Package Biskit :: Module match2seq

Module match2seq

source code

Match 2 sequences against each other, deleting all positions that differ. compareStructures() compares sequences of 2 structures and returns a residue mask for each of them.

Classes

[hide private]

Test
Test case

Functions

[hide private]

[str] sequenceList(model)
Extracts a one letter amino acid sequence list

[tuples] getOpCodes(seq_1, seq_2)
Compares two sequences and returns a list with the information needed to convert the first one sequence into the second.

[tuple], [tuple] getSkipLists(seqDiff)
Extracts information about what residues that have to be removed from sequence 1 (delete code) and sequence 2 (insert code).

[tuple], [tuple] getEqualLists(seqDiff)
Extract information about regions in the sequences that are equal.

str repeateInMatch(deletedRes)
Takes a string and returns a list of strings containing internal repeates.

[str],[int] delete(seqAA, seqNr, delList)
Takes a amino acid and a sequence list and deletes positions according to the information given in the delList.

[str], [int] getEqual(seqAA, seqNr, equalList)
Gets only the postions of the sequences that are equal according to the OpCodes.

[str], [int], [str], [int] iterate(seqAA_1, seqNr_1, seqAA_2, seqNr_2, del_1, del_2)
Delete residues until no more deletions are indicated by the sequence matcher.

([1|0...],[1|0...]) compareModels(model_1, model_2)
Initiates comparison of the sequences of two structure objects and returns two equal sequence lists (new_seqAA_1 and new_seqAA_2 should be identical) and the corresponding residue position lists.

Function Details

[hide private]

sequenceList(model)

source code

Extracts a one letter amino acid sequence list

Parameters:

model (PDBModel) - model

Returns: [str]: sequence ['A','G','R','T',.....]

getOpCodes(seq_1, seq_2)

source code

Compares two sequences and returns a list with the information needed to convert the first one sequence into the second.

Parameters:

seq_1 ([ str ]) - list of single letters
seq_2 ([ str ]) - list of single letters

Returns: [tuples]

Optimization code from difflib:

        [('delete', 0, 1, 0, 0), ('equal', 1, 4, 0, 3),
         ('insert', 4, 4, 3, 4), ('equal', 4, 180, 4, 180)]

getSkipLists(seqDiff)

source code

Extracts information about what residues that have to be removed from sequence 1 (delete code) and sequence 2 (insert code). Returns deletion codes in the format (start_pos, length).

Parameters:

seqDiff ([tuples]) - opcodes

Returns: [tuple], [tuple]

Lists of tuples containing regions of the sequences that should be deteted. Example:

 strucDel_1 = [(0, 1), (180, 4)]
 strucDel_2 = [(3, 1), (207, 4)]

getEqualLists(seqDiff)

source code

Extract information about regions in the sequences that are equal. Returns deletion codes in the format (start_pos, length).

Parameters:

seqDiff ([tuples]) - opcodes

Returns: [tuple], [tuple]

Lists of tuples containing regions of the sequences that are equal. Example:

 strucEqual_1 = [(0, 216)]
 strucEqual_2 = [(0, 216)]

repeateInMatch(deletedRes)

source code

Takes a string and returns a list of strings containing internal repeates.

Parameters:

deletedRes (str) - string of one letter amino acid sequence

Returns: str

smallest self repete. Example:

           'GSGS'     returns  'GS'
           'ABABABAB'    "     'ABAB' and 'AB'
           'FFF'         "     'F'

delete(seqAA, seqNr, delList)

source code

Takes a amino acid and a sequence list and deletes positions according to the information given in the delList.

Furthermore, compares the deleted sequence with the following and preceding sequence. If they are identical also these residues are deleted.

If the sequence contains internal repeates (as in the sequence 'GSGS') and 2) does not apply the preceding and following sequence is also scanned for this sequence (here 'GS').

Parameters:

seqAA ([str]) - list with the amino acid sequence in one letter code
seqNr ([int]) - list with the amino acid postitons
delList ([tuple]) - list of residues to be deleted (postiton, length)

Returns: [str],[int]

sequence and positions, example:

          seqAA - ['A','G','R','T',.....]
          seqNr - [ 0,  1,  2,  3 ,.....]  
          delList - [(0, 2), (180, 4)]
          ->  seqAA - ['R','T',.....]
              seqNr - [ 2,  3 ,.....]

getEqual(seqAA, seqNr, equalList)

source code

Gets only the postions of the sequences that are equal according to the OpCodes. This should not be nessesary but might be usefull to skip 'replace' OpCode.

Parameters:

seqAA ([str]) - list with the amino acid sequence in one letter code
seqNr ([int]) - list with the amino acid postitons
equalList ([tuple], [tuple]) - Lists of tuples containing regions of the sequences that are equal

Returns: [str], [int]: lists of amino acids and positions where equal

iterate(seqAA_1, seqNr_1, seqAA_2, seqNr_2, del_1, del_2)

source code

Delete residues until no more deletions are indicated by the sequence matcher. Return the final sequences

Parameters:

seqAA_1 ([str]) - list with the amino acid sequence in one letter code
seqNr_1 ([int]) - list with the amino acid postitons
seqAA_2 ([str]) - list with the amino acid sequence in one letter code
seqNr_2 ([int]) - list with the amino acid postitons
del_1 ([tuple]) - Lists of tuples containing regions of the sequences that should be deteted
del_2 ([tuple]) - Lists of tuples containing regions of the sequences that should be deteted

Returns: [str], [int], [str], [int]: the final sequence and position lists

compareModels(model_1, model_2)

source code

Initiates comparison of the sequences of two structure objects and returns two equal sequence lists (new_seqAA_1 and new_seqAA_2 should be identical) and the corresponding residue position lists.

Parameters:

model_1 (PDBModel) - model
model_2 (PDBModel) - model

Returns: ([1|0...],[1|0...])

tuple of atom masks for model_1 and model_2:

         e.g. ( [0001011101111111], [1110000111110111] )