BINF 634 Fall 2015 Lect 51 BINF634 Lecture 5 Program 1 Solution Quiz 2 Solution Program 2...

BINF 634 Fall 2015 Lect 5 1

BINF634 Lecture 5 Program 1 Solution

Quiz 2 Solution

Program 2 Discussions

Regular Expressions

Regular Expressions Lab

Time to Work on Program 2

Outline

Program 1 Discussions You must test all of your code on binf

I am testing your code on binf I can’t possibly know what configuration

of what machine that your code runs under

The perl on binf must be the first line in your program #!/usr/bin/perl



Program 1 Solution#!/usr/bin/perluse strict;use warnings;

# File: cpg.pl# Author: Jeff Solka# Date: 01 Aug 2015## Purpose: Read sequences from a FASTA

format file# Programming Assignment #1

# the argument list should contain the file name

die "usage: fasta.pl filename\n" if scalar @ARGV < 1;

# get the filename from the argument listmy ($filename) = @ARGV;

# Open the file given as the first argument on the command line

open(INFILE, $filename) or die "Can't open $filename\n";

# variable declarations:my @header = (); # array of headersmy @sequence = (); # array of

sequencesmy $count = 0; # number of

sequences

# read FASTA filemy $n = -1; # index of current

sequencewhile (my $line = <INFILE>) { chomp $line; # remove training \

n from line if ($line =~ /^>/) { # line

starts with a ">"$n++; # this starts a new header$header[$n] = $line; # save header

line$sequence[$n] = ""; # start a new

(empty) sequence }

Program 1 Solution

Program 1 Solution (cont.) else {next if not @header; # ignore data before first

header$sequence[$n] .= $line # append to end of

current sequence }}$count = $n+1; # set count to the number of

sequencesclose INFILE;

# remove white space from all sequencesfor (my $i = 0; $i < $count; $i++) { $sequence[$i] =~ s/\s//g;}########## Sequence processing starts here:##### REST OF PROGRAM

my $maxlength = 0;my $minlength = 1E99;my $sumlength = 0;my $avlength = 0;

# process the sequencesfor (my $i = 0; $i < $count; $i++) { $sumlength += length($sequence[$i]); if(length($sequence[$i]) > $maxlength){ $maxlength = length($sequence[$i]); } if(length($sequence[$i]) < $minlength){ $minlength = length($sequence[$i]); }}

$avlength = $sumlength/$count;

# print out statisticsprint "Report for file $filename \n";print "There are $count sequences in the

file \n";print "Total sequence length = $sumlength \

n";print "Maximum sequence length = $maxlength

\n";print "Minimum sequence length = $minlength

\n";print "Ave sequence length = $avlength \n";

Program 1 Solution

4BINF 634 Fall 2015 Lect 5


Program 1 Solution (cont.)# print out sequence informationfor (my $i = 0; $i < $count; $i++) { print "$header[$i]\n"; print

"Length:",length($sequence[$i]),"\n";

# Notice that we can use scalar

variables to hold numbers.my $a = 0; my $c = 0; my $g = 0; my $t = 0;my $cg = 0;

# Use a regular expression "trick", and five while loops,

# to find the counts of the four bases plus errors

while($sequence[$i] =~ /a/ig){$a++} while($sequence[$i] =~ /c/ig){$c++} while($sequence[$i] =~ /g/ig){$g++} while($sequence[$i] =~ /t/ig){$t++} while($sequence[$i] =~ /cg/ig){$cg++}

printf "A:%d %0.2f \n", $a, $a/length($sequence[$i]);

printf "C:%d %0.2f \n", $c, $c/length($sequence[$i]);

printf "G:%d %0.2f \n", $g, $g/length($sequence[$i]);

printf "T:%d %0.2f \n", $t, $t/length($sequence[$i]);

printf "CpG:%d %0.2f \n", $cg, $cg/length($sequence[$i]);

}

exit;

Program 1 Solution


Quiz 2 Solution#!/usr/bin/perl -w

use strict;

use warnings;

#quiz2 Fall 2015

#Jeff Solka

my(@a)=(1..10);

print "array a prior to the function call \n";

print "@a \n";

myfun(\@a);

print "array a after the function call \n";

print "@a \n";

exit;

sub myfun{

my($i)=@_;

my $element;

foreach $element(@$i) {

$element = $element**2;

}

}

Program 1 Solution


Quiz 2 Program in Action

Program in action.

