Bio.SeqRecord module

Represent a Sequence Record, a sequence with annotation.

class Bio.SeqRecord.SeqRecord(seq: Optional[Union[Seq, MutableSeq]], id: Optional[str] = '<unknown id>', name: str = '<unknown name>', description: str = '<unknown description>', dbxrefs: Optional[List[str]] = None, features: Optional[List[SeqFeature]] = None, annotations: Optional[Dict[str, Union[str, int]]] = None, letter_annotations: Optional[Dict[str, Sequence[Any]]] = None)

Bases: object

A SeqRecord object holds a sequence and information about it.

Main attributes:

• id - Identifier such as a locus tag (string)

• seq - The sequence itself (Seq object or similar)

Additional attributes:

• name - Sequence name, e.g. gene name (string)

• description - Additional text (string)

• dbxrefs - List of database cross references (list of strings)

• features - Any (sub)features defined (list of SeqFeature objects)

• annotations - Further information about the whole sequence (dictionary). Most entries are strings, or lists of strings.

• letter_annotations - Per letter/symbol annotation (restricted dictionary). This holds Python sequences (lists, strings or tuples) whose length matches that of the sequence. A typical use would be to hold a list of integers representing sequencing quality scores, or a string representing the secondary structure.

You will typically use Bio.SeqIO to read in sequences from files as SeqRecord objects. However, you may want to create your own SeqRecord objects directly (see the __init__ method for further details):

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF"),
...                    id="YP_025292.1", name="HokC",
...                    description="toxic membrane protein")
>>> print(record)
ID: YP_025292.1
Name: HokC
Description: toxic membrane protein
Number of features: 0
Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF')

If you want to save SeqRecord objects to a sequence file, use Bio.SeqIO for this. For the special case where you want the SeqRecord turned into a string in a particular file format there is a format method which uses Bio.SeqIO internally:

>>> print(record.format("fasta"))
>YP_025292.1 toxic membrane protein
MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF

You can also do things like slicing a SeqRecord, checking its length, etc

>>> len(record)
44
>>> edited = record[:10] + record[11:]
>>> print(edited.seq)
MKQHKAMIVAIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
>>> print(record.seq)
MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF

__init__(seq: Optional[Union[Seq, MutableSeq]], id: Optional[str] = '<unknown id>', name: str = '<unknown name>', description: str = '<unknown description>', dbxrefs: Optional[List[str]] = None, features: Optional[List[SeqFeature]] = None, annotations: Optional[Dict[str, Union[str, int]]] = None, letter_annotations: Optional[Dict[str, Sequence[Any]]] = None) → None

Create a SeqRecord.

Arguments:

• seq - Sequence, required (Seq or MutableSeq)

• id - Sequence identifier, recommended (string)

• name - Sequence name, optional (string)

• description - Sequence description, optional (string)

• dbxrefs - Database cross references, optional (list of strings)

• features - Any (sub)features, optional (list of SeqFeature objects)

• annotations - Dictionary of annotations for the whole sequence

• letter_annotations - Dictionary of per-letter-annotations, values should be strings, list or tuples of the same length as the full sequence.

You will typically use Bio.SeqIO to read in sequences from files as SeqRecord objects. However, you may want to create your own SeqRecord objects directly.

Note that while an id is optional, we strongly recommend you supply a unique id string for each record. This is especially important if you wish to write your sequences to a file.

You can create a ‘blank’ SeqRecord object, and then populate the attributes later.

dbxrefs: List[str]

annotations: Dict[str, Union[str, int]]

property letter_annotations

Dictionary of per-letter-annotation for the sequence.

For example, this can hold quality scores used in FASTQ or QUAL files. Consider this example using Bio.SeqIO to read in an example Solexa variant FASTQ file as a SeqRecord:

>>> from Bio import SeqIO
>>> record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa")
>>> print("%s %s" % (record.id, record.seq))
slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
>>> print(list(record.letter_annotations))
['solexa_quality']
>>> print(record.letter_annotations["solexa_quality"])
[40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0, -1, -2, -3, -4, -5]

The letter_annotations get sliced automatically if you slice the parent SeqRecord, for example taking the last ten bases:

>>> sub_record = record[-10:]
>>> print("%s %s" % (sub_record.id, sub_record.seq))
slxa_0001_1_0001_01 ACGTNNNNNN
>>> print(sub_record.letter_annotations["solexa_quality"])
[4, 3, 2, 1, 0, -1, -2, -3, -4, -5]

Any python sequence (i.e. list, tuple or string) can be recorded in the SeqRecord’s letter_annotations dictionary as long as the length matches that of the SeqRecord’s sequence. e.g.

