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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 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

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 ‘-‘.
Raises InvalidSequence:
 

When the sequence string contains forbidden characters. In the future, ‘?’ and ‘.’ will also raise this exception.

class SequenceHandle

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.

GetName()

Returns the name of the sequence. Also available as the property name

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.

SetName()

Set name of the sequence. Also available as the property name.

gapless_string

Shorthand for GetGaplessString()

name

Shorthand for GetName()/SetName()

attached_view

Shorthand for GetAttachedView().

offset

Shorthand for GetOffset()/SetOffset()

__len__()

Returns the length of the sequence (including insertions and deletions)

__str__()

Returns the sequence as a string.

Match(s1, s2)
Parameters:

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.

The SequenceList

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 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
Raises:InvalidAlignment if the sequences do not have the same length.
class AlignmentHandle

Note

Several of these methods just forward calls to the sequence. For more detailed information, have a look at the SequenceHandle documentation.

GetSequence(index)

Returns the sequence at the given index, raising an IndexError when trying to access an inexistent sequence.

GetSequences()

Returns a list of all sequence of the alignment.

GetLength()

Returns the length of the alignment.

GetCount()

Returns the number of sequences in the alignment.

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
FindSequence(name)

Find 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

SetSequenceOffset(seq_index, offset)

Set the sequence offset of sequence at index seq_index

Copy()

Create a deep copy of the alignment

GetPos(seq_index, res_index)

Get position of residue with index equal to res_index in sequence at index seq_index.

GetResidueIndex(seq_index, pos)

Get residue index of residue at position pos in sequence at index seq_index.

AttachView(seq_index, view)
AttachView(seq_index, view, chain_name)

Attach the given view to the sequence at index seq_index.

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
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 match
Parameters:sequence (ConstSequenceHandle) – Sequence to be added
GetSequenceOffset(index)
SetSequenceOffset(index, offset)

Get/set the offset for sequence at index.

Parameters:
  • index (int) – The index of the sequence
  • offset (int) – The new offset
Return type:

int

GetSequenceRole(index)
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
Return type:

str

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.
RemoveSequence(index)

Remove sequence at index from the alignment.

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.

GetFreq(aa)
Parameters:aa (str) – One letter code of standard amino acid
Returns:Frequency of aa
SetFreq(aa, freq)
Parameters:
  • aa (str) – One letter code of standard amino acid
  • freq (float) – The frequency of the given amino acid
entropy

Shannon entropy based on the columns amino acid frequencies

class ProfileHandle
__len__()

Returns the length of the sequence for which we have profile.

Return type:int
AddColumn(col)

Appends column in the internal column list.

Parameters:col (ProfileColumn) – Column to add
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:

ProfileHandle

Raises:

Error if if to <= from or to > __len__().

SetSequence(sequence)

Sets sequence.

SetNullModel(null_model)

Sets null_model.

sequence

Sequence for which we have this profile. Note: user must enforce consistency between sequence length and number of profile columns.

columns

Iterable columns of the profile

null_model

Null model of the profile

avg_entropy

Average entropy of all the columns

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.

GetProfile(name)
Parameters:name (str) – Name of profile to be returned
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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