Package Bio :: Module SeqRecord :: Class SeqRecord
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Class SeqRecord

source code

object --+
         |
        SeqRecord
Known Subclasses:

A SeqRecord object holds a sequence and information about it.

Main attributes:
Additional attributes:

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
>>> from Bio.Alphabet import IUPAC
>>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
...                         IUPAC.protein),
...                    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', IUPACProtein())

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
<BLANKLINE>

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
Instance Methods [hide private]
 
__init__(self, seq, id='<unknown id>', name='<unknown name>', description='<unknown description>', dbxrefs=None, features=None, annotations=None, letter_annotations=None)
Create a SeqRecord.
source code
 
_set_per_letter_annotations(self, value) source code
 
_set_seq(self, value) source code
 
__getitem__(self, index)
Returns a sub-sequence or an individual letter.
source code
 
__iter__(self)
Iterate over the letters in the sequence.
source code
 
__contains__(self, char)
Implements the 'in' keyword, searches the sequence.
source code
 
__str__(self)
A human readable summary of the record and its annotation (string).
source code
 
__repr__(self)
A concise summary of the record for debugging (string).
source code
 
format(self, format)
Returns the record as a string in the specified file format.
source code
 
__format__(self, format_spec)
Returns the record as a string in the specified file format.
source code
 
__len__(self)
Returns the length of the sequence.
source code
 
__bool__(self)
Boolean value of an instance of this class (True).
source code
 
__nonzero__(self)
Boolean value of an instance of this class (True).
source code
 
__add__(self, other)
Add another sequence or string to this sequence.
source code
 
__radd__(self, other)
Add another sequence or string to this sequence (from the left).
source code
 
upper(self)
Returns a copy of the record with an upper case sequence.
source code
 
lower(self)
Returns a copy of the record with a lower case sequence.
source code
 
reverse_complement(self, id=False, name=False, description=False, features=True, annotations=False, letter_annotations=True, dbxrefs=False)
Returns new SeqRecord with reverse complement sequence.
source code

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Properties [hide private]
  letter_annotations
Dictionary of per-letter-annotation for the sequence.
  seq
The sequence itself, as a Seq or MutableSeq object.

Inherited from object: __class__

Method Details [hide private]

__init__(self, seq, id='<unknown id>', name='<unknown name>', description='<unknown description>', dbxrefs=None, features=None, annotations=None, letter_annotations=None)
(Constructor)

source code 

Create a SeqRecord.

Arguments:
  • seq - Sequence, required (Seq, MutableSeq or UnknownSeq)
  • 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.

If you don't have the actual sequence, but you do know its length, then using the UnknownSeq object from Bio.Seq is appropriate.

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

Overrides: object.__init__

__getitem__(self, index)
(Indexing operator)

source code 

Returns a sub-sequence or an individual letter.

Slicing, e.g. my_record[5:10], returns a new SeqRecord for that sub-sequence with approriate annotation preserved. The name, id and description are kept.

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).

However, 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 explictly 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, FeatureLocation
>>> from Bio.Alphabet import IUPAC
>>> rec = SeqRecord(Seq("MAAGVKQLADDRTLLMAGVSHDLRTPLTRIRLAT"
...                     "EMMSEQDGYLAESINKDIEECNAIIEQFIDYLR",
...                     IUPAC.protein),
...                 id="1JOY", name="EnvZ",
...                 description="Homodimeric domain of EnvZ from E. coli")
>>> rec.letter_annotations["secondary_structure"] = "  S  SSSSSSHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTT  "
>>> rec.features.append(SeqFeature(FeatureLocation(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', IUPACProtein())
>>> print(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', IUPACProtein())
>>> print(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', IUPACProtein())

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', IUPACProtein())

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', IUPACProtein())

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__(self)

source code 

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__(self, char)
(In operator)

source code 

Implements 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
>>> from Bio.Alphabet import generic_dna
>>> Seq("AAA") in record
True
>>> Seq("AAA", generic_dna) in record
True

See also the Seq object's __contains__ method.

__str__(self)
(Informal representation operator)

source code 

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
>>> from Bio.Alphabet import IUPAC
>>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
...                         IUPAC.protein),
...                    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', IUPACProtein())

In this example you don't actually need to call str explicity, 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', IUPACProtein())

Note that long sequences are shown truncated.

Overrides: object.__str__

__repr__(self)
(Representation operator)

source code 

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
>>> from Bio.Alphabet import generic_protein
>>> rec = SeqRecord(Seq("MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKAT"
...                    +"GEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQ"
...                    +"SGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQ"
...                    +"PQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF",
...                    generic_protein),
...                 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', ProteinAlphabet()), 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', ProteinAlphabet()), 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).

Overrides: object.__repr__

format(self, format)

source code 

Returns 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
>>> from Bio.Alphabet import IUPAC
>>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
...                         IUPAC.protein),
...                    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
<BLANKLINE>

The python print command 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).

__format__(self, format_spec)

source code 

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

This method supports the python format() function added in Python 2.6/3.0. The format_spec should be a lower case string supported by Bio.SeqIO as an output file format. See also the SeqRecord's format() method.

Under Python 3 please note that for binary formats a bytes string is returned, otherwise a (unicode) string is returned.

Overrides: object.__format__

__len__(self)
(Length operator)

source code 

Returns 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

__bool__(self)

source code 

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)!

__nonzero__(self)
(Boolean test operator)

source code 

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__(self, other)
(Addition operator)

source code 

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__(self, other)
(Right-side addition operator)

source code 

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))
[]

upper(self)

source code 

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

All the annotation is preserved unchanged. e.g.

>>> from Bio.Alphabet import generic_dna
>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> record = SeqRecord(Seq("acgtACGT", generic_dna), 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
+
"#$%&'()
<BLANKLINE>

Naturally, there is a matching lower method:

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

lower(self)

source code 

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

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

reverse_complement(self, id=False, name=False, description=False, features=True, annotations=False, letter_annotations=True, dbxrefs=False)

source code 

Returns new SeqRecord with reverse complement 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,

>>> 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', IUPACAmbiguousDNA())
>>> 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', IUPACAmbiguousDNA())
>>> 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']
<BLANKLINE>
>>> 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']
<BLANKLINE>

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 ammended, and would need correction after the reverse complement.

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

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

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

>>> from Bio.SeqRecord import SeqRecord
>>> from Bio.Seq import MutableSeq
>>> from Bio.Alphabet import generic_dna
>>> rec = SeqRecord(MutableSeq("ACGT", generic_dna), 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

Property Details [hide private]

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
{}
Get Method:
unreachable(self)
Set Method:
_set_per_letter_annotations(self, value)

seq

The sequence itself, as a Seq or MutableSeq object.
Get Method:
unreachable(self)
Set Method:
_set_seq(self, value)