Computational Genomics Elhanan Borenstein A quick review Arguments and return values: Returning multiple values from a function: return [sum, prod] Pass-by-reference vs. pass-by-value Default Arguments def printMulti(text, n=3): Keyword Arguments runBlast(“my_f.txt”, matrix=“PAM40”)
Modules: A file containing a set of related functions Easy to create and use your own modules First import it: import utils … Then use dot notation: utils.makeDict() A quick review – cont’ Recursion: A function that calls itself Divide and conquer algorithms Every recursion must have two key features: 1. There are one or more base cases for which no recursion is applied. 2. All recursion chains eventually end up at one of the base cases.
Examples: Factorial, string reversal Binary search Traversing trees Merge sort
Recursion vs. iteration
Strings ‘abc’
A B C “abc”
‘’’ abc’’’
r’abc’ Newlines are a bit more complicated ‘abc\n’
A B C “abc\n”
‘’’abc ’’’ A B C \ n r’abc\n’ Why so many? ‘ vs “ lets you put the other kind inside a string. Very Useful. ‘’’ lets you run across multiple lines. All 3 let you include and show invisible characters (using \n, \t, etc.) r’...’ (raw strings) do not support invisible character, but avoid problems with backslash. Will become useful very soon. open(’C:\new\text.dat’) vs. open(’C:\\new\\text.dat’) vs. open(r’C:\new\text.dat’) String operations As you recall, the string data type supports a verity of operations: >>> my_str = 'tea for too‘ >>> print my_str.replace('too','two') 'tea for two'
>>> print my_str.upper()
TEA FOR TOO
>>> my_str.split(‘ ‘) [‘tea’, ‘for’, ‘too’]
>>> print my_str.find(“o")
5 >>> print my_str.count(“o") 3 But … What if we want to do more complex things? Get rid of all punctuation marks Find all dates in a long text and convert them to a specific format Delete duplicated words Find all email addresses in a long text Find everything that “looks” like a gene name in some output file Split a string whenever a certain word (rather than a certain character) occurs Find DNA motifs in a Fasta file Well … We can always write a program that does that … # assume we have a genome sequence in string variable myDNA for index in range(0,len(myDNA)-20) : if (myDNA[index] == "A" or myDNA[index] == "G") and (myDNA[index+1] == "A" or myDNA[index+1] == "G") and (myDNA[index+2] == "A" or myDNA[index+2] == "G") and (myDNA[index+3] == "C") and (myDNA[index+4] == “A") and # and on and on! … (myDNA[index+19] == "C" or myDNA[index+19] == "T") : print "Match found at ",index break
6 Regular expressions Regular expressions (a.k.a. RE, regexp, regexes, regex) are a highly specialized text-matching tool.
Regex can be viewed as a tiny programming language
embedded in Python and made available through the re module.
They are extremely useful in searching and modifying
(long) string
http://docs.python.org/library/re.html Not only in Python REs are very widespread: Unix utility “grep” Perl TextWrangler TextPad Python
So, … learning the “RE language” would serve you in
many different environments as well. Do you absolutely need regexes? No, everything they do, you could do yourself!
BUT … pattern-matching is:
Widely used (especially in bioinf applications)! Tedious to program! Error-prone!
RE give you a flexible, systematic, compact, and
automatic way to do it. (In truth, it’s still somewhat error-prone, but in a different way). Regexe vs. Python The regular expression language is relatively small and restricted Not all possible string processing tasks can be done using regular expressions. Some tasks can be done with RE, but the expressions turn out to be extremely complicated.
In these cases, you may be better off writing a Python
code to do the processing: Python code may take longer to write It will be slower than an elaborate regular expression But … it will also probably be more understandable. Let’s get to it: How do regexes work?
Valentine Day Special!
It’s all about finding a great match Finding a good match Using this RE tiny language, you can specify patterns that you want to match
You can then ask match questions such as:
“Does this string match this pattern?” “Is there a match to this pattern anywhere in this string?” “What are all the matches to this pattern in this string?”