[binf:binf634/quizzs/myquizzes] jsolka% ./quiz2.pl

array a prior to the function call

1 2 3 4 5 6 7 8 9 10

array a after the function call

1 4 9 16 25 36 49 64 81 100

Quiz 2 Solution

ANY QUESTIONS ON PROGRAM 2?


Program 2 Discussions

Regular Expression Humor

A relevant cartoon


Regular Expression (Humor)


Regular Expressions Bioinformatics programs often have to look for patterns in strings:

Find a DNA sequences containing only C's and G's Look for a sequence that begins with ATG and ends with TAG

Regular expressions are a way of describing a PATTERN: "all the words that begin with the letter A" "every 10-digit phone number“

We create regular expression to match the different parts of the pattern we're looking for

Ordinary characters match themselves Meta-characters are special symbols that match a group of characters

for example \d matches any digit

Regular Expression (Why?)

Meta Characters(see Camel Book, Ch. 5)

. match any single character

[atcg] match any single a, t, c, or g

[A-Z] match any character in given range

[^atcg] match any character NOT in the set

\CHAR takes away meta meaning of character CHAR[\.\|\*] matches "." or "|" or "*"

^ or \A true at start of string

$ or \z true at end of string

\b\B

true at word boundarytrue when not at word boundary

\d\D

match any digitmatch any non-digit

\n\t

match newline charactermatch tab character

\s\S

match any white space charactermatch any non-whitespace character

\w\W

match any "word" character (alphanumeric plus "_")match any non-word character

Regular Expression (How?)


Ways to Control Patterns(see Camel Book, Ch. 5)

PATTERN1|PATTERN2 matches either PATTER1 or PATTERN2

PATTERN* matches zero or more instances of pattern. [A-Z]* = any number of capital letters (including 0)

PATTERN+ matches one or more instances of pattern. [A-Z]+ = one or more capital letters

PATTERN{N} matches exactly N instances of pattern[ATCG]{3} = one codon

PATTERN{MIN,MAX}

PATTERN{MIN,}

matches at least MIN but not more than MAX timesA[C]{2,4}G matches ACCG, ACCCG, or ACCCCGmatches at least MIN times

*?+?{MIN,MAX}?

matches 0 or more time, minimallymatches 1 or more time, minimallymatches MIN to MAX times, minimally

Regular Expression (How?)


Examples

# match if string $str contains 0 or more white space characters

$str =~ /^\s*$/;

# string $str contains all capital letters (at least one)

$str =~ /^[A-Z]+$/;

# string $str contains a capital letter followed by 0 or more digits

$str =~ /[A-Z]\d*/;

# number $n contains some digits before and after a decimal point

$n =~ /^\d+\.\d+$/;

# string contains A and B separated by any two characters

$s =~ /A..B/;

# string does NOT contains ATG

$s !~ /ATG/;

Regular Expression (Practice)


Examples

# match if string $str contains any sequence of three consecutive A's

$str =~ /AAA/;

$str =~ /A{3}/;

# match if string $str consist of exactly three A's

$str =~ /^AAA$/;

$str =~ /^A{3}$/;

# match if $str contains a codon for Alanine (GCA, GCT, GCC, GCG)

$str =~ /GC./;

# match if $str contains a STOP codon (TAA, TAG, TGA)

$str =~ /TA[AG]|TGA/;

$str =~ /T(AA|AG|GA)/;

$str =~ /T(A[AG]|GA)/;



