Introduction to Programming: Perl for Biologists
Timothy M. Kunau
Center for Biomedical Research Informatics
Academic Health Center
University of Minnesota
[email protected]
Bioinformatics Summer Institute 2007
1
Introduction to Programming: Day two
Timothy M. Kunau
Center for Biomedical Research Informatics
Academic Health Center
University of Minnesota
[email protected]
Bioinformatics Summer Institute 2007
2
Day I
•Art and Programming
•Getting Started
•Biology and Computer Science
•Bioinformatics Data
•Perl basics:
•Strings and Variables
•Math and Logic
•Looping, operators, and functions
3
Day II
•Assignment discussion
•Data from outside the program
•Writing out data
•Data into arrays and hashes
•Array operations
•Scope and Good practices
•RegEx
4
Day I: assignment review.
1. Calculate the reverse complement of a DNA strand using the tr/// operation.
2. Read about file handling. (Safari on-line documentation is available.)
3. Read about Regular Expressions (regex). (Safari)
4. Find CPAN.ORG and locate a module that would be useful to you as a biologist.
5. Read about that module and email me ([email protected]) the following details:
1. Name of the module.
2. The name of the person who wrote it.
3. What it does.
4. How it would be useful to you?
5
Day I: assignment review.
1. Calculate the reverse complement of a DNA
strand using the tr/// operation.
6
The tr/// operator (translate)
• Match and replace what is in the first section,
in order, with what is in the second.
• $dna
=~ tr/[A-Z]/[a-z]/;
# lowercase
• $dna
=~ tr/[A-Z]/[B-ZA]/;
# shift cipher
• $dna
=~ tr/[ACGT]/[TGCA]/;
# revcom
• $dna
= reverse($dna);
7
7
s/// operator (substitute)
• Allows you to substitute whatever is matched in
first section with value in the second section. (See
m//.)
• $sport
=~ s/football/soccer/g;
• $tdfwinner
=~ s/Lance Armstrong/Ivan Basso/g;
8
8
Reverse compliment of a DNA strand
#!/usr/bin/perl -w
# Calculating the reverse complement of a strand of DNA
# The DNA
my $DNA = 'ACGGGAGGACGGGAAAATTACTACGGCATTAGC';
print "Here is the starting DNA:\n\n$DNA\n\n";
# Calculate the reverse complement
my $revcom = reverse $DNA;
# The Perl translate/transliterate command is just what we need:
$revcom =~ tr/ACGTacgt/TGCAtgca/;
print "Here is the reverse complement DNA:\n\n$revcom\n";
9
CPAN
10
Day I: assignment review, CPAN modules
1. Name of the module.
2. The name of the person who wrote it.
3. What it does.
4. How it would be useful to you.
11
Getting Data from Files
open(HANDLE, "contig2_MT.fa") || die $!;
while (defined($line = <HANDLE>)) {
if( $line =~ /^\>/ ) {
print $line, "\n";
}
}
close(HANDLE);
% ./file-handles.pl
>ContigId:Contig2 AssemblyProcessId:MtSC AssemblyProcessVersion:1
12
12
Getting Data from Files
open(HANDLE, "contig2_MT.fa") || die $!;
while (<HANDLE>) {
if( $_ =~ /^\>/ ) { # tests first line
print $_, "\n"; # prints first line
}
}
close(HANDLE);
% ./file-handlesII.pl
>ContigId:Contig2 AssemblyProcessId:MtSC AssemblyProcessVersion:1
13
13
Getting Data from Files
open(HANDLE, "contig2_MT.fa") || die $!;
@slurp = <HANDLE>;
print @slurp;
close(HANDLE);
% ./file-handlesIII.pl
>ContigId:Contig2 AssemblyProcessId:MtSC AssemblyProcessVersion:1
GGGTATACTTCCTCCTCCATTGTTTGAGATATCACAAGACTTGAAATTGA
GCACGACCCATATTCTACTTCAAGGCGTTGAAGCAAAAACTCACCATGGG
AAACTAAACAGGTTAGTAAGTAGGCATCACCATCATTTTATATCGATATG
GATAATAATGCACAAGACTTTCAAAGTTATCTTCAGATTCTTCCCCCTGT
TGAGTTTGCTTGCGTTTATGGATCATCTCTTCATCCAACCAATCATGACA
AGACAACCATGGTTGATTATATTCTTGGAGTTTCTGACCCTATACAATGG
CATTCTGAGAATCCGAAAATGAATAAGCATCACTATGCGTCATGGATGGT
GCACCTTGGTGGAGAGAGGCTGATTACCGCAGATGCAGATAAAATTGGTG
TGGGAGTACATTTCAACCCTTTTG
14
14
Pass data into a program
while(<STDIN>) {
print “stdin read: $_”;
}
15
15
Pass data into a program
open(GREP, “grep ‘>’ $filename”) || die $!;
my $i = 0;
while(<GREP>) {
$i++;
}
close(GREP);
print “$i sequences in file\n”;
16
16
Writing out data
open(OUT, “>outname”) || die $!;
print OUT “sequence report\n”;
close(OUT);
17
17
Writing out data
# appending with >>
open(OUT, “>>outname”) || die $!;
print OUT “append this\n”;
close(OUT);
18
18
Filehandles as variables
my $var = \*STDIN;
19
19
Filehandles as variables
open($fh, “>report.txt”) || die $!;
print $fh “line 1\n”;
20
20
Filehandles as variables
open($fh2, “report”) || die $!;
$fh = $fh2;
while(<$fh>) {
something interesting goes here;
}
21
21
Zero based economy...
