Help on class SeqRecord in module Bio.SeqRecord:
class SeqRecord(builtins.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
| >>> 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
|
| Methods defined here:
|
| __add__(self, other)
| 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[:]
|
| __bool__(self)
| 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)!
|
| __contains__(self, char)
| 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
| >>> 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.
|
| __eq__(self, other)
| Define the equal-to operand (not implemented).
|
| __format__(self, format_spec)
| 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
| <BLANKLINE>
|
| See also the SeqRecord's format() method.
|
| __ge__(self, other)
| Define the greater-than-or-equal-to operand (not implemented).
|
| __getitem__(self, index)
| 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.
| * 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, 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())
| >>> 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())
| >>> 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'
|
| __gt__(self, other)
| Define the greater-than operand (not implemented).
|
| __init__(self, seq, id='<unknown id>', name='<unknown name>', description='<unknown description>', dbxrefs=None, features=None, annotations=None, letter_annotations=None)
| 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.
|
| __iter__(self)
| 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.
|
| __le___(self, other)
| Define the less-than-or-equal-to operand (not implemented).
|
| __len__(self)
| 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__(self, other)
| Define the less-than operand (not implemented).
|
| __ne__(self, other)
| Define the not-equal-to operand (not implemented).
|
| __radd__(self, other)
| 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))
| []
|
| __repr__(self)
| 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
| >>> 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).
|
| __str__(self)
| 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
| >>> 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.
|
| format(self, format)
| 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
| >>> 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 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).
|
| lower(self)
| 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
| <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)
| 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', 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
| amended, 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
|
| translate(self, table='Standard', stop_symbol='*', to_stop=False, cds=False, gap=None, id=False, name=False, description=False, features=False, annotations=False, letter_annotations=False, dbxrefs=False)
| 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
| <BLANKLINE>
|
| 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
| <BLANKLINE>
|
| upper(self)
| Return 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>
|
| ----------------------------------------------------------------------
| Data descriptors defined here:
|
| __dict__
| dictionary for instance variables (if defined)
|
| __weakref__
| list of weak references to the object (if defined)
|
| 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.
|
| seq
| The sequence itself, as a Seq or MutableSeq object.
|
| ----------------------------------------------------------------------
| Data and other attributes defined here:
|
| __hash__ = None
