seq
– Sequences and Alignments¶
The seq
module helps you working with sequence data of various kinds. It
has classes for single sequences
, lists of
sequences
and alignments
of two or
more sequences.
Attaching Structures to Sequences¶
As OpenStructure is a computational structural biology framework, it is not
surprising that the sequence classes have been designed to work together with
structural data. Each sequence can have an attached EntityView
allowing for fast mapping between residues in the entity view and position in
the sequence.
Sequence Offset¶
When using sequences and structures together, often the start of the structure and the beginning of the sequence do not fall together. In the following case, the alignment of sequences B and C only covers a subsequence of structure A:
A acefghiklmnpqrstuvwy
B ghiklm
C 123-45
We would now like to know which residue in protein A is aligned to which residue in sequence C. This is achieved by setting the sequence offset of sequence C to 4. In essence, the sequence offset influences all the mapping operations from position in the sequence to residue index and vice versa. By default, the sequence offset is 0.
Loading and Saving Sequences and Alignments¶
The io
module supports input and output of common sequence formats.
Single sequences can be loaded from disk with LoadSequence()
,
alignments are loaded with LoadAlignment()
and lists of sequences
are loaded with LoadSequenceList()
. In addition to the file based
input methods, sequences can also be loaded from a string:
seq_string = '''>sequence
abcdefghiklmnop'''
s = io.SequenceFromString(seq_string, 'fasta')
print s.name, s # will print "sequence abcdefghiklmnop"
Note that, in that case specifying the format is mandatory.
The SequenceHandle¶
-
CreateSequence
(name, sequence, role="UNKNOWN")¶ Create a new
SequenceHandle
with the given name and sequence.Parameters: - name (
str
) – Name of the sequence - sequence (
str
) – String of characters representing the sequence. Only ‘word’ characters (no digits), ‘?’, ‘-‘ and ‘.’ are allowed. In an upcoming release, ‘?’ and ‘.’ will also be forbidden so its best to translate those to ‘X’ or ‘-‘. - role (
str
) – Role of the sequence (optional)
Raises InvalidSequence: When the sequence string contains forbidden characters. In the future, ‘?’ and ‘.’ will also raise this exception.
- name (
-
class
SequenceHandle
¶ -
class
ConstSequenceHandle
¶ Represents a sequence. New instances are created with
CreateSequence()
.-
GetPos
(residue_index)¶ Get position of residue with index in sequence. This is best illustrated in the following example:
s=seq.CreateSequence("A", "abc---def") print s.GetPos(1) # prints 1 print s.GetPos(3) # prints 6
The reverse mapping, that is from position in the sequence to residue index can be achieved with
GetResidueIndex()
.
-
GetResidueIndex
(pos)¶ Get residue index of character at given position. This method is the inverse of
GetPos()
. If the sequence contains a gap at that position, anError
is raised. Admires the sequence offset.s=seq.CreateSequence("A", "abc--def") print s.GetResidueIndex(1) # prints 1 print s.GetResidueIndex(6) # prints 4 # the following line raises an exception of type # Error with the message "requested position contains # a gap" print s.GetResidueIndex(3)
-
GetResidue
(pos)¶ As,
GetResidueIndex()
, but directly returns the residue view. If no view is attached, or if the position is a gap, an invalid residue view is returned.Return type: ResidueView
-
GetLastNonGap
()¶ Get position of last non-gap character in sequence. In case of an empty sequence, or, a sequence only consisting of hyphens, -1 is returned
-
GetFirstNonGap
()¶ Get position of first non-gap character in sequence. In case of an empty sequence, or, a sequence only consisting of hyphens, -1 is returned.
-
AttachView
(view)¶ -
AttachView
(view, chain_name) Attach an
EntityView
to sequence. The first signature requires that the view contains one chain. If not, anIntegrityError
is raised. The second signature will select the chain with the given name. If no such chain exists, anIntegrityError
is raised.
-
HasAttachedView
()¶ Returns True when the sequence has a view attached, False if not.
-
GetAttachedView
()¶ Returns the attached
EntityView
, or an invalidEntityView
if no view has been attached. Also available as the propertyattached_view
.
-
SetOffset
()¶ Set the sequence offset. By default, the offset is 0. Also available as the property
offset
.
-
GetOffset
()¶ Returns the sequence offset. Also available as
offset
.
-
GetGaplessString
()¶ Returns a string version of this sequence with all hyphens removed. Also available as the property
gapless_string
.
-
Normalise
()¶ Remove ‘-‘ and ‘.’ as gaps from the sequence and make it all upper case. Works in place.
