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.
First supported in release 1.75.
First supported in release 1.73.
Triggers 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 1.69, having triggered a warning with release 1.66 onwards.
No longer supported as of Release 1.63, having triggered a warning with Release 1.62, with advance notice in the release notes for Release 1.61.
No longer supported as of Release 1.59, having triggered a warning since Release 1.55, with advance notice in the release notes for Release 1.54.
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.
Declared obsolete in release 1.79. 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.
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 (ingoring 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. 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. Instead of myseq.ungap(), please use myseq.replace("-", "").
Deprecated in release 1.79.
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.
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).
This was removed in Release 1.62, when MMCIF2Dict was updated to use shlex from the standard library instead. This had required manual intervention to include when installing Biopython from source due to a dependency on flex.
The sort and get_atom methods of the Residue class were removed in
Release 1.79.
Use of the PDB_TO_XYZR bash script was removed from get_surface in
Release 1.79.
With the introduction of the CompoundLocation in Release 1.62, the SeqFeature attribute sub_features was deprecated. It was removed in Release 1.68.
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.
Before this, CompareAceParser and CompareAceConsumer from
Bio.Motif.Parsers.AlignAce were declared obsolete in Release 1.53,
deprecated in Release 1.55 final, and removed in Release 1.57.
AlignAceConsumer, AlignAceParser, and AlignAceScanner were
declared obsolete in Release 1.53 and deprecated in Release 1.55 final;
their functionality is now available through a read() function in
Bio.Motif.Parsers.AlignAce.
MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer,
MASTParser, _MASTScanner, and MASTRecord were declared obsolete in
Release 1.54 and deprecated in Release 1.55 final; their functionality is now
available through a read() function in Bio.Motif.Parsers.MEME and
Bio.Motif.Parsers.MAST, respectively.
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.
Deprecated in Release 1.59, removed in Release 1.62. Use Python's built in set object.
The arguments to create these fuzzy positions changed in Release 1.59.
Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and removed in Release 1.57.
Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and removed in Release 1.57.
This module was a parser for the EBI InterPro webpages, but no longer worked with their current website. Deprecated in Release 1.55, and removed in Release 1.58.
This module used to be used for parsing GenBank and EMBL feature locations. It has been replaced with faster code using regular expressions, and is no longer needed. Declared obsolete in Release 1.55, deprecated in Release 1.56, and removed in Release 1.59.
This module was a copy of John Aycock's SPARK parser included with Biopython solely for use in Bio.GenBank.LocationParser. Declared obsolete in Release 1.55, deprecated in Release 1.56, and removed in Release 1.59.
This module (originally in C) offered complement and antiparallel functions (duplicating functionality in Bio.Seq) and a rather odd function called check_bases (also available as Bio.Restriction.Restriction.check_bases). Deprecated in Release 1.53, removed in Release 1.57.
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.
For some time now, both the NCBI and Biopython have encouraged people to parse the XML output instead, however Bio.SearchIO will initially attempt to support plain text BLAST output.
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.
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).
Declared obsolete in Release 1.52, deprecated in Release 1.55 final, and removed in Release 1.58. Replaced with Bio.AlignIO for parsing and writing clustal format alignments (since Release 1.46), and Bio.Align.Applications for calling the ClustalW command line tool (since Release 1.51). See the Tutorial for examples.
Support for psycopg (version one) in Biopython's BioSQL code was deprecated in Release 1.51, and removed in Release 1.55. Please use psycopg2 instead.
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.
Declared obsolete in Release 1.51, deprecated in Release 1.53, and removed in Release 1.57. Please use the Python subprocess module instead, or as of Release 1.55 the application wrappers can be used directly to execute the command.
As of Easter 2009, the NCBI have stopped supporting the unofficial return type of "genbank" in EFetch. Instead we should be using "gb" (GenBank) or "gp" (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this automatically, but issues a deprecation warning. The code to check and correct for "genbank" was removed in Biopython 1.55 final.
Declared obsolete in Release 1.50, deprecated in Release 1.51, and removed in Release 1.56. Most of the functionality in Bio.SwissProt.SProt is available from Bio.SwissProt.
Declared obsolete in Release 1.50, deprecated in Release 1.53, and removed in Release 1.57. Most of the functionality has moved to Bio.ExPASy.Prosite and Bio.ExPASy.Enzyme, respectively.
Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed in Release 1.56.
Bio.File.SGMLHandle was declared obsolete in Release 1.50, deprecated in Release 1.52, and removed in Release 1.56. Bio.File.SGMLStripper was deprecated in Release 1.57, removed in Release 1.61. Bio.File.StringHandle was deprecated in Release 1.59, removed in Release 1.61.