>>> len(sub_record.letter_annotations)
1
>>> sub_record.letter_annotations["dummy"] = "abcdefghij"
>>> len(sub_record.letter_annotations)
2

You can delete entries from the letter_annotations dictionary as usual:

>>> del sub_record.letter_annotations["solexa_quality"]
>>> sub_record.letter_annotations
{'dummy': 'abcdefghij'}

You can completely clear the dictionary easily as follows:

>>> sub_record.letter_annotations = {}
>>> sub_record.letter_annotations
{}

Note that if replacing the record’s sequence with a sequence of a different length you must first clear the letter_annotations dict.

property seq

The sequence itself, as a Seq or MutableSeq object.

__getitem__(index: int) → str

__getitem__(index: slice) → Bio.SeqRecord.SeqRecord

Return a sub-sequence or an individual letter.

Slicing, e.g. my_record[5:10], returns a new SeqRecord for that sub-sequence with some annotation preserved as follows:

• The name, id and description are kept as-is.

• Any per-letter-annotations are sliced to match the requested sub-sequence.

• Unless a stride is used, all those features which fall fully within the subsequence are included (with their locations adjusted accordingly). If you want to preserve any truncated features (e.g. GenBank/EMBL source features), you must explicitly add them to the new SeqRecord yourself.

• With the exception of any molecule type, the annotations dictionary and the dbxrefs list are not used for the new SeqRecord, as in general they may not apply to the subsequence. If you want to preserve them, you must explicitly copy them to the new SeqRecord yourself.

Using an integer index, e.g. my_record[5] is shorthand for extracting that letter from the sequence, my_record.seq[5].

For example, consider this short protein and its secondary structure as encoded by the PDB (e.g. H for alpha helices), plus a simple feature for its histidine self phosphorylation site:

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> from Bio.SeqFeature import SeqFeature, SimpleLocation
>>> rec = SeqRecord(Seq("MAAGVKQLADDRTLLMAGVSHDLRTPLTRIRLAT"
...                     "EMMSEQDGYLAESINKDIEECNAIIEQFIDYLR"),
...                 id="1JOY", name="EnvZ",
...                 description="Homodimeric domain of EnvZ from E. coli")
>>> rec.letter_annotations["secondary_structure"] = "  S  SSSSSSHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTT  "
>>> rec.features.append(SeqFeature(SimpleLocation(20, 21),
...                     type = "Site"))

Now let’s have a quick look at the full record,

>>> print(rec)
ID: 1JOY
Name: EnvZ
Description: Homodimeric domain of EnvZ from E. coli
Number of features: 1
Per letter annotation for: secondary_structure
Seq('MAAGVKQLADDRTLLMAGVSHDLRTPLTRIRLATEMMSEQDGYLAESINKDIEE...YLR')
>>> rec.letter_annotations["secondary_structure"]
'  S  SSSSSSHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTT  '
>>> print(rec.features[0].location)
[20:21]

Now let’s take a sub sequence, here chosen as the first (fractured) alpha helix which includes the histidine phosphorylation site:

>>> sub = rec[11:41]
>>> print(sub)
ID: 1JOY
Name: EnvZ
Description: Homodimeric domain of EnvZ from E. coli
Number of features: 1
Per letter annotation for: secondary_structure
Seq('RTLLMAGVSHDLRTPLTRIRLATEMMSEQD')
>>> sub.letter_annotations["secondary_structure"]
'HHHHHTTTHHHHHHHHHHHHHHHHHHHHHH'
>>> print(sub.features[0].location)
[9:10]

You can also of course omit the start or end values, for example to get the first ten letters only:

