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object --+ | Seq
A read-only sequence object (essentially a string with an alphabet).
Like normal python strings, our basic sequence object is immutable. This prevents you from doing my_seq[5] = "A" for example, but does allow Seq objects to be used as dictionary keys.
The Seq object provides a number of string like methods (such as count, find, split and strip), which are alphabet aware where appropriate.
In addition to the string like sequence, the Seq object has an alphabet property. This is an instance of an Alphabet class from Bio.Alphabet, for example generic DNA, or IUPAC DNA. This describes the type of molecule (e.g. RNA, DNA, protein) and may also indicate the expected symbols (letters).
The Seq object also provides some biological methods, such as complement, reverse_complement, transcribe, back_transcribe and translate (which are not applicable to sequences with a protein alphabet).
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data Sequence as a string (DEPRECATED). |
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Inherited from |
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Add another sequence or string to this sequence. If adding a string to a Seq, the alphabet is preserved: >>> from Bio.Seq import Seq >>> from Bio.Alphabet import generic_protein >>> Seq("MELKI", generic_protein) + "LV" Seq('MELKILV', ProteinAlphabet()) When adding two Seq (like) objects, the alphabets are important. Consider this example: >>> from Bio.Seq import Seq >>> from Bio.Alphabet.IUPAC import unambiguous_dna, ambiguous_dna >>> unamb_dna_seq = Seq("ACGT", unambiguous_dna) >>> ambig_dna_seq = Seq("ACRGT", ambiguous_dna) >>> unamb_dna_seq Seq('ACGT', IUPACUnambiguousDNA()) >>> ambig_dna_seq Seq('ACRGT', IUPACAmbiguousDNA()) If we add the ambiguous and unambiguous IUPAC DNA alphabets, we get the more general ambiguous IUPAC DNA alphabet: >>> unamb_dna_seq + ambig_dna_seq Seq('ACGTACRGT', IUPACAmbiguousDNA()) However, if the default generic alphabet is included, the result is a generic alphabet: >>> Seq("") + ambig_dna_seq Seq('ACRGT', Alphabet()) You can't add RNA and DNA sequences: >>> from Bio.Alphabet import generic_dna, generic_rna >>> Seq("ACGT", generic_dna) + Seq("ACGU", generic_rna) Traceback (most recent call last): ... TypeError: Incompatable alphabets DNAAlphabet() and RNAAlphabet() You can't add nucleotide and protein sequences: >>> from Bio.Alphabet import generic_dna, generic_protein >>> Seq("ACGT", generic_dna) + Seq("MELKI", generic_protein) Traceback (most recent call last): ... TypeError: Incompatable alphabets DNAAlphabet() and ProteinAlphabet() |
Compare the sequence to another sequence or a string (README). Historically comparing Seq objects has done Python object comparison. After considerable discussion (keeping in mind constraints of the Python language, hashes and dictionary support) a future release of Biopython will change this to use simple string comparison. The plan is that comparing incompatible alphabets (e.g. DNA to RNA) will trigger a warning. This version of Biopython still does Python object comparison, but with a warning about this future change. During this transition period, please just do explicit comparisons: >>> seq1 = Seq("ACGT") >>> seq2 = Seq("ACGT") >>> id(seq1) == id(seq2) False >>> str(seq1) == str(seq2) True Note - This method indirectly supports ==, < , etc. |
Implements the 'in' keyword, like a python string. e.g. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import generic_dna, generic_rna, generic_protein >>> my_dna = Seq("ATATGAAATTTGAAAA", generic_dna) >>> "AAA" in my_dna True >>> Seq("AAA") in my_dna True >>> Seq("AAA", generic_dna) in my_dna True Like other Seq methods, this will raise a type error if another Seq (or Seq like) object with an incompatible alphabet is used: >>> Seq("AAA", generic_rna) in my_dna Traceback (most recent call last): ... TypeError: Incompatable alphabets DNAAlphabet() and RNAAlphabet() >>> Seq("AAA", generic_protein) in my_dna Traceback (most recent call last): ... TypeError: Incompatable alphabets DNAAlphabet() and ProteinAlphabet() |
Hash for comparison. See the __cmp__ documentation - we plan to change this!