•The first element is ‘0’ for an index or first character in a string
•computer scientists like it this way
•as do most programming languages, including Perl
•Biologists often number first base in a sequence as ‘1’
•GenBank
•BioPerl
•Interbase coordinates (Kent-UCSC, Chado-GMOD)
22
22
Coordinate systems
• Zero based, interbase coordinates
A A T G G G T A G A
0 1 2 3 4 5 6 7 8 9
• 1 based coordinates
A T G G G T A G A
1 2 3 4 5 6 7 8 9
23
23
Arrays as Lists
• Lists are sets of items
• Can be mixed types of scalars (numbers, strings, floats)
• Perl uses lists extensively
• Variables are prefixed by @
24
24
List operations
• reverse # reverse list order
• $list[$n] # get the $n-th item
• $two = $list[2]; # get which item?
25
25
List operations
• reverse # reverse list order
• $list[$n] # get the $n-th item
• $three = $list[2]; # get the third
item
26
26
List operations
• scalar # get length of array
• $len = scalar @list;
• $last_index = $#list;
• delete $list[10]; # delete entry
27
27
Autovivication
• Autovivify : to bring oneself to life.
• Automatically allocates space for an array item element:
$array[0] = ‘apple’;
$array[4] = ‘elephant’;
$array[25] = ‘zebra’;
delete $array[25];
28
28
29
pop,push,shift,unshift
# remove last item
$last = pop @list;
# remove first item
$first = shift @list;
# add to end of list
push @list, $last;
# add to beginning of list
unshift @list, $first;
30
30
splicing an array
splice ARRAY,OFFSET,LENGTH,LIST
splice ARRAY,OFFSET,LENGTH
splice ARRAY,OFFSET
splice ARRAY
31
31
splicing an array
@list = (‘alice’,’chad’,’rod’);
($x,$y) = splice(@list,1,2);
splice(@list, 1,0,(‘marvin’,’alex’));
32
32
Sorting with sort
@list = (‘tree’,’frog’, ‘log’);
@sorted = sort @list;
# reverse order
@sorted = sort { $b cmp $a } @list;
33
33
Sorting with arrays of numbers
@list = (25,21,12,17,9,8);
# sort based on numerics
@sorted = sort { $a <=> $b } @list;
# reverse order of sort
@revsorted = sort { $b <=> $a } @list;
34
34
LAB: files
% pico files2arrays.pl
#!/usr/bin/perl -w
#
# Reading protein sequence data file.
# File containing the sequence data
my $fastafilename = 'contig2_MT.fa';
# First we have to "open" the file
open(FASTAFILE, $fastafilename);
# Read the fastafrom file, and store it
# into the array variable @protein
@fasta = <FASTAFILE>;
# Print the protein onto the screen
print @fasta;
# Close the file.
close FASTAFILE;
exit;
35
LAB: files
% pico files2arrays.pl
#!/usr/bin/perl -w
#
# Reading protein sequence data file.
# File containing the sequence data
my $fastafilename = 'contig2_MT.fa';
# First we have to "open" the file
open(FASTAFILE, $fastafilename) || die $!;
# Read the fastafrom file, and store it
# into the array variable @protein
@fasta = <FASTAFILE>;
# Print the protein onto the screen
print @fasta;
# Close the file.
close FASTAFILE;
exit;
36
LAB: get a file in FASTA format
http://www.ncbi.nlm.nih.gov/
37
LAB: navigate to GenBank
38
LAB: search for your favorite protein
39
LAB: favorite protein entries, change display
40
LAB: change display to FASTA
41
LAB: we return to our
program, already in
progress
% pico kinase.fa
#!/usr/bin/perl -w
#
# Reading protein sequence data file.
# File containing the sequence data
my $fastafilename = 'kinase.fa';
% pico files2arrays.pl
# First we have to "open" the file
open(FASTAFILE, $fastafilename) || die $!;
Add the name of the
FASTA file you created to
the program.