>>> print(rec[:10])
ID: 1JOY
Name: EnvZ
Description: Homodimeric domain of EnvZ from E. coli
Number of features: 0
Per letter annotation for: secondary_structure
Seq('MAAGVKQLAD')

Or for the last ten letters:

>>> print(rec[-10:])
ID: 1JOY
Name: EnvZ
Description: Homodimeric domain of EnvZ from E. coli
Number of features: 0
Per letter annotation for: secondary_structure
Seq('IIEQFIDYLR')

If you omit both, then you get a copy of the original record (although lacking the annotations and dbxrefs):

>>> print(rec[:])
ID: 1JOY
Name: EnvZ
Description: Homodimeric domain of EnvZ from E. coli
Number of features: 1
Per letter annotation for: secondary_structure
Seq('MAAGVKQLADDRTLLMAGVSHDLRTPLTRIRLATEMMSEQDGYLAESINKDIEE...YLR')

Finally, indexing with a simple integer is shorthand for pulling out that letter from the sequence directly:

>>> rec[5]
'K'
>>> rec.seq[5]
'K'

__iter__() → Iterable[Union[Bio.Seq.Seq, Bio.Seq.MutableSeq]]

Iterate over the letters in the sequence.

For example, using Bio.SeqIO to read in a protein FASTA file:

>>> from Bio import SeqIO
>>> record = SeqIO.read("Fasta/loveliesbleeding.pro", "fasta")
>>> for amino in record:
...     print(amino)
...     if amino == "L": break
X
A
G
L
>>> print(record.seq[3])
L

This is just a shortcut for iterating over the sequence directly:

>>> for amino in record.seq:
...     print(amino)
...     if amino == "L": break
X
A
G
L
>>> print(record.seq[3])
L

Note that this does not facilitate iteration together with any per-letter-annotation. However, you can achieve that using the python zip function on the record (or its sequence) and the relevant per-letter-annotation:

>>> from Bio import SeqIO
>>> rec = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa")
>>> print("%s %s" % (rec.id, rec.seq))
slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
>>> print(list(rec.letter_annotations))
['solexa_quality']
>>> for nuc, qual in zip(rec, rec.letter_annotations["solexa_quality"]):
...     if qual > 35:
...         print("%s %i" % (nuc, qual))
A 40
C 39
G 38
T 37
A 36

You may agree that using zip(rec.seq, …) is more explicit than using zip(rec, …) as shown above.

__contains__(char: str) → bool

Implement the ‘in’ keyword, searches the sequence.

e.g.

>>> from Bio import SeqIO
>>> record = SeqIO.read("Fasta/sweetpea.nu", "fasta")
>>> "GAATTC" in record
False
>>> "AAA" in record
True

This essentially acts as a proxy for using “in” on the sequence:

>>> "GAATTC" in record.seq
False
>>> "AAA" in record.seq
True

Note that you can also use Seq objects as the query,

>>> from Bio.Seq import Seq
>>> Seq("AAA") in record
True

See also the Seq object’s __contains__ method.

__bytes__() → bytes

__str__() → str

Return a human readable summary of the record and its annotation (string).

The python built in function str works by calling the object’s __str__ method. e.g.

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF"),
...                    id="YP_025292.1", name="HokC",
...                    description="toxic membrane protein, small")
>>> print(str(record))
ID: YP_025292.1
Name: HokC
Description: toxic membrane protein, small
Number of features: 0
Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF')

In this example you don’t actually need to call str explicitly, as the print command does this automatically:

>>> print(record)
ID: YP_025292.1
Name: HokC
Description: toxic membrane protein, small
Number of features: 0
Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF')

Note that long sequences are shown truncated.

__repr__() → str

Return a concise summary of the record for debugging (string).

The python built in function repr works by calling the object’s __repr__ method. e.g.

