computer programming for biologists

Computer Programming for Biologists

Class 5

Nov 20st, 2014

Karsten Hokamp

http://bioinf.gen.tcd.ie/GE3M25/programming


Project

Program Exit

Random numbers

Regular Expressions

Overview


Task 1: Report length of a sequence in Fasta format

Understand the problem, consider input/output:

>Tmsb10ATGGCAGACAAGCCGGACATGGGGGAAATCGCCAGCTTCGATAAGGCCAAGCTGAAGAAAACCGAGACGCAGGAGAAGAACACCCTGCCGACCAAAGAGACCATTGAACAGGAAAAGAGGAGTGAAATCTCCTAA

Sequence length is 135 bp.

Project


Problems:

1.File contains header line

2.Sequence contains line-breaks

>Tmsb10ATGGCAGACAAGCCGGACATGGGGGAAATCGCCAGCTTCGATAAGGCCAAGCTGAAGAAAACCGAGACGCAGGAGAAGAACACCCTGCCGACCAAAGAGACCATTGAACAGGAAAAGAGGAGTGAAATCTCCTAA

Project


Steps:

1.Read in file content (line-by-line)

2. Remove line-breaks

3. Skip header line

4. Concatenate sequence into one long string

5. Calculate and report length

Project


Steps:

# 1. Read in file content (line-by-line)

while ($input = <>) {

}

Project


Steps:



# 2. Remove line-breaks

# 3. Skip header line

# 4. Concatenate sequence into one long

string

}

Project


Steps:




chomp $input;



string

}

Project


Steps:




chomp $input;



string

$sequence .= $input;

}

Project





chomp $input;


# 4. Concatenate sequence into one long string


}

# 5. Calculate and report length

$length = length($sequence);

print "Sequence length: $length bp\n";

Project





chomp $input;

# 3. Skip header line (check for '>' in first position)

# extract first character:

$first = substr $input, 0, 1;

# is it a '>'?

if ($first eq '>') {

# skip this line

next;

}


Project





chomp $input;

# 3. Skip header line (check for '>' in first position)

# extract first character:

$first = substr $input, 0, 1;

# is it a '>'?

unless ($first eq '>') {

# this must be part of the sequence


}

}

Project

alternativeversionalternativeversion


# 1. Read in file content (line-by-line)while ($input = <>) {

# 2. Remove line-breakschomp $input;# 3. Skip header line (check for '>' in first position)# extract first character:$first = substr $input, 0, 1;# is it a '>'?if ($first eq '>') {

# skip this linenext;

}# 4. Concatenate sequence into one long string$sequence .= $input;

}# 5. Calculate and report length$length = length($sequence);print "Sequence length: $length bp\n";

Project


# Suggestions for the start of the script:

# make sure a file has been providedunless (@ARGV) {

die "Please specify file name on command line!";}

# initialise sequence variable$sequence = '';

# 1. Read in file content (line-by-line)while ($input = <>) {

…

Project


1. automatic exit at end of script

2. explicit exit with value:

exit 0; # default

or

exit 1; # normally indicates an error

3. exit on failure:

die "error message";

("\n" supresses line number)

Exiting a program


Example:

Exiting a program


Practical:

Project

http://bioinf.gen.tcd.ie/GE3M25/programming/class5


• constructs that describe patterns

• powerful methods for text processing

• search for patterns in a string

• search and extract patterns

• search and replace patterns

• pattern at which to split a string

Regular Expressions


Examples:

• Look for a motif in a dna/protein sequence

• Find low complexity repeats and mask with x's

• Find start of sequence string in GenBank record

• Extract e-mail addresses from a web-page

• Replace strings, e.g.: '@tcd.ie' with '@gmail.com'

Regular Expressions


Find a pattern in a string (stored in a variable):

$sequence = 'ataggctagctaga';

if ( $sequence =~ /ctag/ ) { print 'Found!';}

Regular Expressions

string in which to

search





Regular Expressions

binding operator





Regular Expressions

pattern





Regular Expressions

delimiters





Regular Expressions

binding operator pattern

delimitersstring in which to

search



$_ = 'ataggctagctaga';

if ( /ctag/ ) { print 'Found!';}

Regular Expressions

pattern

delimiters

without binding // to a variable, regular expression works on $_


Search modifier:

i = make search case-insensitive


if ( $sequence =~ /TAG/i ) {

print 'Found!';

