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 subpart 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 io.LoadSequence(),
alignments are loaded with io.LoadAlignment() and lists of sequences are loaded with io.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
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CreateSequence(name, sequence)
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 ‘-‘.
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Raises InvalidSequence: |
| When the sequence string contains forbidden
characters. In the future, ‘?’ and ‘.’ will also raise this exception.
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class SequenceHandle
Represents a sequence. New instances are created with CreateSequence().
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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().
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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.
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)
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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.
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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
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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.
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AttachView(view)
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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.
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HasAttachedView()
Returns True when the sequence has a view attached, False if not.
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GetAttachedView()
Returns the attached EntityView, or an invalid
EntityView if no view has been attached. Also available as
the property attached_view.
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GetName()
Returns the name of the sequence. Also available as the property
name
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SetOffset()
Set the sequence offset. By default, the offset is
0. Also available as the property offset.
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GetOffset()
Returns the sequence offset. Also available as
offset.
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GetGaplessString()
Returns a string version of this sequence with all hyphens removed. Also
available as the property gapless_string.
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SetName()
Set name of the sequence. Also available as the property name.
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gapless_string
Shorthand for GetGaplessString()
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name
Shorthand for GetName()/SetName()
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attached_view
Shorthand for GetAttachedView().
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offset
Shorthand for GetOffset()/SetOffset()
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__len__()
Returns the length of the sequence (including insertions and deletions)
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__str__()
Returns the sequence as a string.
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Match(s1, s2)
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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 wildcard character that always matches the other sequence.
The SequenceList
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class SequenceList
Represents a list of sequences. The class provides a row-based interface. New
instances are created with CreateSequenceList().
The AlignmentHandle
The AlignmentHandle represents a list of aligned sequences. In
constrast 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 GetSequenceList().
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
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CreateAlignment()
Creates and returns a new AlignmentHandle with no sequences.
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AlignmentFromSequenceList(sequences)
Create a new alignment from the given list of sequences
Parameters: | sequences (ConstSequenceList) – the list of sequences |
Raises : | InvalidAlignment if the sequences do not have the same length. |
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class AlignmentHandle
Note
Several of these methods just forward calls to the sequence. For more
detailed information, have a look at the SequenceHandle
documentation.
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GetSequence(index)
Returns the sequence at the given index, raising an IndexError when trying
to access an inexistent sequence.
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GetSequenceList()
Returns a list of all sequence of the alignment.
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GetLength()
Returns the length of the alignment.
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GetCount()
Returns the number of sequences in the alignment.
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ToString(width=80)
Returns a formatted string version of the alignment. The sequences are
split into smaller parts to fit into the number columns specified.
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
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FindSequence(name)
Find 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
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SetSequenceOffset(seq_index, offset)
Set the sequence offset of sequence at index seq_index
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Copy()
Create a deep copy of the alignment
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GetPos(seq_index, res_index)
Get position of residue with index equal to res_index in sequence at index
seq_index.
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GetResidueIndex(seq_index, pos)
Get residue index of residue at position pos in sequence at index
seq_index.
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AttachView(seq_index, view)
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AttachView(seq_index, view, chain_name)
Attach the given view to the sequence at index seq_index.
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Cut(start, end)
Removes the columns in the half-closed interval start, end from the
alignment.
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
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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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ShiftRegion(start, end, amount, master=-1)
Shift columns in the half-closed interval start, end. If amount is a
positive number, the columns are shifted to the right, if negative, the
columns are shifted to the left.
If master is set to -1, all sequences in the region are affected, otherwise
only the sequence at index equal to master is shifted.
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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: |
- index1 – The index of the first sequence
- index2 – The index of the second sequence.
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Raises : | In case one of the two sequences doesn’t have an attached view, a
RuntimeError is raised.
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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 |
Parameters: | sequence (ConstSequenceHandle) – Sequence to be added |
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GetSequenceOffset(index)
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SetSequenceOffset(index, offset)
Get/set the offset for sequence at index.
Parameters: |
- index (int) – The index of the sequence
- offset (int) – The new offset
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Return type: | int
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GetSequenceRole(index)
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SetSequenceRole(index, role)
Get/Set the sequence role for sequence at index.
Parameters: |
- index (int) – The index of the sequence
- role (str) – The new role
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Return type: | str
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GetCoverage(index)
Get coverage of sequence at index to the first sequence.
Parameters: | index (int) – The index of the sequence |
Returns: | Coverage as a number between 0 and 1. |
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RemoveSequence(index)
Remove sequence at index from the alignment.
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