Examples

# string contains any word containing all capital letters

$str =~ /\b[A-Z]+\b/;

# A followed by any number of C or G's followed by T or A

$str =~ /A[CG]*(T|A)/;

$str =~ /A[CG]{0,}[TA]/;

# TT followed by one or more CA's followed by anything except G

$str =~ /TT(CA)+[^G]/;

# string begins with B and has between 5 and 10 letters

$str =~ /^B.{4,9}$/;

# string consists of a 10 digit phone number: ddd-ddd-dddd$str =~ /^\d\d\d\-\d\d\d\-\d\d\d\d$/; $str =~ /^\d{3}\-\d{3}\-\d{4}$/;




Capturing Matches When we match a string with a regular expression, we may want to find

out what matched Do this by surrounding the part of interest with ( ) Then access special variables $1, $2, etc to get matches:

$str = "Perl is a programming language used for bioinformatics.";

$str =~ /(.*) is.*(b.*)\./;

$first = $1;

$second = $2;

print "$first $second\n"; # prints "Perl bioinformatics"

# or, you can capture the results in a list assignment:

($first, $second) = $str =~ /(.*) is.*(b.*)\./;

print "$first $second\n"; # prints "Perl bioinformatics"

Regular Expression (What Did We Match?)


Capturing Matches When we match a string with a regular expression, we may want to find out

what matched Do this by surrounding the part of interest with ( ) Then access special variables $1, $2, etc to get matches:

$str = "Perl is a programming language used for bioinformatics.";

$str =~ /(P.*l)/;

$word = $1;

print $word; # prints "Perl is a programming l"

$str =~ /(P.*?l)/;

$word = $1;

print $word; # prints "Perl"

$str =~ /\b(u.*?)\b/;

$word = $1;

print $word; # prints "used"



Capturing Matches If no string is given to the match operators, $_ is assumed

@A = qw / ATGGCT CCCCGGTAT GCAGTGG /;

for (@A) {

($first, $second) = /(.+)GG(.+)/;

print "$first $second\n" if ($first and $second);

}

OUTPUT:

AT CT

CCCC TAT

Q. Why no output for third string?


#!/usr/bin/perluse strict;use warnings;

my $string = "Several rapidly developing RNA interference (RNAi)methodologies hold the promise to selectively inhibit gene expression inmammals. RNAi is an innate cellular process activated when adouble-stranded RNA (dsRNA) molecule of greater than 19 duplexnucleotides enters the cell, causing the degradation of not only theinvading dsRNA molecule, but also single-stranded (ssRNAs) RNAs ofidentical sequences, including endogenous mRNAs.";

# find all words containing "RNA"while ( $string =~ /(\w*RNA\w*)/g ) { print "$1\n";}exit;

Output:RNARNAiRNAiRNAdsRNAdsRNAssRNAsRNAsmRNAs





# find all words containing "RNA"while ( $string =~ /(\w+RNA\w+)/g ) { print "$1\n";}exit;

Output:ssRNAsmRNAs





# find all words containing "RNA"while ( $string =~ /(\S+RNA\S+)/g ) { print "$1\n";}exit;

Output:(RNAi)(dsRNA)(ssRNAs)mRNAs.




Capturing MatchesWhen we match a string with a regular expression, several special variables

get set automatically:

$string =~ /REGEXP/;$` = part of string to the left of the match$& = part of string matched by the regular expression REGEXP$’ = part of string the the right the match

$string = "ATCGCAT";$string =~ /T.G/;print "left part: $` \n";print "match: $& \n";print "right part: $’ \n";

Output:left part: Amatch: TCGright part: CAT



A Nice Application of Capturing Matches#!/usr/bin/perlprint ("\nEnter string or cntl-D to quit\n");print ("Square brackets indicate text that matched pattern\n\n");$prompt = "test> ";print $prompt;while(<STDIN>) {chomp;if(/REGEXP Goes Here/) {print("$`\[$&]$'\n");}else {print("no match\n");}print $prompt;}exit;

