work, e.g. you can no longer do this:
>>> from Bio.SVDSuperimposer.SVDSuperimposer import SVDSuperimposer
>>> super_imposer = SVDSuperimposer()Due to a long standing name shadowing problem, Bio.PDB.Vector was
both a class and a module, which defined the class and various other
functions imported to the Bio.PDB namespace.
As of Release 1.70, the module has been renamed Bio.PDB.vectors, leaving
Bio.PDB.Vector to unambiguously mean the class. This is in line with the
PEP8 naming conventions. A deprecated compatibility stub was left in place
so that any imports via the old module name will work but raise a warning.
This compatibility stub was removed in Release 1.74.
We expect this to have no impact for the majority of users, unless you do
something like from Bio.PDB.Vector import calc_dihedral in which case
use from Bio.PDB import calc_dihedral (which will work on older versions
of Biopython as well).
The get_atom and sort methods of the Residue class were deprecated
in Release 1.71 and 1.70 respectively, and removed in Release 1.79.
Use of the PDB_TO_XYZR bash script was removed from get_surface in
Release 1.79.
The Bio.PDB.QCPSuperimposer module was deprecated in release 1.80, and
removed in release 1.82. Please use the Bio.PDB.qcprot module instead.
Release 1.82 unfortunately removed the .strand, .ref, and .ref_db
attributes of the SeqFeature without a deprecation period. Release 1.83
restored but deprecated them. Please use .location.strand etc instead.
With the introduction of the CompoundLocation in Release 1.62, the SeqFeature attribute sub_features was deprecated. It was removed in Release 1.68.
Note that in Release 1.80 the location_operator argument can no longer be used, instead do this via the CompoundLocation object. The location_operator argument was removed from the SeqFeature initializer in Release 1.82.
There were multiple deprecations in Release 1.80, listed below. The deprecated code was removed in Release 1.82.
- Class
FeatureLocationrenamed toSimpleLocation, with the old name preserved for now solely for backward compatibility. - Arguments
strand,refandref_dbto theSeqFeatureclass - set them via the location object - Unused class
PositionGap- originally for very old GenBank files. - Location attributes
location.nofuzzy_startandlocation.nofuzzy_end- use the location directly or if requiredint(location.start)andint(location.end). This will fail for theUnknownPositionwhere the nofuzzy aliases returnedNone. - Position attribute
.positionreturned the (left) position as an integer - use the location directly or if requiredint(position), however forOneOfPosition,BetweenPosition, andWithinPositionthat will give the default position rather than the left-most (minimum) value. - Position attribute
.extensionreturned the "width", typically zero except forOneOfPosition,BetweenPosition, andWithinPositionwhere this must be handled explicitly now. - Base class
AbstractPositionwas renamed toPosition.
Declared obsolete with a PendingDeprecationWarning in Release 1.61, formally deprecated in Release 1.62, removed in Release 1.67. Please use the newer Bio.motifs module instead.
Deprecated in release 1.62, removed in Release 1.67. An up to date version of the software cannot be obtained anymore (affects Bio.Motif and its replacement Bio.motifs).
Unused class InterlacedSequenceIterator was deprecated in Release 1.61, and removed in Release 1.64.
Class SequentialSequenceWriter was declared obsolete in Release 1.77, deprecated in Release 1.78, and removed in Release 1.80.
Obsolete file Bio/HotRand.py was deprecated in Release 1.61, and removed in Release 1.64. Consider using an alternative RNG, or the Python module "randomdotorg".
Long obsolete file Bio/Search.py was deprecated in Release 1.61, and removed in Release 1.64.
The three functions for calling the "legacy" NCBI BLAST command line tools blastall, blastpgp and rpsblast were declared obsolete in Biopython Release 1.53, deprecated in Release 1.61, and removed in Release 1.64. Please use the BLAST+ wrappers in Bio.Blast.Applications instead.
The remainder of this module is a parser for the plain text BLAST output, which was declared obsolete in Release 1.54, and deprecated in Release 1.63. The module was removed in Release 1.72 from the public API. It lives now in maintenance mode in Bio.SearchIO._legacy to preserve existing functionality. A BiopythonDeprecationWarning was added to this module in Release 1.80. The Bio.SearchIO._legacy module was removed from Biopython in Release 1.82.
For some time now, both the NCBI and Biopython have encouraged people to parse the XML output instead.
NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline, BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release 1.53, deprecated in Release 1.61, and removed in Release 1.64, having been replaced with wrappers for the new NCBI BLAST+ tools (e.g. NcbiblastpCommandline and NcbipsiblastCommandline).
The parser in Bio.Blast.ParseBlastTable for tabular output generated by
NCBI blastpgp was deprecated in Biopython release 1.80, and removed in release
1.82. To parse tabular output generated by BLAST programs, please use the
parse function in Bio.Align.
The remove_database and get_all_primary_ids methods were removed from
the DBServer class in Release 1.79.
The get_Seq_by_primary_id method was removed from the BioSeqDatabase
class in Release 1.79.