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> rec = SeqRecord(Seq("MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKAT"
...                     "GEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQ"
...                     "SGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQ"
...                     "PQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF"),
...                 id="NP_418483.1", name="b4059",
...                 description="ssDNA-binding protein",
...                 dbxrefs=["ASAP:13298", "GI:16131885", "GeneID:948570"])
>>> print(repr(rec))
SeqRecord(seq=Seq('MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTE...IPF'), id='NP_418483.1', name='b4059', description='ssDNA-binding protein', dbxrefs=['ASAP:13298', 'GI:16131885', 'GeneID:948570'])

At the python prompt you can also use this shorthand:

>>> rec
SeqRecord(seq=Seq('MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTE...IPF'), id='NP_418483.1', name='b4059', description='ssDNA-binding protein', dbxrefs=['ASAP:13298', 'GI:16131885', 'GeneID:948570'])

Note that long sequences are shown truncated. Also note that any annotations, letter_annotations and features are not shown (as they would lead to a very long string).

format(format: str) → str

Return the record as a string in the specified file format.

The format should be a lower case string supported as an output format by Bio.SeqIO, which is used to turn the SeqRecord into a string. e.g.

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF"),
...                    id="YP_025292.1", name="HokC",
...                    description="toxic membrane protein")
>>> record.format("fasta")
'>YP_025292.1 toxic membrane protein\nMKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF\n'
>>> print(record.format("fasta"))
>YP_025292.1 toxic membrane protein
MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF

The Python print function automatically appends a new line, meaning in this example a blank line is shown. If you look at the string representation you can see there is a trailing new line (shown as slash n) which is important when writing to a file or if concatenating multiple sequence strings together.

Note that this method will NOT work on every possible file format supported by Bio.SeqIO (e.g. some are for multiple sequences only, and binary formats are not supported).

__format__(format_spec: str) → str

Return the record as a string in the specified file format.

This method supports the Python format() function and f-strings. The format_spec should be a lower case string supported by Bio.SeqIO as a text output file format. Requesting a binary file format raises a ValueError. e.g.

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF"),
...                    id="YP_025292.1", name="HokC",
...                    description="toxic membrane protein")
...
>>> format(record, "fasta")
'>YP_025292.1 toxic membrane protein\nMKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF\n'
>>> print(f"Here is {record.id} in FASTA format:\n{record:fasta}")
Here is YP_025292.1 in FASTA format:
>YP_025292.1 toxic membrane protein
MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF

See also the SeqRecord’s format() method.

__len__() → int

Return the length of the sequence.

For example, using Bio.SeqIO to read in a FASTA nucleotide file:

>>> from Bio import SeqIO
>>> record = SeqIO.read("Fasta/sweetpea.nu", "fasta")
>>> len(record)
309
>>> len(record.seq)
309

__lt__(other: Any) → NoReturn

Define the less-than operand (not implemented).

__le__(other: Any) → NoReturn

Define the less-than-or-equal-to operand (not implemented).

__eq__(other: object) → NoReturn

Define the equal-to operand (not implemented).

__ne__(other: object) → NoReturn

Define the not-equal-to operand (not implemented).

__gt__(other: Any) → NoReturn

Define the greater-than operand (not implemented).

__ge__(other: Any) → NoReturn

Define the greater-than-or-equal-to operand (not implemented).

__bool__() → bool

Boolean value of an instance of this class (True).

This behaviour is for backwards compatibility, since until the __len__ method was added, a SeqRecord always evaluated as True.

Note that in comparison, a Seq object will evaluate to False if it has a zero length sequence.

WARNING: The SeqRecord may in future evaluate to False when its sequence is of zero length (in order to better match the Seq object behaviour)!

__add__(other: Union[Bio.SeqRecord.SeqRecord, Bio.Seq.Seq, Bio.Seq.MutableSeq, str]) → Bio.SeqRecord.SeqRecord

Add another sequence or string to this sequence.

The other sequence can be a SeqRecord object, a Seq object (or similar, e.g. a MutableSeq) or a plain Python string. If you add a plain string or a Seq (like) object, the new SeqRecord will simply have this appended to the existing data. However, any per letter annotation will be lost:

>>> from Bio import SeqIO
>>> record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa")
>>> print("%s %s" % (record.id, record.seq))
slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
>>> print(list(record.letter_annotations))
['solexa_quality']

>>> new = record + "ACT"
>>> print("%s %s" % (new.id, new.seq))
slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNNACT
>>> print(list(new.letter_annotations))
[]

The new record will attempt to combine the annotation, but for any ambiguities (e.g. different names) it defaults to omitting that annotation.