You can also use REs to modify a string
Replace parts of a string (sub) that match the pattern with something else Break stings into smaller pieces (split) wherever this pattern is matched A simple example Consider the following example: >>> import re >>> re.findall(r'\bf[a-z]*', 'which foot or hand fell fastest')
['foot', 'fell', 'fastest']
This RE means: A word that starts with ‘f’ followed by any number of alphabetical characters
Note the re. prefix – findall is a function in the re
module findall: Format: findall(<regexe>, <string>) Returns a list of all non-overlapping substrings that matches the regexe. REs are provided as strings. Remember: It’s all about matching
Regular expressions are patterns;
they “match” sequences of characters Basic RE matching Most letters and numbers match themselves For example, the regular expression test will match the string test exactly Normally case sensitive >>> re.findall(r’test’, “Tests are testers’ best testimonials”) [‘test', ‘test']
Most punctuation marks have special meanings!
Metacharacters: . ^ $ * + ? { [ ] \ | ( ) needs to be escaped by backslash (e.g., “\.” instead of “.”) to get non-special behavior Therefore, “raw” string literals (r’C:\new.txt’) are generally recommended for regexes (unless you double your backslashes judiciously) Sets Square brackets mean that any of the listed characters will do (matching one of several alternatives) [abc] means either ”a” , ”b” , or “c”
You can also give a range:
[a-d] means ”a”, ”b”, ”c”, or ”d”
Negation: caret means not
[^a-d] means anything but a, b, c or d [^5] means anything but 5
Metacharacters are not active inside sets.
[ak$] will match “a”, “k”, or “$”. Normally, “$” is a metacharacter. Inside a set it’s stripped of its special nature. Predefined sets \d matches any decimal digit (equivalent to [0-9]). \D matches any non-digit character (equivalent to [^0-9]). \s matches any whitespace character Note the pairs. Easy to remember! (equivalent to [ \t\n\r\f\v]). \S matches any non-whitespace character (equivalent to [^ \t\n\r\f\v]). \w matches any alphanumeric character (equivalent to [a-zA-Z0-9_]). \W matches any non-alphanumeric character (equivalent to the class [^a-zA-Z0-9_]. Matching boundaries ^ matches the beginning of the string $ matches the end of the string
\b matches a word boundary
\B matches position that is not a word boundary
(A word boundary is a position that changes from a word
character to a non-word character, or vice versa).
For example, \bcat will match catalyst but not location
Wildcards . matches any character (except newline) If you really mean “.” you must use a backslash
WARNING: backslash is special in Python strings It’s special again in RE This means you need too many backslashes Use ”raw strings” to make things simpler
What does this RE means: r’\d\.\d’?
Repetitions Allows you to specify that a portion of the RE must/can be repeated a certain number of times. * : The previous character can repeat 0 or more times ca*t matches ”ct”, ”cat”, ”caat”, ”caaat” etc.
+ : The previous character can repeat 1 or more times
ca+t matches ”cat”, ”caat” etc. but not ”ct”
Braces provide a more detailed way to indicate repeats
A{1,3} means at least one and no more than three A’s A{4,4} means exactly four A’s A quick example Remember this PSSM:
re.findall(r’[AG]{3,3}CATG[TC]{4,4}[AG]{2,2}C[AT]TG[CT][CG][TC]’, myDNA) More examples >>> re.sub('\d', 'x', 'a_b - 12') 'a_b - xx' >>> re.sub('\D', 'x', 'a_b - 12') 'xxxxxx12' >>> re.sub('\s', 'x', 'a_b - 12') 'a_bx-x12' >>> re.sub('\S', 'x', 'a_b - 12') 'xxx x xx' >>> re.sub('\w', 'x', 'a_b - 12') 'xxx - xx' >>> re.sub('\W', 'x', 'a_b - 12') 'a_bxxx12‘ >>> re.sub('^', 'x', 'a_b - 12') 'xa_b - 12' >>> re.sub('$', 'x', 'a_b - 12') 'a_b - 12x' >>> re.sub('\b', 'x', 'a_b - 12') 'a_b - 12' >>> re.sub('\\b', 'x', 'a_b - 12') 'xa_bx - x12x' >>> re.sub(r'\b', 'x', 'a_b - 12') 'xa_bx - x12x' >>> re.sub('\B', 'x', 'a_b - 12') 'ax_xb x-x 1x2' RE Semantics If R, S are regexes: RS matches the concatenation of strings matched by R, S individually R|S matches the union (either R or S)
Parentheses can be used for grouping
(abc)+ matches ‘abc’, ‘abcabc’, ‘abcabcabc’, etc. this|that matches ‘this’ and ‘that’, but not ‘thisthat’. Conflicts? Check this example: >>> import re >>> mystring = "This contains 2 files, hw3.py and uppercase.py." >>> all_matches = re.findall(r’.+\.py’, mystring) >>> print all_matches
What do you think all_matchs contains?