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Create a Seq object. Arguments:
You will typically use Bio.SeqIO to read in sequences from files as SeqRecord objects, whose sequence will be exposed as a Seq object via the seq property. However, will often want to create your own Seq objects directly: >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF", ... IUPAC.protein) >>> my_seq Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein()) >>> print my_seq MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF >>> my_seq.alphabet IUPACProtein()
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Adding a sequence on the left. If adding a string to a Seq, the alphabet is preserved: >>> from Bio.Seq import Seq >>> from Bio.Alphabet import generic_protein >>> "LV" + Seq("MELKI", generic_protein) Seq('LVMELKI', ProteinAlphabet()) Adding two Seq (like) objects is handled via the __add__ method. |
Returns a (truncated) representation of the sequence for debugging.
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Returns the full sequence as a python string, use str(my_seq). Note that Biopython 1.44 and earlier would give a truncated version of repr(my_seq) for str(my_seq). If you are writing code which need to be backwards compatible with old Biopython, you should continue to use my_seq.tostring() rather than str(my_seq).
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string/Seq/MutableSeq to string, checking alphabet (PRIVATE). For a string argument, returns the string. For a Seq or MutableSeq, it checks the alphabet is compatible (raising an exception if it isn't), and then returns a string. |
Returns the DNA sequence from an RNA sequence. New Seq object. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG", ... IUPAC.unambiguous_rna) >>> messenger_rna Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA()) >>> messenger_rna.back_transcribe() Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA()) Trying to back-transcribe a protein or DNA sequence raises an exception: >>> my_protein = Seq("MAIVMGR", IUPAC.protein) >>> my_protein.back_transcribe() Traceback (most recent call last): ... ValueError: Proteins cannot be back transcribed! |
Returns the complement sequence. New Seq object. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> my_dna = Seq("CCCCCGATAG", IUPAC.unambiguous_dna) >>> my_dna Seq('CCCCCGATAG', IUPACUnambiguousDNA()) >>> my_dna.complement() Seq('GGGGGCTATC', IUPACUnambiguousDNA()) You can of course used mixed case sequences, >>> from Bio.Seq import Seq >>> from Bio.Alphabet import generic_dna >>> my_dna = Seq("CCCCCgatA-GD", generic_dna) >>> my_dna Seq('CCCCCgatA-GD', DNAAlphabet()) >>> my_dna.complement() Seq('GGGGGctaT-CH', DNAAlphabet()) Note in the above example, ambiguous character D denotes G, A or T so its complement is H (for C, T or A). Trying to complement a protein sequence raises an exception. >>> my_protein = Seq("MAIVMGR", IUPAC.protein) >>> my_protein.complement() Traceback (most recent call last): ... ValueError: Proteins do not have complements! |
Non-overlapping count method, like that of a python string. This behaves like the python string method of the same name, which does a non-overlapping count! Returns an integer, the number of occurrences of substring argument sub in the (sub)sequence given by [start:end]. Optional arguments start and end are interpreted as in slice notation. Arguments:
e.g. >>> from Bio.Seq import Seq >>> my_seq = Seq("AAAATGA") >>> print my_seq.count("A") 5 >>> print my_seq.count("ATG") 1 >>> print my_seq.count(Seq("AT")) 1 >>> print my_seq.count("AT", 2, -1) 1 HOWEVER, please note because python strings and Seq objects (and MutableSeq objects) do a non-overlapping search, this may not give the answer you expect: >>> "AAAA".count("AA") 2 >>> print Seq("AAAA").count("AA") 2 A non-overlapping search would give the answer as three! |
Does the Seq end with the given suffix? Returns True/False. This behaves like the python string method of the same name. Return True if the sequence ends with the specified suffix (a string or another Seq object), False otherwise. With optional start, test sequence beginning at that position. With optional end, stop comparing sequence at that position. suffix can also be a tuple of strings to try. e.g. >>> from Bio.Seq import Seq >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG") >>> my_rna.endswith("UUG") True >>> my_rna.endswith("AUG") False >>> my_rna.endswith("AUG", 0, 18) True >>> my_rna.endswith(("UCC","UCA","UUG")) True |
