Strings in Python

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Strings in Python
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Computers store text as strings
gtgtgt s "GATTACA"
s
Each of these are characters
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Why are strings important?

• Sequences are strings
• ..catgaaggaa ccacagccca gagcaccaag ggctatccat..
• Database records contain strings
• LOCUS AC005138
• DEFINITION Homo sapiens chromosome 17, clone
  hRPK.261_A_13, complete sequence
• AUTHORS Birren,B., Fasman,K., Linton,L.,
  Nusbaum,C. and Lander,E.
• HTML is one (big) string

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Getting Characters
gtgtgt s "GATTACA" gtgtgt s0 'G' gtgtgt s1 'A' gtgtgt
s-1 'A' gtgtgt s-2 'C' gtgtgt s7 Traceback (most
recent call last) File "ltstdingt", line 1, in
? IndexError string index out of range gtgtgt
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Getting substrings
gtgtgt s13 'AT' gtgtgt s3 'GAT' gtgtgt
s4 'ACA' gtgtgt s35 'TA' gtgtgt
s 'GATTACA' gtgtgt s2 'GTAA' gtgtgt
s-22-1 'CAT' gtgtgt







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Creating strings
Strings start and end with a single or double
quote characters (they must be the same)
"This is a string" "This is another
string" "" "Strings can be in double quotes" Or
in single quotes. 'Theres no difference.' Okay,
there\s a small one.
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Special Characters andEscape Sequences
Backslashes (\) are used to introduce special
characters
gtgtgt s 'Okay, there\'s a small one.'
The \ escapes the following single quote
gtgtgt print s Okay, there's a small one.
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Some special characters
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Working with strings
length concatenation repeat substring
test substring location substring count
gtgtgt len("GATTACA") 7 gtgtgt "GAT"
"TACA" 'GATTACA' gtgtgt "A" 10 'AAAAAAAAAA' gtgtgt
"G" in "GATTACA" True gtgtgt "GAT" in
"GATTACA" True gtgtgt "AGT" in "GATTACA" False gtgtgt
"GATTACA".find("ATT") 1 gtgtgt "GATTACA".count("T") 2
gtgtgt
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Converting from/to strings
gtgtgt "38" 5 Traceback (most recent call last)
File "ltstdingt", line 1, in ? TypeError cannot
concatenate 'str' and 'int' objects gtgtgt int("38")
5 43 gtgtgt "38" str(5) '385' gtgtgt int("38"),
str(5) (38, '5') gtgtgt int("2.71828") Traceback
(most recent call last) File "ltstdingt", line
1, in ? ValueError invalid literal for int()
2.71828 gtgtgt float("2.71828") 2.71828 gtgtgt
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Change a string?
Strings cannot be modified They are
immutable Instead, create a new one
gtgtgt s "GATTACA" gtgtgt s3 "C" Traceback (most
recent call last) File "ltstdingt", line 1, in
? TypeError object doesn't support item
assignment gtgtgt s s3 "C" s4 gtgtgt
s 'GATCACA' gtgtgt
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Some more methods
gtgtgt "GATTACA".lower() 'gattaca' gtgtgt
"gattaca".upper() 'GATTACA' gtgtgt
"GATTACA".replace("G", "U") 'UATTACA' gtgtgt
"GATTACA".replace("C", "U") 'GATTAUA' gtgtgt
"GATTACA".replace("AT", "") 'GTACA' gtgtgt
"GATTACA".startswith("G") True gtgtgt
"GATTACA".startswith("g") False gtgtgt
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Ask for a string
The Python function raw_input asks the user
(thats you!) for a string
gtgtgt seq raw_input("Enter a DNA sequence
") Enter a DNA sequence ATGTATTGCATATCGT gtgtgt
seq.count("A") 4 gtgtgt print "There are",
seq.count("T"), "thymines" There are 7
thymines gtgtgt "ATA" in seq True gtgtgt substr
raw_input("Enter a subsequence to find ") Enter
a subsequence to find GCA gtgtgt substr in
seq True gtgtgt
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Assignment 1
Ask the user for a sequence then print its length
Enter a sequence ATTAC It is 5 bases long
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Assignment 2
Modify the program so it also prints the number
of A, T, C, and G characters in the sequence
Enter a sequence ATTAC It is 5 bases
long adenine 2 thymine 2 cytosine 1 guanine 0
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Assignment 3
Modify the program to allow both lower-case and
upper-case characters in the sequence
Enter a sequence ATTgtc It is 6 bases
long adenine 1 thymine 3 cytosine 1 guanine 1
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Assignment 4
Modify the program to print the number of unknown
characters in the sequence
Enter a sequence ATTUgtc It is 7 bases
long adenine 1 thymine 3 cytosine 1 guanine
1 unknown 2