>>> from Bio import SeqIO
>>> with open("GenBank/pBAD30.gb") as handle:
...     plasmid = SeqIO.read(handle, "gb")
>>> print("%s %i" % (plasmid.id, len(plasmid)))
pBAD30 4923

Now let’s cut the plasmid into two pieces, and join them back up the other way round (i.e. shift the starting point on this plasmid, have a look at the annotated features in the original file to see why this particular split point might make sense):

>>> left = plasmid[:3765]
>>> right = plasmid[3765:]
>>> new = right + left
>>> print("%s %i" % (new.id, len(new)))
pBAD30 4923
>>> str(new.seq) == str(right.seq + left.seq)
True
>>> len(new.features) == len(left.features) + len(right.features)
True

When we add the left and right SeqRecord objects, their annotation is all consistent, so it is all conserved in the new SeqRecord:

>>> new.id == left.id == right.id == plasmid.id
True
>>> new.name == left.name == right.name == plasmid.name
True
>>> new.description == plasmid.description
True
>>> new.annotations == left.annotations == right.annotations
True
>>> new.letter_annotations == plasmid.letter_annotations
True
>>> new.dbxrefs == left.dbxrefs == right.dbxrefs
True

However, we should point out that when we sliced the SeqRecord, any annotations dictionary or dbxrefs list entries were lost. You can explicitly copy them like this:

>>> new.annotations = plasmid.annotations.copy()
>>> new.dbxrefs = plasmid.dbxrefs[:]

__radd__(other: Union[Bio.Seq.Seq, Bio.Seq.MutableSeq, str]) → Bio.SeqRecord.SeqRecord

Add another sequence or string to this sequence (from the left).

This method handles adding a Seq object (or similar, e.g. MutableSeq) or a plain Python string (on the left) to a SeqRecord (on the right). See the __add__ method for more details, but for example:

>>> from Bio import SeqIO
>>> record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa")
>>> print("%s %s" % (record.id, record.seq))
slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
>>> print(list(record.letter_annotations))
['solexa_quality']

>>> new = "ACT" + record
>>> print("%s %s" % (new.id, new.seq))
slxa_0001_1_0001_01 ACTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
>>> print(list(new.letter_annotations))
[]

count(sub, start=None, end=None)

Return the number of non-overlapping occurrences of sub in seq[start:end].

Optional arguments start and end are interpreted as in slice notation. This method behaves as the count method of Python strings.

upper() → Bio.SeqRecord.SeqRecord

Return a copy of the record with an upper case sequence.

All the annotation is preserved unchanged. e.g.

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> record = SeqRecord(Seq("acgtACGT"), id="Test",
...                    description = "Made up for this example")
>>> record.letter_annotations["phred_quality"] = [1, 2, 3, 4, 5, 6, 7, 8]
>>> print(record.upper().format("fastq"))
@Test Made up for this example
ACGTACGT
+
"#$%&'()

Naturally, there is a matching lower method:

>>> print(record.lower().format("fastq"))
@Test Made up for this example
acgtacgt
+
"#$%&'()

__annotations__ = {'_per_letter_annotations': '_RestrictedDict', 'annotations': typing.Dict[str, typing.Union[str, int]], 'dbxrefs': typing.List[str]}

__hash__ = None

lower() → Bio.SeqRecord.SeqRecord

Return a copy of the record with a lower case sequence.

All the annotation is preserved unchanged. e.g.