-
GetOneLetterCode
(pos)¶ -
__getitem__
(pos)¶ -
__getitem__
(slice) Returns: Character at position pos of sequence (also supports pythonic slicing with [] operator) Return type: str
-
gapless_string
¶ Shorthand for
GetGaplessString()
-
attached_view
¶ Shorthand for
GetAttachedView()
.
-
offset
¶ Shorthand for
GetOffset()
/SetOffset()
-
role
¶ Role of this sequence.
Type: str
-
__len__
()¶ Returns: The length of the sequence (including insertions and deletions)
-
__str__
()¶ Returns: The sequence as a string.
-
Copy
()¶ Create a deep copy of the sequence. The newly created sequence has the same attached view (not a deep copy of the view!).
-
-
SequenceFromChain
(name, chain)¶ Returns: Sequence extracted from one letter codes in given chain with a view to the chain attached to it
Return type: Parameters: - name (
str
) – Name of the sequence - chain (
ChainHandle
/ChainView
) – Chain from which to extract sequence
- name (
-
Match
(s1, s2)¶ Parameters: - s1 (
SequenceHandle
, orstr
) – The first sequence - s2 (
SequenceHandle
, orstr
) – The second sequence
Check whether the two sequences s1 and s2 match. This function performs are case-insensitive comparison of the two sequences. The character ‘X’ is interpreted as a wild card character that always matches the other sequence.
- s1 (
The SequenceList¶
-
CreateSequenceList
()¶ Creates and returns a new
SequenceList
with no sequences.
-
class
SequenceList
¶ -
class
ConstSequenceList
¶ Represents a list of sequences. The class provides a row-based interface.
-
AddSequence
(sequence)¶ Append a sequence to the list.
-
GetMinLength
()¶ -
GetMaxLength
()¶ Returns: Minimal / maximal length of the sequences in this list. Return type: int
-
FindSequence
(name)¶ Find sequence with given name. If the alignment contains several sequences with the same name, the first sequence is returned.
-
SequencesHaveEqualLength
()¶ Returns: True if all sequences have same length.
-
Take
(n)¶ Returns: First n (or last -n if n negative) sequences.
-
Slice
(first, n)¶ Returns: n sequences starting from first.
-
__getitem__
(key)¶ Returns: Sequence(s) indexed by key (supports pythonic slicing).
-
The AlignmentHandle¶
The AlignmentHandle
represents a list of aligned sequences. In
contrast to SequenceList
, an alignment requires all sequences to be of
the same length. New instances of alignments are created with
CreateAlignment()
and AlignmentFromSequenceList()
.
Typically sequence alignments are used column-based, i.e by looking at an
aligned columns in the sequence alignment. To get a row-based (sequence) view
on the sequence list, use GetSequences()
.
All functions that operate on an alignment will again produce a valid alignment. This mean that it is not possible to change the length of one sequence, without adjusting the other sequences, too.
The following example shows how to iterate over the columns and sequences of an alignment:
aln=io.LoadAlignment('aln.fasta')
# iterate over the columns
for col in aln:
print col
# iterate over the sequences
for s in aln.sequences:
print s
-
CreateAlignment
()¶ Creates and returns a new
AlignmentHandle
with no sequences.
-
AlignmentFromSequenceList
(sequences)¶ Create a new alignment from the given list of sequences
Parameters: sequences ( ConstSequenceList
) – the list of sequencesRaises: InvalidAlignment
if the sequences do not have the same length.
-
class
AlignmentHandle
¶ -
GetSequence
(index)¶ Returns: Sequence at the given index, raising an IndexError when trying to access an inexistent sequence. Return type: ConstSequenceHandle
-
GetSequences
()¶ Returns: List of all sequence of the alignment. Also available as sequences
.Return type: ConstSequenceList
-
GetCount
()¶ Returns: Number of sequences in the alignment. Also available as sequence_count
.Return type: int
-
ToString
(width=80)¶ Returns: Formatted string version of the alignment. The sequences are split into smaller parts to fit into the number columns specified. Return type: str
aln=seq.CreateAlignment() aln.AddSequence(seq.CreateSequence("A", "abcdefghik")) aln.AddSequence(seq.CreateSequence("B", "1234567890")) # The following command will print the output given below print aln.ToString(7) # A abcde # B 12345 # # A fghik # B 67890
-
FindSequence
(name)¶ Returns: Sequence with given name. If the alignment contains several sequences with the same name, the first sequence is returned.