# Read the fastafrom file, and store it
# into the array variable @protein
@fasta = <FASTAFILE>;
Run the program.
# Print the protein onto the screen
print @fasta;
# Close the file.
close FASTAFILE;
exit;
42
LAB: break it.
What happens when?:
1.
You added the file?
2.
Did the error message go away?
How would you protect your user from an error
like this?
3.
Did you think that was harder than it needed to be?
43
LAB: a safer method
% pico files2arrays.pl
% ./files2arrays.pl
Run the program.
#!/usr/bin/perl -w
# Reading data from a file using a loop
# File containing the sequence data
my $fastafilename = 'kinase.fa';
open(FASTAFILE, $fastafilename) || die $!;
# Read file one line at a time and print
while ($protein = <FASTAFILE>) {
print $protein;
}
close FASTAFILE;
exit;
44
LAB:
breaking it.
Why is this
more safe
than reading
the file into an
array?
#!/usr/bin/perl -w
# Reading data from a file using a loop
# File containing the sequence data
my $fastafilename = 'kinase.fa';
open(FASTAFILE, $fastafilename) || die $!;
# Read file one line at a time and print
while ($protein = <FASTAFILE>) {
print $protein;
}
close FASTAFILE;
exit;
45
A brief break
46
Scope
TM proctor & gamble
• Section or subsection of a program where a
variable is valid.
• Defined by braces { }
• Use ‘my’ to declare variables.
• use
strict;
variables.
• use
warnings;
# mandates declaration of
# or ‘-w’ on shebang line
47
47
Good practices
•
‘my’ operator declares a variable or a list of variables to be local (private)
to the enclosed block, subroutine, or file. It will also be recognized in
blocks contained by that region.
•
The region in which the private variable is recognized is called its scope,
variables declared with ‘my’ are called lexically scoped variables.
•
Lexical (private) variables are not recognized outside of their scope.
•
A private variable of a function will not be recognized in another function
called by that function. If you want that to happen, declare the variable as
‘local’.
•
It is recommended that you declare all of your variables with ‘my’.
48
48
Someone else’s code
@list = (‘aardvark’, ‘baboon’, ‘cat’,
‘dog’,’lamb’,’kangaroo’);
for $animal ( @list )
if( length($animal)
print “$animal is
} else {
print “$animal is
}
}
{
<= 3 ) {
noisy\n”;
quiet\n”;
49
49
Made more safe.
use warnings;
use strict;
my @list = (‘aardvark’, ‘baboon’, ‘cat’,
‘dog’,’lamb’,’kangaroo’);
for my $animal ( @list ) {
if( length($animal) <= 3 ) {
print “$animal is noisy\n”;
} else {
print “$animal is quiet\n”;
}
}
50
50
Associative arrays or Hashes
Array
5
‘sue’
4
‘juan’
3
‘max’
2
‘aaron’
1
‘steve’
‘john’
0
Hash
apple
12
pear
3
cherry
30
lemon
2
peach
6
kiwi
3
51
51
Associative arrays or Hashes
• Like arrays, but instead of numbers as indices
hashes use strings.
my @array = (‘john’, ‘steve’, ‘aaron’,
‘max’, ‘juan’, ‘sue’);
my %fruithash = ( ‘apple’ => 12, ‘pear’ =>
3, ‘cherry’ =>30, ‘lemon’ => 2, ‘peach’ =>
6, ‘kiwi’ => 3);
52
52
Using hashes
• { } operator
• Set a value
$fruithash{‘cherry’} = 10;
• Access a value
print $fruithash{‘cherry’}, “\n”;
• Remove an entry
delete $fruithash{‘cherry’};
53
53
Get the Keys
• ‘keys’ function will return a list of the hash keys
my @keys = keys %fruithash;
for my $key ( keys %fruithash ) {
print “$key => $hash{$key}\n”;
}
• produces: ‘apple’, ‘pear’, ...
• Order of keys is NOT guaranteed!