>>> from Bio import SeqIO
>>> record = SeqIO.read("Fasta/aster.pro", "fasta")
>>> print(record.format("fasta"))
>gi|3298468|dbj|BAA31520.1| SAMIPF
GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLLLKFVTNDMAVGVFSLSAGVG
VTNALVFEIVMTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI

>>> print(record.lower().format("fasta"))
>gi|3298468|dbj|BAA31520.1| SAMIPF
gghvnpavtfgafvggnitllrgivyiiaqllgstvaclllkfvtndmavgvfslsagvg
vtnalvfeivmtfglvytvyataidpkkgslgtiapiaigfivgani

To take a more annotation rich example,

>>> from Bio import SeqIO
>>> old = SeqIO.read("EMBL/TRBG361.embl", "embl")
>>> len(old.features)
3
>>> new = old.lower()
>>> len(old.features) == len(new.features)
True
>>> old.annotations["organism"] == new.annotations["organism"]
True
>>> old.dbxrefs == new.dbxrefs
True

isupper()

Return True if all ASCII characters in the record’s sequence are uppercase.

If there are no cased characters, the method returns False.

islower()

Return True if all ASCII characters in the record’s sequence are lowercase.

If there are no cased characters, the method returns False.

reverse_complement(id: bool = False, name: bool = False, description: bool = False, features: bool = True, annotations: bool = False, letter_annotations: bool = True, dbxrefs: bool = False) → Bio.SeqRecord.SeqRecord

Return new SeqRecord with reverse complement sequence.

By default the new record does NOT preserve the sequence identifier, name, description, general annotation or database cross-references - these are unlikely to apply to the reversed sequence.

You can specify the returned record’s id, name and description as strings, or True to keep that of the parent, or False for a default.

You can specify the returned record’s features with a list of SeqFeature objects, or True to keep that of the parent, or False to omit them. The default is to keep the original features (with the strand and locations adjusted).

You can also specify both the returned record’s annotations and letter_annotations as dictionaries, True to keep that of the parent, or False to omit them. The default is to keep the original annotations (with the letter annotations reversed).

To show what happens to the pre-letter annotations, consider an example Solexa variant FASTQ file with a single entry, which we’ll read in as a SeqRecord:

>>> from Bio import SeqIO
>>> record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa")
>>> print("%s %s" % (record.id, record.seq))
slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
>>> print(list(record.letter_annotations))
['solexa_quality']
>>> print(record.letter_annotations["solexa_quality"])
[40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0, -1, -2, -3, -4, -5]

Now take the reverse complement, here we explicitly give a new identifier (the old identifier with a suffix):

>>> rc_record = record.reverse_complement(id=record.id + "_rc")
>>> print("%s %s" % (rc_record.id, rc_record.seq))
slxa_0001_1_0001_01_rc NNNNNNACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT

Notice that the per-letter-annotations have also been reversed, although this may not be appropriate for all cases.

>>> print(rc_record.letter_annotations["solexa_quality"])
[-5, -4, -3, -2, -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]

Now for the features, we need a different example. Parsing a GenBank file is probably the easiest way to get an nice example with features in it…

>>> from Bio import SeqIO
>>> with open("GenBank/pBAD30.gb") as handle:
...     plasmid = SeqIO.read(handle, "gb")
>>> print("%s %i" % (plasmid.id, len(plasmid)))
pBAD30 4923
>>> plasmid.seq
Seq('GCTAGCGGAGTGTATACTGGCTTACTATGTTGGCACTGATGAGGGTGTCAGTGA...ATG')
>>> len(plasmid.features)
13

Now, let’s take the reverse complement of this whole plasmid:

>>> rc_plasmid = plasmid.reverse_complement(id=plasmid.id+"_rc")
>>> print("%s %i" % (rc_plasmid.id, len(rc_plasmid)))
pBAD30_rc 4923
>>> rc_plasmid.seq
Seq('CATGGGCAAATATTATACGCAAGGCGACAAGGTGCTGATGCCGCTGGCGATTCA...AGC')
>>> len(rc_plasmid.features)
13

Let’s compare the first CDS feature - it has gone from being the second feature (index 1) to the second last feature (index -2), its strand has changed, and the location switched round.

>>> print(plasmid.features[1])
type: CDS
location: [1081:1960](-)
qualifiers:
    Key: label, Value: ['araC']
    Key: note, Value: ['araC regulator of the arabinose BAD promoter']
    Key: vntifkey, Value: ['4']

>>> print(rc_plasmid.features[-2])
type: CDS
location: [2963:3842](+)
qualifiers:
    Key: label, Value: ['araC']
    Key: note, Value: ['araC regulator of the arabinose BAD promoter']
    Key: vntifkey, Value: ['4']

You can check this new location, based on the length of the plasmid:

>>> len(plasmid) - 1081
3842
>>> len(plasmid) - 1960
2963

Note that if the SeqFeature annotation includes any strand specific information (e.g. base changes for a SNP), this information is not amended, and would need correction after the reverse complement.