Find method, like that of a python string. This behaves like the python string method of the same name. Returns an integer, the index of the first occurrence of substring argument sub in the (sub)sequence given by [start:end]. Arguments:
Returns -1 if the subsequence is NOT found. e.g. Locating the first typical start codon, AUG, in an RNA sequence: >>> from Bio.Seq import Seq >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG") >>> my_rna.find("AUG") 3 |
Returns a lower case copy of the sequence. This will adjust the alphabet if required. Note that the IUPAC alphabets are upper case only, and thus a generic alphabet must be substituted. >>> from Bio.Alphabet import Gapped, generic_dna >>> from Bio.Alphabet import IUPAC >>> from Bio.Seq import Seq >>> my_seq = Seq("CGGTACGCTTATGTCACGTAG*AAAAAA", Gapped(IUPAC.unambiguous_dna, "*")) >>> my_seq Seq('CGGTACGCTTATGTCACGTAG*AAAAAA', Gapped(IUPACUnambiguousDNA(), '*')) >>> my_seq.lower() Seq('cggtacgcttatgtcacgtag*aaaaaa', Gapped(DNAAlphabet(), '*')) See also the upper method. |
Returns a new Seq object with leading (left) end stripped. This behaves like the python string method of the same name. Optional argument chars defines which characters to remove. If ommitted or None (default) then as for the python string method, this defaults to removing any white space. e.g. print my_seq.lstrip("-") See also the strip and rstrip methods. |
Returns the reverse complement sequence. New Seq object. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> my_dna = Seq("CCCCCGATAGNR", IUPAC.ambiguous_dna) >>> my_dna Seq('CCCCCGATAGNR', IUPACAmbiguousDNA()) >>> my_dna.reverse_complement() Seq('YNCTATCGGGGG', IUPACAmbiguousDNA()) Note in the above example, since R = G or A, its complement is Y (which denotes C or T). You can of course used mixed case sequences, >>> from Bio.Seq import Seq >>> from Bio.Alphabet import generic_dna >>> my_dna = Seq("CCCCCgatA-G", generic_dna) >>> my_dna Seq('CCCCCgatA-G', DNAAlphabet()) >>> my_dna.reverse_complement() Seq('C-TatcGGGGG', DNAAlphabet()) Trying to complement a protein sequence raises an exception: >>> my_protein = Seq("MAIVMGR", IUPAC.protein) >>> my_protein.reverse_complement() Traceback (most recent call last): ... ValueError: Proteins do not have complements! |
Find from right method, like that of a python string. This behaves like the python string method of the same name. Returns an integer, the index of the last (right most) occurrence of substring argument sub in the (sub)sequence given by [start:end]. Arguments:
Returns -1 if the subsequence is NOT found. e.g. Locating the last typical start codon, AUG, in an RNA sequence: >>> from Bio.Seq import Seq >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG") >>> my_rna.rfind("AUG") 15 |
Right split method, like that of a python string. This behaves like the python string method of the same name. Return a list of the 'words' in the string (as Seq objects), using sep as the delimiter string. If maxsplit is given, at most maxsplit splits are done COUNTING FROM THE RIGHT. If maxsplit is ommited, all splits are made. Following the python string method, sep will by default be any white space (tabs, spaces, newlines) but this is unlikely to apply to biological sequences. e.g. print my_seq.rsplit("*",1) See also the split method. |
Returns a new Seq object with trailing (right) end stripped. This behaves like the python string method of the same name. Optional argument chars defines which characters to remove. If ommitted or None (default) then as for the python string method, this defaults to removing any white space. e.g. Removing a nucleotide sequence's polyadenylation (poly-A tail): >>> from Bio.Alphabet import IUPAC >>> from Bio.Seq import Seq >>> my_seq = Seq("CGGTACGCTTATGTCACGTAGAAAAAA", IUPAC.unambiguous_dna) >>> my_seq Seq('CGGTACGCTTATGTCACGTAGAAAAAA', IUPACUnambiguousDNA()) >>> my_seq.rstrip("A") Seq('CGGTACGCTTATGTCACGTAG', IUPACUnambiguousDNA()) See also the strip and lstrip methods. |