Regular Expression (A Regular Expression Tester)

An Even Nicer Implementation of This Idea - I

#!/usr/bin/perl

use strict;

use warnings;

# File: regex_tester.pl

# Author: Jim Logan

#

# Fully interactive version (i.e., no recompiles required) a regular expression

# tester based on a script by Fernando J. Pineda as presented to

# class of BINF623 by Jeff Solka on 10/1/12.

# Particularly useful in an Eclipse environment using its cut and paste facility.

# instructions for use

print "\nAccepts keyboard entry of a regular expression and then permits\n";

print "successive entry of strings to test that expression.\n";

print "Square brackets in output indicate the text that matched pattern\n\n";

print "Note: Depending upon the environment (e.g. Eclipse), you may be\n";

print "able to cut and paste into both the \"Next expression\" and the\n";

print "\"New test string\" fields and then edit as desired.\n";


Regular Expression (A Nicer Regular Expression Tester)

An Even Nicer Implementation of This Idea - II

# initialization

my $regex = '/^.*$/'; #default regex to start and to demonstrate

my $string = 'This is a test string';

my $input = "";

my $stripped_regex = "";

while (1) { # outer loop to sequence regular expressions

print "\nCurrent regular expresssion: $regex\n";

print "Enter a new expression to change or ENTER to continue without change.\n";

print "(\"quit\" terminates the program)\n";

print "New expression: ";

$input = <STDIN>;

chomp $input;

if ($input =~ /^q.*$/i) {exit};

if ($input !~ /^$/) {

$regex = $input;

}

$stripped_regex = substr ($regex, 1, length ($regex) -2);



An Even Nicer Implementation of This Idea - III

# User includes the two slashes for a regular expresssion

# but they are stripped here so that variable is just the pattern

# that will be interpolated in /pattern/ context.

while (1) { # inner loop to sequence strings to test the expression

print "\nCurrent test string: $string\n";

print "Enter a new expression to change or ENTER to reset the regex.\n";

print "New test string: ";

$input = <STDIN>;

chomp $input;

if ($input =~ /^$/) { # for blank line, go back to set expresssion

last; }

else {

$string = $input; # else run regex over input

}



An Even Nicer Implementation of This Idea - IV

if( $string =~ /$stripped_regex/) {

print("$`\[$&]$'\n"); } # show match in context of input

else {

print("no match\n");

}

}

}

exit;




Finding the position of matches

If we use the global modifier g, then pos($string) returns position after the match:

$string = "ATCGCATGGAA";

$string =~ /T.G/g;

print "$& ends at position ", pos($string)-1, "\n\";

$string =~ /T.G/g;

print "$& ends at position ", pos($string)-1, "\n";

Output:

TCG ends at position 3

TGG ends at position 8

Regular Expression (Where Did the Match Occur?)



# find all words containing "RNA"while ( $string =~ /(\S+RNA\S+)/g ) { print "$1 ends at position ", pos($string)-1, "\n";}exit;

Output:(RNAi) ends at position 49(dsRNA) ends at position 211(ssRNAs) ends at position 374mRNAs. ends at position 431

Regular Expression (Where Did the Match Occur?)



Some Useful URLs http://docs.python.org/library/re.html http://www.regular-expressions.info/ http://www.regular-expressions.info/tutorial.html http://www.troubleshooters.com/codecorn/littperl/perlreg.htm

Additional Reading


Homework Remember we meet Tuesday of week 10/13/15 at the usual

place and time due to the Columbus day Holiday. Program 2 due Tuesday 10/13/14at 7:00 pm. Quiz 3 will occur next week. Remember that on Tuesday October 19, 2015 we will have our

in class midterm exam. It will be open book and notes.

On the Horizon


Regular Expression Lab Counts as a quiz grade

100 possible points

Our Regular Expression Lab

BINF 634 Fall 2015 Lect 51 BINF634 Lecture 5 Program 1 Solution Quiz 2 Solution Program 2...

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