-
SetSequenceName
(seq_index, name)¶ Set the name of the sequence at index seq_index to name (see
SequenceHandle.name
).
-
Copy
()¶ Create a deep copy of the alignment by copying each contained sequence (see
SequenceHandle.Copy()
)
-
GetPos
(seq_index, res_index)¶ Returns: Position of residue with index equal to res_index in sequence at index seq_index (see SequenceHandle.GetPos()
)
-
GetResidueIndex
(seq_index, pos)¶ Returns: Residue index of residue at position pos in sequence at index seq_index (see SequenceHandle.GetResidueIndex()
)
-
GetResidue
(seq_index, pos)¶ Returns: Attached residue at position pos in sequence at index seq_index (see SequenceHandle.GetResidue()
).
-
AttachView
(seq_index, view)¶ -
AttachView
(seq_index, view, chain_name) Attach the given view to the sequence at index seq_index (see
SequenceHandle.AttachView()
).
-
Cut
(start, end)¶ Removes the columns in the half-closed interval start, end from the alignment. Note that this function does not update offsets!
aln=seq.CreateAlignment() aln.AddSequence(seq.CreateSequence("A", "abcd---hik")) aln.AddSequence(seq.CreateSequence("B", "1234567890")) aln.Cut(4, 7) print aln.ToString(80) # will print # A abcdhik # B 1234890
-
Replace
(new_region, start, end)¶ Replace the columns in the half-closed interval start, end with the columns in new_region.
Parameters: new_region ( AlignedRegion
orAlignmentHandle
) – The region to be inserted
-
GetMatchingBackboneViews
(index1=0, index2=1)¶ Returns a tuple of entity views containing matching backbone atoms for the two sequences at index1 and index2, respectively. For each aligned column in the alignment, backbone atoms are added to the view if both aligned residues have them. It is guaranteed that the two views contain the same number of atoms and that the order of the atoms in the two views is the same.
The output of this function can be used to superpose two structures with
SuperposeSVD()
.Parameters: - index1 – The index of the first sequence
- index2 – The index of the second sequence.
Raises: In case one of the two sequences doesn’t have an attached view, a
RuntimeError
is raised.
-
AddSequence
(sequence)¶ Append a sequence to the alignment. The sequence must have the same length as sequences already present in the alignment.
Raises: RuntimeError
if the sequence length does not matchParameters: sequence ( ConstSequenceHandle
) – Sequence to be added
-
GetSequenceOffset
(index)¶ -
SetSequenceOffset
(index, offset)¶ Get/set the offset for sequence at index (see
SequenceHandle.offset
).Parameters: - index (
int
) – The index of the sequence - offset (
int
) – The new offset
Return type: int
- index (
-
GetSequenceRole
(index)¶ -
SetSequenceRole
(index, role)¶ Get/Set the sequence role for sequence at index (see
SequenceHandle.role
).Parameters: - index (
int
) – The index of the sequence - role (
str
) – The new role
Return type: str
- index (
-
GetCoverage
(index)¶ Get coverage of sequence at index to the first sequence.
Parameters: index ( int
) – The index of the sequenceReturns: Coverage as a number between 0 and 1.
-
RemoveSequence
(index)¶ Remove sequence at index from the alignment.
-
sequences
¶ Shorthand for
GetSequences()
-
sequence_count
¶ Shorthand for
GetCount()
-
__getitem__
(pos)¶ Returns: Column at position pos of alignment. Return type: AlignedColumn
-
__getitem__
(slice) Returns: Columns defined by by pythonic slicing. Return type: AlignedRegion
-
-
class
AlignedRegion
¶ Represents a slice of an
AlignmentHandle
.-
GetAlignmentHandle
()¶ Returns: Alignment from which we slices. Return type: AlignmentHandle
-
__getitem__
(pos)¶ Returns: Column at position pos within this slice. Return type: AlignedColumn
-
start
¶ Starting position in alignment.
-
end
¶ One after end position in alignment.
-
-
class
AlignedColumn
¶ -
GetIndex
()¶ Returns: Position in alignment.
-
GetRowCount
()¶ Returns: Number of rows in the column.
-
GetResidue
(row)¶ Returns: Attached residue for sequence at given row of this column (see AlignmentHandle.GetResidue()
).
-
__getitem__
(row)¶ Returns: Character at given row of this column. Return type: str
-
__str__
()¶ Returns: String representation of column in alignment.