Split method, like that of a python string. This behaves like the python string method of the same name. Return a list of the 'words' in the string (as Seq objects), using sep as the delimiter string. If maxsplit is given, at most maxsplit splits are done. If maxsplit is ommited, all splits are made. Following the python string method, sep will by default be any white space (tabs, spaces, newlines) but this is unlikely to apply to biological sequences. e.g. >>> from Bio.Seq import Seq >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG") >>> my_aa = my_rna.translate() >>> my_aa Seq('VMAIVMGR*KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*')) >>> my_aa.split("*") [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))] >>> my_aa.split("*",1) [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))] See also the rsplit method: >>> my_aa.rsplit("*",1) [Seq('VMAIVMGR*KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))] |
Does the Seq start with the given prefix? Returns True/False. This behaves like the python string method of the same name. Return True if the sequence starts with the specified prefix (a string or another Seq object), False otherwise. With optional start, test sequence beginning at that position. With optional end, stop comparing sequence at that position. prefix can also be a tuple of strings to try. e.g. >>> from Bio.Seq import Seq >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG") >>> my_rna.startswith("GUC") True >>> my_rna.startswith("AUG") False >>> my_rna.startswith("AUG", 3) True >>> my_rna.startswith(("UCC","UCA","UCG"),1) True |
Returns a new Seq object with leading and trailing ends stripped. This behaves like the python string method of the same name. Optional argument chars defines which characters to remove. If ommitted or None (default) then as for the python string method, this defaults to removing any white space. e.g. print my_seq.strip("-") See also the lstrip and rstrip methods. |
Returns the full sequence as a MutableSeq object. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAAL", ... IUPAC.protein) >>> my_seq Seq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein()) >>> my_seq.tomutable() MutableSeq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein()) Note that the alphabet is preserved. |
Returns the full sequence as a python string (semi-obsolete). Although not formally deprecated, you are now encouraged to use str(my_seq) instead of my_seq.tostring(). |
Returns the RNA sequence from a DNA sequence. New Seq object. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG", ... IUPAC.unambiguous_dna) >>> coding_dna Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA()) >>> coding_dna.transcribe() Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA()) Trying to transcribe a protein or RNA sequence raises an exception: >>> my_protein = Seq("MAIVMGR", IUPAC.protein) >>> my_protein.transcribe() Traceback (most recent call last): ... ValueError: Proteins cannot be transcribed! |
Turns a nucleotide sequence into a protein sequence. New Seq object. This method will translate DNA or RNA sequences, and those with a nucleotide or generic alphabet. Trying to translate a protein sequence raises an exception. Arguments:
e.g. Using the standard table: >>> coding_dna = Seq("GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG") >>> coding_dna.translate() Seq('VAIVMGR*KGAR*', HasStopCodon(ExtendedIUPACProtein(), '*')) >>> coding_dna.translate(stop_symbol="@") Seq('VAIVMGR@KGAR@', HasStopCodon(ExtendedIUPACProtein(), '@')) >>> coding_dna.translate(to_stop=True) Seq('VAIVMGR', ExtendedIUPACProtein()) Now using NCBI table 2, where TGA is not a stop codon: >>> coding_dna.translate(table=2) Seq('VAIVMGRWKGAR*', HasStopCodon(ExtendedIUPACProtein(), '*')) >>> coding_dna.translate(table=2, to_stop=True) Seq('VAIVMGRWKGAR', ExtendedIUPACProtein()) In fact, GTG is an alternative start codon under NCBI table 2, meaning this sequence could be a complete CDS: >>> coding_dna.translate(table=2, cds=True) Seq('MAIVMGRWKGAR', ExtendedIUPACProtein()) It isn't a valid CDS under NCBI table 1, due to both the start codon and also the in frame stop codons: >>> coding_dna.translate(table=1, cds=True) Traceback (most