54
54
Get just the values
• Similarly:
# creates an array of hash values
my @fruitcnt = values %fruithash;
for my $itemcount ( @fruitcnt ) {
print “val is $itemcount\n”;
}
55
55
Iterate through a set
• Order is not guaranteed!
while( my ($key,$value) = each %fruithash){
print “$key => $value\n”;
}
56
56
References
• Are “pointers” to the data object instead of object
itself.
• A shorthand to refer to a variable and pass it
around.
• Must “dereference” whatever is pointed at to get its
actual value, the “reference” is just a location in
memory.
57
57
Reference Operators
•
\ in front gets its memory location
my $ptr = \@vals;
• Pointers can be assigned directly:
•[
] for arrays, { } for hashes
my $ptr = [ (‘owlmonkey’, ‘lemur’)];
my $hashptr = { ‘cdrom’ => ‘III’,
‘start’ => 23};
58
58
Dereferencing
• Need to cast reference back to datatype:
my @list = @$ptr;
my %hash = %$hashref;
• Can also use ‘{ }’ to clarify
my @list = @{$ptr};
my %hash = %{$hashref};
59
59
Really not so hard...
my @list = (‘fugu’, ‘human’, ‘worm’, ‘fly’);
my $list_ref = \@list;
my $list_ref_copy = [@list];
for my $item ( @$list_ref ) {
print “$item\n”;
}
60
60
Why use references?
• Simplify argument passing to subroutines
• Allows updating data without making multiple copies.
• What if we wanted to pass in 2 arrays to a
subroutine?
sub func { my (@v1,@v2) = @_; }
• How do we know when one stops and another
starts?
61
61
Why use references?
• Passing in two arrays to intermix.
sub func {
my ($v1,$v2) = @_;
my @mixed;
while( @$v1 || @$v2 ) {
push @mixed, shift @$v1 if @$v1;
push @mixed, shift @$v2 if @$v2;
}
return \@mixed;
}
62
62
References also allow Arrays of Arrays
my @lst;
push @lst, [‘milk’, ‘butter’, ‘cheese’];
push @lst, [‘wine’, ‘sherry’, ‘port’];
push @lst, [‘bread’, ‘bagels’, ‘croissants’];
my @matrix = [ [1, 0, 0],
[0, 1, 0],
[0, 0, 1] ];
63
63
Hashes of arrays
$hash{‘dogs’} = [‘beagle’, ‘shepherd’, ‘lab’];
$hash{‘cats’} = [‘calico’, ‘tabby’, ‘siamese’];
$hash{‘fish’} = [‘gold’,’beta’,’tuna’];
for my $key (keys %hash ) {
print “$key => “, join(“\t”, @{$hash{$key}}), “\n”;
}
64
64
Subroutines
• Set of code that can be
reused.
• Can also be referred to as
procedures and functions.
the result of re• Often
factoring and refining your
solution.
little to do with
• Have
submarines.
65
65
Defining a subroutine
•
sub routine_name { }
•
Calling the routine:
# declaring a subroutine
routine_name;
&routine_name;
# & is optional
66
66
Passing data to a subroutine
• Pass in a list of data
&dosomething($var1,$var2);
sub dosomething {
my ($v1,$v2) = @_;
}
sub dosomethingelse {
my $v1 = shift @_;
my $v2 = shift;
}
67
67
Returning data from a subroutine
• The last line of the routine sets the return value.
sub dothis {
my $c = 10 + 20;
}
print dothis(), “\n”;
• Better to specify return value and/or a condition to leave
routine early.
68
68
Subroutine returns true (1) if codon is a stop codon
(standard genetic code)
sub is_stopcodon {
my $val = shift @_;
if( length($val) != 3 ) {
return -1;
} elsif( $val eq ‘TAA’ || $val eq ‘TAG’ ||
$val eq ‘TGA’ ) {
return 1;
} else {
return 0;
}
}
69
69
#!/usr/bin/perl -w
# A program with a subroutine to append AAAAT to DNA
LAB: subroutines
% pico subroutine.pl
# The original DNA
$dna = 'CGACGTCTTCTCAGGCGA';
# The call to the subroutine "addPOLYA".
# argument passed in is $dna; result is $longer_dna
$longer_dna = addPOLYA($dna);
print "I added AAAAT to $dna and got $longer_dna\n\n";
# Here is the definition for subroutine "addPOLYA"
sub addPOLYA {
my($dna) = @_;
$dna .= 'AAAAT';
return $dna;
}
exit;
70
LAB: break it.
Can you?:
1.
Create better variable names?
