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.
No longer supported as of Release 1.51, having triggered a warning with Release 1.50, with a mention in the release notes for Release 1.49.
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 1.63, 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 1.69, having triggered a warning with release 1.66 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.
Still suported but deprecated as of Release 1.67, triggering a warning at installation time.
This was deprecated in Biopython 1.69.
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 added in Release 1.62 (August 2013).
For backward compatibility and/or to silence the warnings, please use explicit string comparision, str(seq1) == str(seq2), or object comparison, id(seq1) == id(seq2), as required.
Deprecated as of Release 1.64. You should now use str(Bio.Seq.Seq) or str(Bio.Seq.MutableSeq) instead of the tostring() methods.
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.
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()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.
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.
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.
Earlier the function pairlist_to_dict was deprecated in Release 1.45, and
removed in Release 1.53.
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.
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.
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.
Deprecated in Release 1.47, removed in Release 1.52.
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.
Following the Release of 1.48, Numeric support in Biopython is discontinued. Please move to NumPy for Biopython 1.49 or later.
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 gives a DeprecationWarning. The Seq object's .data property was removed in Release 1.61.
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.
Bio.distance was deprecated in Release 1.49, at which point its C code implementation Bio.cdistance was removed (this was not intended as a public API). Removed in Release 1.53.
Deprecated in Release 1.49, as the website this parsed has been redesigned. Removed in Release 1.53.
Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed in Release 1.51. The source code for Martel is still in our repository if anyone wanted to develop this outside of Biopython.
Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders, Bio.Std, Bio.StdHandler, Bio.Decode and Bio.DBXRef modules
Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium sized files, use Bio.SeqIO.to_dict() to make an in memory dictionary of SeqRecord objects. Biopython 1.52 onwards provides Bio.SeqIO.index() which is suitable even for very large files.
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. Please use Bio.AlignIO or the Alignment object's format method instead.
Deprecated in Release 1.48, and removed in Release 1.51, this parser was replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
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.
Deprecated in Release 1.48, and removed in Release 1.51, this was a parser for the output of MetaTool 3.5 which is now obsolete.
The online functionality (search_for, download_many, and NCBIDictionary) was declared obsolete in Release 1.48, deprecated in Release 1.50, and removed in Release 1.54. Please use Bio.Entrez instead.
Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed in Release 1.53. Please use Bio.Entrez instead.
Deprecated in favor of Bio.Entrez in Release 1.48, removed in Release 1.52.
A revised API was added and the old one deprecated in Release 1.48, and removed in Biopython 1.52: Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle) Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle) Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle) Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle) Bio.Medline.RecordParser --> Bio.Medline.read(handle) Bio.Medline.Iterator --> Bio.Medline.parse(handle)
The HTML BLAST parser was deprecated in Release 1.48, and removed in 1.52. The deprecated functions blast and blasturl were removed in Release 1.44.
Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser for this "simple alignment format" could be developed for Bio.AlignIO instead.
Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO, removed in Release 1.51.
Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO, removed in Release 1.51.
You can still use the "phylip", "clustal", "nexus" and "stockholm" formats in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
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.
Deprecated as of Release 1.47, as it appears to have no users, and the code does not seem relevant for ECell 3. Removed in Release 1.49.
Deprecated as of Release 1.45, removed in Release 1.49.
Deprecated as of Release 1.45, removed in Release 1.49. The NCBI's LocusLink was superseded by Entrez Gene.
Deprecated as of Release 1.46, removed in Release 1.49.
Deprecated as of Release 1.46, removed in Release 1.49.
Deprecated as of Release 1.46, removed in Release 1.49.
Deprecated as of Release 1.46, removed in Release 1.49.
Deprecated as of Release 1.45, removed in Release 1.48
The modules under Bio.WWW were deprecated in Release 1.45, and removed in Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48, and removed in Release 1.53.
The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro, Bio.WWW.ExPASy and Bio.WWW.NCBI is now available from Bio.SCOP, Bio.InterPro, Bio.ExPASy and Bio.Entrez instead.
The old Bio.SeqIO.FASTA and Bio.SeqIO.generic were deprecated in favour of the new Bio.SeqIO module as of Release 1.44, removed in Release 1.47.
Deprecated in Release 1.44, removed in 1.46.
Deprecated in Release 1.44, removed in 1.46.
Deprecated in Release 1.44, removed in 1.46.
Deprecated in favor of Bio.SeqUtils.lcc in Release 1.44, removed in 1.46.
Deprecated in favor of Bio.SeqUtils.CheckSum in Release 1.44, removed in 1.46.
This was removed in Release 1.44 (a deprecation was not possible).
These were deprecated in Release 1.44, and removed in Release 1.49.
This was deprecated in Release 1.43 and removed in Release 1.44.
Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated in Release 1.31, and removed in Release 1.43. Function 'translate' was deprecated in Release 1.49, and removed in Release 1.53. Use the functions and methods in Bio.Seq 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 functions forward_complement and antiparallel in Bio.GFF.easy
have been deprecated as of Release 1.31, and removed in Release 1.43.
Use the functions complement and reverse_complement in Bio.Seq
instead.
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).
Deprecated as of Release 1.30, removed in Release 1.42. Use Bio.SeqUtils
instead.
Deprecated as of Release 1.30, removed in Release 1.42. The Support Vector Machine code in Biopython has been superseded by a more robust (and maintained) SVM library, which includes a python interface. We recommend using LIBSVM:
http://www.csie.ntu.edu.tw/~cjlin/libsvm/
Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't completely implemented and duplicates the work of most standard parsers.
Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use the function kcluster in Bio.Cluster which performs k-means or k-medians clustering.
The module Bio.SCOP.FileIndex was deprecated in Release 1.46, and removed in Release 1.53. The class Parser in Bio.SCOP.Dom was removed in Release 1.55 final. The class Iterator in Bio.SCOP.Dom was removed in Release 1.56.
Dictionary to_one_letter_code in module Bio.SCOP.three_to_one_dict was moved to protein_letters_3to1 in module Bio.Data.SCOPData in Release 1.62. The old alias was preserved with a deprecation warning, until it was removed in Release 1.66.
Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe', and 'back_transcribe' were deprecated in Release 1.49, and removed in Release 1.53. 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. It will be removed in
Release 1.70.
Bio.PopGen.FDist was deprecated in Release 1.68. It will be 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. It will be 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 get_column and add_sequence of the MultipleSeqAlignment class were deprecated in Release 1.57 and removed in Release 1.69.
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.
Bio.ParserSupport.SGMLStrippingConsumer was deprecated in Release 1.59, and
removed in Release 1.61.