recent call last): ... TranslationError: First codon 'GTG' is not a start codon If the sequence has no in-frame stop codon, then the to_stop argument has no effect: >>> coding_dna2 = Seq("TTGGCCATTGTAATGGGCCGC") >>> coding_dna2.translate() Seq('LAIVMGR', ExtendedIUPACProtein()) >>> coding_dna2.translate(to_stop=True) Seq('LAIVMGR', ExtendedIUPACProtein()) NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid or a stop codon. These are translated as "X". Any invalid codon (e.g. "TA?" or "T-A") will throw a TranslationError. NOTE - Does NOT support gapped sequences. NOTE - This does NOT behave like the python string's translate method. For that use str(my_seq).translate(...) instead. |
Return a copy of the sequence without the gap character(s). The gap character can be specified in two ways - either as an explicit argument, or via the sequence's alphabet. For example: >>> from Bio.Seq import Seq >>> from Bio.Alphabet import generic_dna >>> my_dna = Seq("-ATA--TGAAAT-TTGAAAA", generic_dna) >>> my_dna Seq('-ATA--TGAAAT-TTGAAAA', DNAAlphabet()) >>> my_dna.ungap("-") Seq('ATATGAAATTTGAAAA', DNAAlphabet()) If the gap character is not given as an argument, it will be taken from the sequence's alphabet (if defined). Notice that the returned sequence's alphabet is adjusted since it no longer requires a gapped alphabet: >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC, Gapped, HasStopCodon >>> my_pro = Seq("MVVLE=AD*", HasStopCodon(Gapped(IUPAC.protein, "="))) >>> my_pro Seq('MVVLE=AD*', HasStopCodon(Gapped(IUPACProtein(), '='), '*')) >>> my_pro.ungap() Seq('MVVLEAD*', HasStopCodon(IUPACProtein(), '*')) Or, with a simpler gapped DNA example: >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC, Gapped >>> my_seq = Seq("CGGGTAG=AAAAAA", Gapped(IUPAC.unambiguous_dna, "=")) >>> my_seq Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '=')) >>> my_seq.ungap() Seq('CGGGTAGAAAAAA', IUPACUnambiguousDNA()) As long as it is consistent with the alphabet, although it is redundant, you can still supply the gap character as an argument to this method: >>> my_seq Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '=')) >>> my_seq.ungap("=") Seq('CGGGTAGAAAAAA', IUPACUnambiguousDNA()) However, if the gap character given as the argument disagrees with that declared in the alphabet, an exception is raised: >>> my_seq Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '=')) >>> my_seq.ungap("-") Traceback (most recent call last): ... ValueError: Gap '-' does not match '=' from alphabet Finally, if a gap character is not supplied, and the alphabet does not define one, an exception is raised: >>> from Bio.Seq import Seq >>> from Bio.Alphabet import generic_dna >>> my_dna = Seq("ATA--TGAAAT-TTGAAAA", generic_dna) >>> my_dna Seq('ATA--TGAAAT-TTGAAAA', DNAAlphabet()) >>> my_dna.ungap() Traceback (most recent call last): ... ValueError: Gap character not given and not defined in alphabet |
Returns an upper case copy of the sequence. >>> from Bio.Alphabet import HasStopCodon, generic_protein >>> from Bio.Seq import Seq >>> my_seq = Seq("VHLTPeeK*", HasStopCodon(generic_protein)) >>> my_seq Seq('VHLTPeeK*', HasStopCodon(ProteinAlphabet(), '*')) >>> my_seq.lower() Seq('vhltpeek*', HasStopCodon(ProteinAlphabet(), '*')) >>> my_seq.upper() Seq('VHLTPEEK*', HasStopCodon(ProteinAlphabet(), '*')) This will adjust the alphabet if required. See also the lower method. |
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dataSequence as a string (DEPRECATED). This is a read only property provided for backwards compatility with older versions of Biopython (as is the tostring() method). We now encourage you to use str(my_seq) instead of my_seq.data or the method my_seq.tostring(). In recent releases of Biopython it was possible to change a Seq object by updating its data property, but this triggered a deprecation warning. Now the data property is read only, since Seq objects are meant to be immutable: >>> from Bio.Seq import Seq >>> from Bio.Alphabet import generic_dna >>> my_seq = Seq("ACGT", generic_dna) >>> str(my_seq) == my_seq.tostring() == "ACGT" True >>> my_seq.data = "AAAA" Traceback (most recent call last): ... AttributeError: can't set attribute
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