Find a potential problem with subroutines and variable
scope?
2.
3.
Get it to work with GLOBAL variables?
4.
Explain why this might be a problem?
71
LAB: add to it.
Can you?:
1.
Find another way to concatenate the strings?
Add a subroutine that provides a reverse transcription
service?
2.
Test for a poly-A tail before adding a poly-A tail and add
one only if it isn’t already there?
3.
Create a file of FASTA entries and run them through your
program?
4.
72
Funny operators
my @bases = qw(C A G T);
my $msg = <<EOF
In his return from the ship to New York, he was
discovered by the enemy as he passed near Governors
Island, They took chase and in an effort to escape,
Ezra Lee cast off the timed mine, as he imagined it
retarded him in the heavy swells of the harbor. He was
then spotted by his men waiting for his return on the
shore and was safely retrieved. The freed magazine,
which was set to go off at one hour, “drifted past
Governors Island into the East River where it exploded
with great violence, throwing large columns of water
and pieces of wood high in the air.”
EOF
;
73
73
Regular Expressions (reg’-ex)
• Part of “amazing power” of Perl
• Considered by some to be the heart and soul of Perl.
• Provide a set of very powerful and flexible facilities for
parsing and manipulating text.
• Syntax can be tricky.
• Worth the effort to learn!
• Do not be afraid.
74
74
Regular Expressions: the secret
• Regular Expressions represent a small, nearly
unrelated, programming language within the Perl
programming language.
• ‘Regexes’ are symbiotic DNA.
• A state machine operating on strings.
• Do not be afraid.
75
75
A simple regex
if( $fruit eq ‘apple’ ||
$fruit eq ‘Apple’ ||
$fruit eq ‘pear’) {
print “ matched fruit $fruit\n”;
}
# becomes this
if( $fruit =~ /[Aa]pple|pear/ ){
print “matched fruit $fruit\n”;
}
76
76
Regular Expression syntax
• use the =~ operator to match
•
•
•
•
•
•
if( $var =~ /pattern/ ) {}
# scalar context
my ($a,$b) = ( $var =~ /(\S+)\s+(\S+)/ );
if( $var !~ m// ) { }
m/REGEXPHERE/
# true if pattern doesn’t
# match
s/REGEXP/REPLACE/
# substitute
tr/VALUES/NEWVALUES/
# translate
77
77
DNA ambiguity chars: (reverse compliment)
• aMino - {A,C}, Keto - {G,T}
• puRines - {A,G}, prYmidines - {C,T}
• Strong - {G,C}, Weak - {A,T}
• H (Not G)- {ACT}, B (Not A), V (Not T), D(Not C)
$str =~ tr/
acgtrymkswhbvdnxACGTRYMKSWHBVDNX/
tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/;
78
78
m// operator (match)
• Search a string for a pattern match
• If no string is specified, will match $_
• Pattern can contain variables which will be interpolated (and
pattern recompiled)
while (<>) {
print if /$pat/;
}
while (<>) {
print if /$pat/o;
}
79
79
Pattern extras: suffixes
•
/i # case insensitive
•
/g # global match (more than one)
•
/x # extended regex (comments and whitespace)
•
/o # compile regex once
80
80
Regex Operators
\
.
x!
^x !
[x] !
escape character - used to a metacharacter like a period, brackets, etc.
(period) match any character except newline
match any instance of x
match any character except x
match any instance of x in the bracketed range - [abxyz] will match any
instance of a, b, x, y, or z
|
(pipe) an OR operator - [x|y] will match an instance of x or y
() ! used to group sequences of characters or matches
{} ! used to define numeric quantifiers
{x} ! match must occur exactly x times
{x,} !match must occur at least x times
{x,y} !match must occur at least x times, but no more than y times
? ! preceding match is optional or one only, same as {0,1}
* ! find 0 or more of preceding match, same as {0,}
+ ! find 1 or more of preceding match, same as {1,}
^ ! match the beginning of the line
$ ! match the end of a line
81
Regex: Character Operators
\d !matches a digit, same as [0-9]
\D !matches a non-digit, same as [^0-9]
\s ! matches a whitespace character (space, tab, newline, etc.)