GenomeDiagram originally used colour and centre (UK spelling of color and center) for argument names. As part of its integration into Biopython 1.50, this will support both colour and color, and both centre and center, to help people port existing scripts written for the standalone version of GenomeDiagram. However, these were deprecated in Release 1.55 final. Support for centre was removed in Release 1.62, and we intend to eventually remove support for colour in later releases of Biopython.
Direct use of the Seq object (and MutableSeq object) .data property is deprecated. As of Release 1.49, writing to the Seq object's .data property triggered a warning, and this property was made read only in Release 1.53. In Release 1.55 final, accessing the .data property of a Seq object gives a DeprecationWarning. The Seq object's .data property was removed in Release 1.61. Starting from Release 1.78, accessing the .data property of a MutableSeq object similarly gives a deprecation warning.
Function quick_FASTA_reader was declared obsolete in Release 1.61, deprecated in Release 1.64, and removed in Release 1.67. Use function list(SimpleFastaParser(handle)) from Bio.SeqIO.FastaIO instead (but ideally convert your code to using an iterator approach).
The 'title2ids' argument to FastaIterator in Bio.SeqIO.FastaIO and FastqPhredIterator in Bio.SeqIO.QualityIO was deprecated in Release 1.80, and removed in Release 1.82. Please use a generator function to modify the records returned by the parser.
Function Tm_staluc in Bio.SeqUtils.MeltingTemp was deprecated in Release 1.78, and removed in Release 1.80.
The modules Bio.SeqUtils.CodonUsage and Bio.SeqUtils.CodonUsageIndices were deprecated in Release 1.80, and removed in Release 1.82. Please use the new CodonAdaptationIndex class in Bio.SeqUtils instead. Note that this class has been updated to use modern Python, and may give slightly different results from the CodonAdaptationIndex class in Bio.SeqUtils.CodonUsage, as the calculation was updated to be consistent with the calculated values by Sharp & Li.
Function 'GC' in Bio.SeqUtils was deprecated in Release 1.80, and removed in Release 1.82. Instead use function 'gc_fraction'.
Function get_amino_acids_percent in Bio.SeqUtils.ProteinAnalysis was deprecated in Release 1.85. Use the amino_acids_percent property instead.
Bio.PopGen.Async was deprecated in Release 1.68, removed in Release 1.70.
Bio.PopGen.FDist was deprecated in Release 1.68, removed in Release 1.70.
Bio.PopGen.SimCoal was deprecated in Release 1.68, and removed in Release
1.70.
Submodule Bio.UniGene.UniGene which was an HTML parser was declared obsolete in Release 1.59, deprecated in Release 1.61, and removed in Release 1.64.
The methods print_full_mat and print_mat were removed from the
SeqMat` class in Bio.SubsMat in Release 1.79.
The Bio.SubsMat module was deprecated in Release 1.78, and removed in Release
1.80. As an alternative, please consider using Bio.Align.substitution_matrices.
The infer_coordinates class method of the Alignment class in
Bio.Align was deprecated in Release 1.84. Instead,please use the
parse_printed_alignment method, which is much faster, and returns both the
sequences after removing the gaps and the coordinates.
The get_column method of the MultipleSeqAlignment was deprecated in
Release 1.57 and removed in Release 1.69.
The add_sequence method of the MultipleSeqAlignment was deprecated in
Release 1.57 and should have been removed in Release 1.69. It was actually
removed in Release 1.79.
The format method of the MultipleSeqAlignment class and the
PairwiseAlignment class were deprecated in Release 1.76. This decision was
reversed in Release 1.79.
The __format__ method of the Array class in Bio.Align.substitution_matrices
was deprecated in Release 1.79.
The PairwiseAlignment class was deprecated in Release 1.80, and removed in Release 1.82. Please use the new Alignment class instead.
This module which defined to original (Multiple-Sequence) Alignment class was deprecated in Release 1.57 and removed in Release 1.69.
Bio.ParserSupport was declared obsolete in Release 1.59, and deprecated in
Release 1.63. The Martel specific EventGenerator was removed in Release
1.67, and the entire module was removed in Release 1.72.
This module was declared obsolete in Release 1.72, deprecated in Release 1.74,
and removed in Release 1.77. As of Release 1.72, KDTree data structures and
the functionality previously available in Bio.KDTree are provided in a new
module Bio.PDB.kdtrees.
These modules were declared obsolete in Release 1.72, deprecated in Release 1.73, and removed in Release 1.77. We suggest pygtrie as an alternative library implementing a trie data structure.
This module was declared obsolete in Release 1.74, deprecated in Release 1.76, and removed in Release 1.79.
The UndoHandle class was deprecated in Release 1.77, and moved to Bio/SearchIO/_legacy/ParserSupport.py, which was the only module in Biopython still using this class. The UndoHandle class in Bio.File was removed in Release 1.79.
Deprecated in Release 1.77, and removed in Release 1.79.
The draw_graphviz function was removed in Release 1.79.
The Bio.pairwise2 module was deprecated in Release 1.80.
The Bio.Wise module was deprecated in Release 1.80, and removed in Release
1.82.
The original_taxon_order attribute of the Nexus class in
Bio.Nexus.Nexus was deprecated in Release 1.80, and removed in
Release 1.85. Please use the taxlabels attribute instead.
The is_palindrom function was removed in Release 1.79.