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.
Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed in Release 1.56. Please use Bio.Motif instead.
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.
Declared obsolete in Release 1.49, deprecated in Release 1.51, and removed in Release 1.57. Please use the methods or functions in Bio.Seq instead.
Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were deprecated in Release 1.50, Bio.listfns was deprecated in Release 1.53. The three C implementations were all removed in Release 1.53. Bio.mathfns and Bio.stringfns were removed in Release 1.55. Bio.listfns was removed in Release 1.57.
Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed in Release 1.55 final. Please use the "fasta" support in Bio.SeqIO or Bio.AlignIO instead.
Note that Bio.Fasta could be used with a RecordParser which gave
FastaRecord objects, for example:
# Old code which won't work any more
from Bio import Fasta
handle = open("example.fas")
for record in Fasta.Iterator(handle, Fasta.RecordParser()) :
# Here record was a Bio.Fasta.Record object
print record.title # The full title line as a string
print record.sequence # The sequence as a string
handle.close()
Alternatively using the old SequenceParser would give SeqRecord
objects like those from the new Bio.SeqIO code, for example:
# Old code which won't work any more
from Bio import Fasta
handle = open("example.fas")
for seq_record in Fasta.Iterator(handle, Fasta.SequenceParser()) :
print seq_record.description # The full title line as a string
print str(seq_record.seq) # The sequence as a string
handle.close()
Either of those examples using Bio.SeqIO becomes just:
# Updated versions of above examples using Bio.SeqIO instead
from Bio import SeqIO
for seq_record in SeqIO.parse("example.fas", "fasta") :
print seq_record.description # The full title line as a string
print str(seq_record.seq) # The sequence as a string
You can also continue to use handles with Bio.SeqIO if you want to.
Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed in Release 1.55 final. Instead, please use Bio.AlignIO or call the format built-in function on the Alignment object.
The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared obsolete in Biopython 1.52, deprecated in Release 1.55 final, and removed in release 1.58. please use the wrappers for the "new" EMBOSS PHYLIP tools (e.g. fneighbor) instead. Specifically, EProtDistCommandline, ENeighborCommandline, EProtParsCommandline, EConsenseCommandline, and ESeqBootCommandline are replaced by FProtDistCommandline, FNeighborCommandline, FProtParsCommandline, FConsenseCommandline, and FSeqBootCommandline, respectively.
This function was made obsolete with the introduction of Bio.AlignIO, deprecated in Release 1.54, and removed in Release 1.58. Use either the Bio.AlignIO functions, or the Bio.Align.MultipleSeqAlignment class directly instead.
Function makeTableX and classes ProteinX and MissingTable were deprecated in Release 1.54, and removed in Release 1.58. These were remnants of the removed translate function, and no longer served any useful purpose.
Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, and removed in Release 1.58. Instead just use the string's slice method with a step of minus one.
Functions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and quicker_apply_on_multi_fasta were deprecated in Release 1.55, and removed in Release 1.58.
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 whole of the old Bio.GFF module was deprecated in Release 1.53, and
removed in Release 1.57 (with the intention of reusing this name space for a
GFF parser).
Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead. The whole of Bio.utils was declared obsolete in Release 1.55, deprecated in Release 1.56, and removed in Release 1.57.
The RecordParser and Iterator classes were declared obsolete in Release 1.54, deprecated in Release 1.55, removed in Release 1.59. Their functionality is now available through a read() and a parse() function, respectively.
The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete in Release 1.54, deprecated in Release 1.55 and removed in Release 1.59. Their functionality is now available through a read() function.
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.
Prior to this, the RecordParser, _Scanner, and _RecordConsumer
classes were declared obsolete in Release 1.54, deprecated in Release 1.55,
and removed in Release 1.58. Their functionality is now available through
a read() function.
Bio.PopGen.SimCoal was deprecated in Release 1.68, and removed in Release
1.70.
The classes UnigeneSequenceRecord, UnigeneProtsimRecord, UnigeneSTSRecord, UnigeneRecord, _RecordConsumer, _Scanner, RecordParser, and Iterator in Bio.UniGene were declared obsolete in Release 1.54, deprecated in Release 1.55, and removed in Release 1.59. Their functionality is now available through a read() and a parse() function in Bio.UniGene.
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 letter_sum and all_letters_sum were removed from the
SeqMat class in Bio.SubsMat in Release 1.57.
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. As an alternative,
please consider using Bio.Align.substitution_matrices.
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; 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.
Bio.ParserSupport.SGMLStrippingConsumer was deprecated in Release 1.59, and
removed in Release 1.61.
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 is_palindrom function was removed in Release 1.79.