-
Extracting views from sequences¶
-
ViewsFromSequences
(seq1, seq2)¶ Returns a tuple of entity views containing only the atoms of the aligned residues. The order of residues in the two views is guaranteed to be the same but the order of atoms within each residue may differ. If the order of atoms is crucial (e.g. for
SuperposeSVD()
) either prefilter the attached views to include only one atom per residue or use the slower (approx. 50% more runtime)AlignmentHandle.GetMatchingBackboneViews()
.Returns: Pair of views including all the aligned residues of the two given sequences. An alignment is Return type: tuple
with twoEntityView
Raises: Exception
if sequence lengths do not match or if any of the sequences is lacking an attached view.
-
ViewsFromAlignment
(aln, index1=0, index2=1)¶ Returns: Pair of views as in
ViewsFromSequences()
.Return type: tuple
with twoEntityView
Parameters: - aln (
AlignmentHandle
) – Alignment from which to extract sequences. - index1 (
int
) – Index of first sequence in aln to use. - index2 (
int
) – Index of second sequence in aln to use.
- aln (
Handling Sequence Profiles¶
The ProfileHandle
provides a simple container for profiles for each
residue. It mainly contains:
- N
ProfileColumn
objects (N = number of residues in sequence) which each contains 20 amino acid frequencies - a
sequence
(str
) of length N - a
null_model
to use for this profile
-
class
ProfileColumn
¶ -
BLOSUMNullModel
()¶ Static method, that returns a new
ProfileColumn
with amino acid frequencies given from the BLOSUM62 substitution matrix.
-
HHblitsNullModel
()¶ Static method, that returns a new
ProfileColumn
with amino acid frequencies as set in HHblits output.
-
GetFreq
(aa)¶ Returns: Frequency of aa Return type: float
Parameters: aa ( str
) – One letter code of standard amino acid
-
SetFreq
(aa, freq)¶ Parameters: - aa (
str
) – One letter code of standard amino acid - freq (
float
) – The frequency of the given amino acid
- aa (
-
GetScore
(other, null_model)¶ Returns: Column score as in Soeding-2005 paper.
Return type: float
Parameters: - other (
ProfileColumn
) – Other column to compute score with. - null_model (
ProfileColumn
) – Null model to use for weighting.
- other (
-
entropy
¶ Shannon entropy based on the columns amino acid frequencies
Type: float
-
-
class
ProfileHandle
¶ -
__len__
()¶ Returns the length of the sequence for which we have profile.
Return type: int
-
AddColumn
(col, olc='X')¶ Appends column in the internal column list.
Parameters:
-
Extract
(from, to)¶ Parameters: - from (
int
) – Col Idx to start from - to (
int
) – End Idx, not included in sub-ProfileHandle
Returns: sub-profile as defined by given indices (
null_model
is copied)Return type: Raises: Error
if to <= from or to >__len__()
.- from (
-
GetAverageScore
(other, offset=0)¶ Returns: Average column score between other.columns[i] and this object’s columns[i+offset] for i in [0, len(other)-1] using this object’s
null_model
. SeeProfileColumn.GetScore()
.Return type: float
Parameters: - other (
ProfileHandle
) – Other profile to compare with. - offset (
int
) – Start comparison at column offset of this object.
Raises: Error
if any columns[i+offset] out of bounds.- other (
-
sequence
¶ Sequence for which we have this profile. When setting a new value, the length and the number of profile columns must match (exception thrown otherwise).
Type: str
-
columns
¶ Iterable columns of the profile (read-only).
Type: ProfileColumnList
-
null_model
¶ Null model of the profile. By default this is set to
ProfileColumn.HHblitsNullModel()
.Type: ProfileColumn
-
avg_entropy
¶ Average entropy of all the columns (read-only).
Type: float
-
-
class
ProfileDB
¶ A simple database to gather
ProfileHandle
objects. It is possible to save them to disk in a compressed format with limited accuracy (4 digits for each frequency).-
Save
(filename)¶ Parameters: filename ( str
) – Name of file that will be generated on disk.
-
Load
(filename)¶ Static loading method
Parameters: filename ( str
) – Name of file from which the database should be loaded.Returns: The loaded database
-
AddProfile
(name, prof)¶ Parameters: - name (
str
) – Name of profile to be added - prof (
ProfileHandle
) – Profile to be added
Raises: Exception
when filename is longer than 255 characters.- name (
-
GetProfile
(name)¶ Parameters: name ( str
) – Name of profile to be returnedReturns: The requested ProfileHandle
Raises: Exception
when noProfileHandle
for name exists.
-
Size
()¶ Returns: Number of ProfileHandle
objects in the database
-
GetNames
()¶ Returns: A nonsorted list of the names of all ProfileHandle
objects in the database
-