String Functions and
Regular Expressions
Anastasis Oulas
Evangelos Pafilis
Jacques Lagnel
Strings - Revision
Declaration and value assignment eg.
courseName = 'Introduction to Python'
Concatenation
field = 'computational' + ' ' + 'Biology'
Equality check
stringA == stringB , stringA != stringC
Containment check
stringA in stringB, stringA not in stringB
Relevance to Bioinformatics
In Bioinformatics many of the tasks have to do with sequences
Sequences can be represented as Strings
Elements on sequences are also Strings
Pick your own choice: codons, transcription factor binding sites,
tata-box, restriction enzyme cutting sites, primer sequences,
intron/exon boundary sequences
Data/Result file handling is String manipulation
Strings - Revision
Declaration and value assignment eg.
seqA = 'ACGTC’
Concatenation
seqB = seqA + ‘AAAA’
Equality check
seqA == seqB , seqA != seqB
Containment check
seqA in seqB, seqB not in seqA
Example
seq = 'ACGTCATAATTAGCTGACGAG'
site = 'AATT' #EcoRI cutting site
print('seq contains the site: ', site in seq)
Example
Sometimes you want the position in the sequence:
seq = 'ACGTCATAATTAGCTGACGAG'
site = 'AATT' #EcoRI cutting site
startingPosition = seq.find(site)
print(startingPosition)
find() returns an integer
Example
Sometimes you want the position in the sequence:
0 1 2 3 4 5 6 7.............20
A C G T C A T A A T T A ....G
startingPosition
Example
seqA = 'ACGTCAUUUUUUUU'
seqB = 'ACGT'
if seqA.startswith(seqB):
print('Seq A starts with seq B')
startswith() returns a Boolean (True/False)
Example
seqA = 'ACGTCAUUUUUUUU'
seqB = 'ACGT'
print ('SeqB starts with seqA (t/f):')
print (seqB.startswith(seqA))
startswith() returns a Boolean (True/False)
Example: substring
General view:
substring = mainString[start position:end position]
The character at the 'end position' is NEVER included
Example: substring
Sometimes you want extract pa part of the string:
seq = 'ACGTCATAAT'
Example: substring
Sometimes you want extract pa part of the string:
index: 0123456789
seq = 'ACGTCATAAT'
substr=seq[3:6]
Example: substring
Sometimes you want extract pa part of the string:
index: 0123456789
seq = 'ACGTCATAAT'
substr=seq[3:6]
print (substr)
Gives: TCA
Example: split string
Sometimes you want build a list of words from a string
string1='hello my world'
space as
list1=['hello', 'my', 'world'] Separator
list1=string1.split(' ')
Example: strings join
Sometimes you want the reverse eg you have the list:
list1=['hello', 'my', 'world']
And you want to join the words the a space.
This can be done using join()
listA=['hello', 'my', 'world']
space = ' '
stringA = space.join(listA)
print( stringA )
=> Prints hello my world
String functions
Searching
str1.startswith(str2[, startpos, [endpos]])
– Returns true if str1 starts with str2
str1.endswith(str2[, startpos, [endos]])
– Returns true if str1 ends with str2
str1.find(str2[, startpos[, endpos]])
– Returns the lowest index of str1 at which str2 is found, or −1
if it is not found
str1.index(str2[, startpos[, endpos]])
– Returns the lowest index of str1 at which str2 is found, or
ValueError if it is not found
String functions - Table
Replacing and changing case
str1.lower()
Returns a copy of the string with all of its
characters converted to lowercase
str1.upper()
Returns a copy of the string with all of its
characters converted to uppercase
str1.replace(oldstr, newstr[, count])
Returns a copy of str1 with all occurrences of the
substring oldstr replaced by the string newstr; if
count is specified, only the first count occurrences
are replaced
String functions
●
str1.join( list1)
●
Returns a string containing the elements of list1 separated
by the str1 string
Testing
str1.islower()
– Returns true if str1 contains at least one “cased” character
and all of its cased characters are lowercase
str1.isupper()
– Returns true if str1 contains at least one “cased” character
and all of its cased characters are uppercase
Regular Expressions
However the requirements of Bioinformatics / Computational
Biology exceed what can be achieved with the available String
functions
This has given rise to wide usage of Regular Expressions
What is a Regular Expression and why is it so useful?