Note trying to reverse complement a protein SeqRecord raises an exception:

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> protein_rec = SeqRecord(Seq("MAIVMGR"), id="Test",
...                         annotations={"molecule_type": "protein"})
>>> protein_rec.reverse_complement()
Traceback (most recent call last):
   ...
ValueError: Proteins do not have complements!

If you have RNA without any U bases, it must be annotated as RNA otherwise it will be treated as DNA by default with A mapped to T:

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> rna1 = SeqRecord(Seq("ACG"), id="Test")
>>> rna2 = SeqRecord(Seq("ACG"), id="Test", annotations={"molecule_type": "RNA"})
>>> print(rna1.reverse_complement(id="RC", description="unk").format("fasta"))
>RC unk
CGT

>>> print(rna2.reverse_complement(id="RC", description="RNA").format("fasta"))
>RC RNA
CGU

Also note you can reverse complement a SeqRecord using a MutableSeq:

>>> from Bio.Seq import MutableSeq
>>> from Bio.SeqRecord import SeqRecord
>>> rec = SeqRecord(MutableSeq("ACGT"), id="Test")
>>> rec.seq[0] = "T"
>>> print("%s %s" % (rec.id, rec.seq))
Test TCGT
>>> rc = rec.reverse_complement(id=True)
>>> print("%s %s" % (rc.id, rc.seq))
Test ACGA

translate(table: str = 'Standard', stop_symbol: str = '*', to_stop: bool = False, cds: bool = False, gap: Optional[str] = None, id: bool = False, name: bool = False, description: bool = False, features: bool = False, annotations: bool = False, letter_annotations: bool = False, dbxrefs: bool = False) → Bio.SeqRecord.SeqRecord

Return new SeqRecord with translated sequence.

This calls the record’s .seq.translate() method (which describes the translation related arguments, like table for the genetic code),

By default the new record does NOT preserve the sequence identifier, name, description, general annotation or database cross-references - these are unlikely to apply to the translated sequence.

You can specify the returned record’s id, name and description as strings, or True to keep that of the parent, or False for a default.

You can specify the returned record’s features with a list of SeqFeature objects, or False (default) to omit them.

You can also specify both the returned record’s annotations and letter_annotations as dictionaries, True to keep that of the parent (annotations only), or False (default) to omit them.

e.g. Loading a FASTA gene and translating it,

>>> from Bio import SeqIO
>>> gene_record = SeqIO.read("Fasta/sweetpea.nu", "fasta")
>>> print(gene_record.format("fasta"))
>gi|3176602|gb|U78617.1|LOU78617 Lathyrus odoratus phytochrome A (PHYA) gene, partial cds
CAGGCTGCGCGGTTTCTATTTATGAAGAACAAGGTCCGTATGATAGTTGATTGTCATGCA
AAACATGTGAAGGTTCTTCAAGACGAAAAACTCCCATTTGATTTGACTCTGTGCGGTTCG
ACCTTAAGAGCTCCACATAGTTGCCATTTGCAGTACATGGCTAACATGGATTCAATTGCT
TCATTGGTTATGGCAGTGGTCGTCAATGACAGCGATGAAGATGGAGATAGCCGTGACGCA
GTTCTACCACAAAAGAAAAAGAGACTTTGGGGTTTGGTAGTTTGTCATAACACTACTCCG
AGGTTTGTT

And now translating the record, specifying the new ID and description:

>>> protein_record = gene_record.translate(table=11,
...                                        id="phya",
...                                        description="translation")
>>> print(protein_record.format("fasta"))
>phya translation
QAARFLFMKNKVRMIVDCHAKHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMANMDSIA
SLVMAVVVNDSDEDGDSRDAVLPQKKKRLWGLVVCHNTTPRFV