[’ This contains 2 files, hw3.py and uppercase.py’]
What happened? Matching is greedy >>> import re >>> mystring = "This contains 2 files, hw3.py and uppercase.py." >>> all_matches = re.findall(r’.+\.py’, mystring) >>> print all_matches [’ This contains 2 files, hw3.py and uppercase.py’]
Our RE matches “hw3.py”
Unfortunately … It also matches: “This contains 2 files, hw3.py” And it even matches: “This contains 2 files, hw3.py and uppercase.py” Python will choose the longest match! Solution: Break my text first into words (not an ideal solution) I could specify that no spaces are allowed in my match A better version This will work: >>> import re >>> mystring = "This contains 2 files, hw3.py and uppercase.py." >>> all_matches = re.findall(r’ [^ ]+\.py’, mystring) >>> print all_matches
[’hw3.py’,’uppercase.py’] Code like a pro … TIP OF THE DAY
Suppose you are not sure:
… whether the format you are using for a certain command is the correct one or … whether range(4) returns 0 to 4 or 0 to 3 or … whether string has a method “reverse” or … whether you are allowed to break inside a nested loop or … whether your code is correct
What should you do?
Code like a pro … TIP OF THE DAY
JUST RUN IT!!!
Don’t be afraid: Running a bugged code will not harm your computer! (it also should not hurt your self-esteem) It doesn’t cost anything It will be faster (and more accurate) than you trying to “think it through” In many cases, the error message or output will be extremely informative
“The freedom to run experiments is the most
precious luxury of computational biologists” Nanahle Nietsnerob Sample problem #1 Download the course webpage (e.g., use the “save as” option). Write a program that reads this webpage text and scan for all the email addresses in it. An email address usually follows these guidelines: Upper or lower case letters or digits Starting with a letter Followed by a the “@” symbol Followed by a string of alphanumeric characters. No spaces are allowed Followed by a the dot “.” symbol Followed by a domain extension. Assume domain extensions are always 3 alphanumeric characters long (e.g., “com”, “edu”, “net”. Solution #1 import sys import re
[‘jht@uw.edu’, ‘elbo@uw.edu’] Sample problem #2 1. Download and save warandpeace.txt. Write a program to read it line-by-line. Use re.findall to check whether the current line contains one or more “proper” names ending in “...ski”. If so, print these names: ['Bolkonski'] ['Bolkonski'] ['Bolkonski'] ['Bolkonski'] ['Volkonski'] ['Volkonski'] ['Volkonski']
2. Now, instead of printing these names for each line,
insert them into a dictionary and just print all the “…ski” names that appear in the text at the end of your program (preferably sorted): Aski Bitski Bolkonski Borovitski Bronnitski Czartoryski Golukhovski Gruzinski Solution #2.1 import sys import re
names_dict = {} # A dictionary for storing all names
for line in file: names = re.findall(r'\w+ski', line) for name in names: names_dict[name] = 1
file.close()
name_list = names_dict.keys() name_list.sort()
for name in name_list:
print name Challenge problem “Translate” War and Peace to Pig Latin. The rules of translations are as follows: If a word starts with a consonant: move it to the end and append “ay” Else, for words that starts with a vowel, keep as is, but add “zay” at the end Examples: beast → eastbay dough → oughday happy → appyhay another→ anotherzay if→ ifzay