Why a regular expression
'AATT' #EcoRI cutting site
– 'AATT' in sequence
DsaI possible cutting sites: CC - G or A - T or C - GG
'CCGTGG' in sequence
'CCGCGG' in sequence
Why a regular expression
'AATT' #EcoRI cutting site
– 'AATT' in sequence
DsaI possible cutting sites: CC - G or A - T or C - GG
'CCGTGG' in sequence
'CCGCGG' in sequence
'CCATGG' in sequence
'CCACGG' in sequence
Why a regular expression
'AATT' #EcoRI cutting site
– 'AATT' in sequence
DsaI possible cutting sites: CC - G or A - T or C - GG
'CCGTGG' in sequence
'CCGCGG' in sequence Combinatorial
'CCATGG' in sequence Explosion
'CCACGG' in sequence
What is a regular expression
Regular Expressions provide the tool to manage this
“combinatorial explosion”
A regular expression for DsaI’s site would be:
– 'CC[GA][TC]GG'
[ ] → a set of possible characters at a single position
[GA]: this position will contain either G or A
(ie possible characters)
[TC]: this position will contain either T or C
Regular expressions: Another example
Find the pattern enzym followed by any character (.)
any number of times incl zero (*)
– Eg Reg Expr: enzym.*
• enzyme
• enzymes
• enzymatic
• enzym
Regular Expression Syntax
. Any character
[ ] A character set
[ACTG] One DNA base character
[A-Za-z_] One underscore or letter
[0-9] a digit
Regular Expression Syntax
\n a newline character
\d Any digit
\D Any nondigit
\s Any whitespace character
– space ' ' , tab \t, new line: \n\r
– ie. shorthand for [ \t\n\r]
\S Any non-whitespace character
ie. all characters excluding [ \t\n\r]
Regular Expression Syntax
* Zero or more repetitions of the preceding regular
expression
? Zero or one repetitions of the preceding regular
expression
+ One or more repetitions of the preceding regular
expression
{n} Exactly n repetitions of the preceding regular
expression
{m,n} Between m and n (inclusive) repetitions of the
preceding regular expression
Regular Expressions
( ) : captures a group of characters
eg. (TA) : matches TA in ACGATAGACC
Can be combined with the repetition quantifiers
eg. (TA){3} : matches TATATA in ACGATATATACC
The re Module
import re
By writing the above statement in a python script the
re (regular expression) module is imported and
ready to use.
You are now able to use the methods of the
regular expression library in your algorithm
Example code
import re
seq = 'ACCGTGGCAAATTTCCACGGACGAG'
regEx = 'CC[GA][TC]GG'
aList = re.findall(regEx,seq)
for i in range(0,len(aList)):
print('Found', aList[i])
finds any DsaI cutting sites in the given sequence
The result is : Found CCGTGG
Found CCACGG
Example code
import re
text = 'this is a test paragraph'
regEx = 'A\stest'
aList = re.findall(regEx,text)
if len(aList) == 0:
print('Not Found')
Checks whether the sentence contains “A text”
The result is : Not Found
Example code
import re
seq = 'ACGATATACC'
regEx = '(TA){2}'
aList = re.findall(regEx,seq)
if len(aList) > 0:
print('Found TATA')
else:
print ('Not Found')
The result is : ?
Example code
import re
seq = 'ACGATATACC'
regEx = '(TA){3}'
aList = re.findall(regEx,seq)
if len(aList) > 0:
print('Found TATA')
else:
print ('Not Found')
The result is : ?
Substitution example: re.sub()
Regular expressions can be used to perform substitutions
eg replace all T’s or C’s with a “-” in a sequence
seq = 'AAACGCTGTCAATACAATCTTCTTTCGGATTTGAATTTTGCAAAGCTGCC'
regEx = '[TC]'
replacement = '-'
new_seq = re.sub(regEx , replacement , seq )
print (new_seq )
The result is :
AAA-G--G--AA-A-AA---------GGA---GAA----G-AAAG--G--
findall() function of the re module
re.sub(regEx , replacement , targetString )
Returns a string with all the matches of the regEx in the targetString
substituted with the replacement string
re.findall(pattern, target[, flags])
Returns a list of all nonoverlapping matches in target as a list of
strings or, if the pattern included groups, a list of lists of strings
([, flags]: it is optional and exceeds the scope of this tutorial,
however if required we would be happy to explain you more)
More functions are available at http://docs.python.org/library/re.html
File I/O – reading from a file
F = open('C:\Documents and
Settings\Administrator\Desktop\User\Pyt
hon course\Seq.txt', 'r')
F is the file handler allows you to have
a direct link to the contents of the
file – Seq.txt
lines = F.readlines() # command reads all
the lines of the file into a list
called lines
F.close()
File I/O – writing to a file
F = open('C:\Documents and
Settings\Administrator\Desktop\User\Pyt
hon course\Out.txt', 'w')
F is the file handler allows you to have
a direct link to the contents of the
file – Seq.txt
F.write('Hello') # command writes the
word “Hello” in the file Out.txt
F.close()