}

Regular Expressions


Metacharacters:

^ = match at the beginning of a line

$ = match at the end of the line

. = match any character (except newline)

\ = escape the next metacharacter

$sequence = ">sequence1\natgacctggaataggat";

if ( $sequence =~ /^>/ ) { # line starts with '>'

print 'Found Fasta header!';

}

Regular Expressions

/\.$/ matches dot at end of line


Exercise:

Modify your course project (sequanto.pl) to use a

regular expression for detection of a header line

instead of 'substr' and 'eq' to check first character.

Project


Matching repetition:

a? = match 'a' 1 or 0 times

a* = match 'a' 0 or more times, i.e., any number of times

a+ = match 'a' 1 or more times, i.e., at least once

a{n,m} = match at least "n" times, but not more than "m" times.

a{n,} = match at least "n" or more times

a{n} = match exactly "n" times

$sequence =~ /a{5,}/; # finds repeats of 5 or more 'a's

Regular Expressions


Search for classes of characters

\d = match a digit character

\w = match a word character (alphanumeric and '_')

\D = match a non-digit character

\W = match a non-word character

\s = whitespace

\S = match a non-whitespace character

$date = '30 Jan 2009';

if ( date =~ /\d{1,2} \w+ \d{2,4}/ ) {

print 'Correct date format!';

}

Regular Expressions

also matches '1 February 09'


Match special characters

\t = matches a tabulator (tab)

\b = matches a word boundary

\r = matches return

\n = matches UNIX newline

\cM = matches Control-M (line-ending in Windows)

while (my $line = <>) {

if ($line =~ /\cM/) {

warn "Windows line-ending detected!";

}

}

Regular Expressions


Search for range of characters

[ ] = match at least one of the characters specified within these brackets

- = specifies a range, e.g. [a-z], or [0-9]

^ = match any character not in the list, e.g. [^A-Z]

$sequence = 'ataggctapgctaga';

if ( $sequence =~ /[^acgt]/ ) {

print "Sequence contains non-DNA character: $&";

}

Regular Expressions

$& is a special variable containing the last pattern match$` and $' contain strings before and after match


Search and replace (substitute):

s/pattern1/pattern2/


$rna = $sequence;

$rna =~ s/t/u/;

-> 'auaggctagctaga'

Regular Expressions

Only the first match will be replaced!


Modifiers for substitution:

i = case in-sensitive

g = global

s = match includes newline


$rna = $sequence;

$rna =~ s/t/u/g;

-> 'auaggcuagcuaga'

Regular Expressions

replaces all 't' in the line with 'u'


Example: Clean up a sequence string:

$sequence = "

1 ataggctagctagat

16 ttagagctagta

";

$sequence =~ s/[^actg]//g;

-> 'ataggctagctagatttagagctagta'

Regular Expressions

Deletes everything that is not a, c, t, or g.


Extract matched patterns:

- put patterns in parentheses

- \1, \2, \3, … refers back to ()'s within pattern match

- $1, $2, $3, … refers back to ()'s after pattern match

$sequence = ">test\natgtagagctagta";

if ($sequence =~ /^>(.*)/) { $id = $1; }

or

$email =~ s/(.*)\@(.*)\.(.*)/\1 at \2 dot \3/;

print "Changed address to $1 at $2 dot $3\n";

Regular Expressions

changes '[email protected]' to 'kahokamp at tcd dot ie''


Practical:

Project

http://bioinf.gen.tcd.ie/GE3M25/programming/class5


Change a character into an array:

@array = split //, $string;

Split input line at tabs:

@columns = split /\t/, $input_line;

Default splits $_ on whitespace:

while (<>) {

@colums = split;

…

}

Regular Expressions in split

computer programming for biologists

Documents

file content line

concatenate sequence

sequenceprint sequence

skip header line4

header linesequence

long string5

fasta formatunderstand

karsten hokamphttp