search_myers_IUPAC

IUPAC code

IUPAC	Base
A	A
C	C
G	G
T	T
R	A or G
Y	C or T
S	G or C
W	A or T
K	G or T
M	A or C
B	C or G or T
D	A or G or T
H	A or C or T
V	A or C or G
N	A or C or G or T

Install

Install localy

$ make install

Usage

Import package

>>> import search_myers_IUPAC

List of positions

Find all the end positions of the mapping of the read on the text with at most k errors

>>> search_myers_IUPAC.listofpositions(text,read,k)

Example:

>>> search_myers_IUPAC.listofpositions('HACTADGTRTG','HYC', 1)
[5, 6, 10]

The read 'HYC' appears in the text 'HACTADGTRTG' at the end positions 5, 6 and 10 with an error of at most 1.

List of best positions

Find all the end positions of the mapping of the read on the text with the minimum number of errors error

>>> search_myers_IUPAC.listofbestpositions(text,read)

Example:

>>> search_myers_IUPAC.listofbestpositions('HACTADGTRTG','HYCAC')
(2, [2, 4, 5, 6])

The read 'HYCAC' appears in the text 'HACTADGTRTG' at the end positions 2, 4, 5 and 6 with an error of 2 and does not appear with an error of 0 or 1.

List of first positions

Find the list of pairs (start_position,error) for all the position before the end_position for the mapping of the read on the text with at most k errors.

>>> search_myers_IUPAC.backtrackpositions(text,read, k,end_position)

Example:

>>> search_myers_IUPAC.backtrackpositions('HACTADGTRTG','HYCG', 1,10)
[(8, 1), (4, 1)]

The read 'HYCAC' appears in the text 'HACTADGTRTG' between the positions 8 and 10 and between the positions 4 and 10 with an error of 1.

Find the maximal first position

Find the pair (start_position,error) for maximal position before the end_position for the mapping of the read on the text with at most k errors.

>>> search_myers_IUPAC.backtrackbestposition(text,read, k,end_position)

Example:

>>> search_myers_IUPAC.backtrackbestposition('HACTADGTRTG','HYCG', 1,10)
(8, 1)

The read 'HYCAC' appears in the text 'HACTADGTRTG' between the positions 8 and 10 with an error of 1.

Find the Tag

Find the tag for maximal position before the end_position for the mapping of the read on the text with at most k errors.

• I : insertion
• D : deletion
• M : mutation
• = : same caracter

>>> search_myers_IUPAC.tag(text,read, k,end_position)

Example

>>> search_myers_IUPAC.backtrackbestposition('HACTADGTRTG','HYCG', 1,8)
(4, 1)
>>> 'HACTADGTRTG'[4:9]
'ADGTR'
>>> search_myers_IUPAC.tag('HACTADGTRTG','HYCG', 1,8)
'==MD='