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Parameters: |
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Raises: | InvalidSequence – When the sequence string contains forbidden characters. In the future, ‘?’ and ‘.’ will also raise this exception. |
SequenceHandle
¶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,
an Error
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, an IntegrityError
is
raised. The second signature will select the chain with the given name. If
no such chain exists, an IntegrityError
is raised.
HasAttachedView
()¶Returns True when the sequence has a view attached, False if not.
GetAttachedView
()¶Returns the attached EntityView
, or an invalid
EntityView
if no view has been attached. Also available as
the property attached_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) |
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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 |
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Return type: | |
Parameters: |
|
Match
(s1, s2)¶Parameters: |
|
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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.
CreateSequenceList
()¶Creates and returns a new SequenceList
with no sequences.
SequenceList
¶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. |
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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. |
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Take
(n)¶Returns: | First n (or last -n if n negative) sequences. |
---|
Slice
(first, n)¶Returns: | n sequences starting from first. |
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__getitem__
(key)¶Returns: | Sequence(s) indexed by key (supports pythonic slicing). |
---|
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 sequences |
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Raises: | InvalidAlignment if the sequences do not have the same length. |
AlignmentHandle
¶GetSequence
(index)¶Returns: | Sequence at the given index, raising an IndexError when trying to access an inexistent sequence. |
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Return type: | ConstSequenceHandle |
GetSequences
()¶Returns: | List of all sequence of the alignment. Also available as
sequences . |
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Return type: | ConstSequenceList |
GetCount
()¶Returns: | Number of sequences in the alignment. Also available as
sequence_count . |
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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. |
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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. |
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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() ) |
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GetResidueIndex
(seq_index, pos)¶Returns: | Residue index of residue at position pos in sequence at index
seq_index (see SequenceHandle.GetResidueIndex() ) |
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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 or AlignmentHandle ) – The region to be inserted |
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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: |
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Raises: | In case one of the two sequences doesn’t have an attached view, a
|
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 match |
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Parameters: | sequence (ConstSequenceHandle ) – Sequence to be added |
GetSequenceOffset
(index)¶SetSequenceOffset
(index, offset)¶Get/set the offset for sequence at index
(see SequenceHandle.offset
).
Parameters: |
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Return type: |
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GetSequenceRole
(index)¶SetSequenceRole
(index, role)¶Get/Set the sequence role for sequence at index
(see SequenceHandle.role
).
Parameters: |
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Return type: |
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GetCoverage
(index)¶Get coverage of sequence at index to the first sequence.
Parameters: | index (int ) – The index of the sequence |
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Returns: | 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. |
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Return type: | AlignedColumn |
__getitem__
(slice)Returns: | Columns defined by by pythonic slicing. |
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Return type: | AlignedRegion |
AlignedRegion
¶Represents a slice of an AlignmentHandle
.
GetAlignmentHandle
()¶Returns: | Alignment from which we slices. |
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Return type: | AlignmentHandle |
__getitem__
(pos)¶Returns: | Column at position pos within this slice. |
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Return type: | AlignedColumn |
start
¶Starting position in alignment.
end
¶One after end position in alignment.
AlignedColumn
¶GetIndex
()¶Returns: | Position in alignment. |
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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. |
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Return type: | str |
__str__
()¶Returns: | String representation of column in alignment. |
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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 |
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Return type: | tuple with two EntityView |
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 |
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Return type: |
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Parameters: |
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The ProfileHandle
provides a simple container for profiles for each
residue. It mainly contains:
ProfileColumn
objects (N = number of residues in sequence)
which each contains 20 amino acid frequenciessequence
(str
) of length Nnull_model
to use for this profileOptionally, HMM-related information can be added. This is transition probabilities between Match, Insertion or Deletion states or neff values (number of effective sequences, a measure of local sequence diversity).
HMMTransition
¶The possible HMM-transitions between Match(M), Insertion(I) and Deletion(D) states. Transitions between Deletion and Insertion are disallowed:
HMM_M2M, HMM_M2I, HMM_M2D, HMM_I2M, HMM_I2I, HMM_D2M, HMM_D2D
HMMData
¶Data container for HMM-related information that can be assigned to profile columns.
neff
¶Local diversity of all sequences that have a residue at this column of the full alignment.
neff_i
¶Local diversity of all sequences that have an insertion at this column of the full alignment.
neff_d
¶Same for deletion.
GetProb
(transition)¶Get HMM transition probability
Parameters: transition ( HMMTransition
) – The transition
SetProb
(transition, prob)¶Set HMM transition probability
Parameters:
- transition (
HMMTransition
) – The transition- prob (
float
) – The probablity to be set
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 |
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Return type: | float |
Parameters: | aa (str ) – One letter code of standard amino acid |
SetFreq
(aa, freq)¶Parameters: |
|
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GetScore
(other, null_model)¶Returns: | Column score as in Soeding-2005 paper. |
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Return type: |
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Parameters: |
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GetHMMData
()¶Returns previously set HMMData
object.
Return type: | HMMData |
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Raises: | Error if data has never been set. |
entropy
¶Shannon entropy based on the columns amino acid frequencies
Type: | float |
---|
hmm_data
¶Shortcut for GetHMMData()
/SetHMMData()
ProfileHandle
¶__len__
()¶Returns the length of the sequence for which we have profile.
Return type: | int |
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AddColumn
(col, olc='X')¶Appends column in the internal column list.
Parameters: |
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Extract
(from, to)¶Parameters: |
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Returns: | sub-profile as defined by given indices
( |
Return type: | |
Raises: |
|
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 |
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Return type: |
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Parameters: |
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Raises: |
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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 |
---|
neff
¶Measure for sequence diversity which is defined as the average of the per-column neff values. However, this is just a convenience attribute which can be set to arbitrary values but there is no guarantee that it’s the actual average of the per-column values.
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. |
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Load
(filename)¶Static loading method
Parameters: | filename (str ) – Name of file from which the database should be loaded. |
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Returns: | The loaded database |
AddProfile
(name, prof)¶Parameters: |
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Raises: |
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GetProfile
(name)¶Parameters: | name (str ) – Name of profile to be returned |
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Returns: | The requested ProfileHandle |
Raises: | Exception when no ProfileHandle 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 |
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– Algorithms for Sequences
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