\S ! matches a non-whitespace character
\w !matches a word character
\W !matches a non-word character
82
Regex: POSIX Operators
[:alnum:] !alphabetic and numeric characters
[:alpha:] ! alphabetic characters
[:blank:] !
space and tab
[:cntrl:] ! control characters
[:digit:] ! digits
[:graph:] ! non-blank (not spaces and control characters)
[:lower:] ! lowercase alphabetic characters
[:print:] ! any printable characters
[:punct:] ! punctuation characters
[:space:] ! all whitespace characters (includes [:blank:], newline, carriage return)
[:upper:] ! uppercase alphabetic characters
[:xdigit:] ! digits allowed in a hexadecimal number (i.e. 0-9, a-f, A-F)
83
Regex: Additional Modules, 180+ found
POSIX::Regex
OO interface for the gnu regex engine
POSIX-Regex-0.89 - 18 Aug 2006 - Paul Miller
Regexp::Common::number
provide regexes for numbers
Regexp-Common-2.120 - 15 Mar 2005 - Abigail
Regexp::Common
Provide commonly requested regular
expressions
Regexp-Common-2.120 - 15 Mar 2005 - Abigail
Regexp::Common::profanity
provide regexes for profanity
Regexp-Common-2.120 - 15 Mar 2005 - Abigail
Regexp::Common::CC
provide patterns for credit card numbers.
Regexp-Common-2.120 - 15 Mar 2005 - Abigail
Regexp::English
Perl module to create regular expressions
more verbosely
Regexp-English-1.00 - 10 Jul 2005 - chromatic
Regexp::Common::IRC
provide patterns for parsing IRC messages
Regexp-Common-IRC-0.02 - 18 Dec 2005 Chris Prather
Regexp::Ethiopic
Regular Expressions Support for Ethiopic
Script.
Regexp-Ethiopic-0.15 - 22 Nov 2006
Regexp::Common::URI
provide patterns for URIs.
Regexp-Common-2.120 - 15 Mar 2005 - Abigail
84
Simple regex
my $line = “aardvark”;
if( $line =~ /aa/ ) {
print “has a double aa\n”
}
if( $line =~ /(a{2})/ ) {
print “has double aa\n”
}
if( $line =~ /(a+)/ ) {
print “has 1 or more a\n”
}
85
85
Matching gene names
# YFL001C YAR102W - yeast ORF names
# let-1, unc-7 - worm names
# ENSG000000101 - human Ensembl gene names
while(<IN>) {
if( /^(Y([A-P])(R|L)(\d{3})(W|C)(\-\w)?)/ ) {
printf “yeast gene %s, chrom %d,%s arm, %d %s strand\n”,
$1, (ord($2)-ord(‘A’))+1, $3, $4;
} elsif( /^(ENSG\d+)/ ) { print “human gene $1\n” }
elsif( /^(\w{3,4}\-\d+)/ ) { print “worm gene $1\n”; }
}
86
86
Regex GenBank record into FASTA components
my ($anno, $dna) = ($rec =~ /^(LOCUS.*ORIGIN\s*\n)(.*)\/\/\n/s);
LOCUS appears at the beginning of the GenBank record,
followed by any number of characters including newlines
with .*, followed by the string ORIGIN, followed by possibly
some whitespace with \s*, followed by a newline \n.
This matches the annotation part of the GenBank record.
87
87
Putting it together
A parser for output from a gene
prediction program
88
88
GlimmerM (Version 3.0)
Sequence name: BAC1Contig11
Sequence length: 31797 bp
Predicted genes/exons
Gene Exon Strand Exon
#
#
Type
Exon Range
Exon
Length
1
1
1
1
1
1
2
3
4
5
+
+
+
+
+
Initial
Internal
Internal
Internal
Terminal
13907
14117
14635
14746
15497
13985
14594
14665
15463
15606
79
478
31
718
110
2
2
2
1
2
3
+
+
+
Initial
Internal
Terminal
20662
21190
21624
21143
21618
21990
482
429
367
3
1
-
Single
25351
25485
135
4
4
4
4
4
4
1
2
3
4
5
6
+
+
+
+
+
+
Initial
Internal
Internal
Internal
Internal
Terminal
27744
27858
28091
28636
28746
28852
27804
27952
28576
28647
28792
28954
61
95
486
12
47
103
5
3
-
Terminal
29953
30037
85
89
89
Putting it together
while(<>) {
if(/^(Glimmer\S*)\s+\((.+)\)/ {
$method = $1; $version = $2;
} elsif( /^(Predicted genes)|(Gene)|(\s+\#)/ ||
/^\s+$/ ) { next
} elsif(
# glimmer 3.0 output
/^\s+(\d+)\s+
# gene num
(\d+)\s+
# exon num
([\+\-])\s+
# strand
(\S+)\s+
# exon type
(\d+)\s+(\d+) # exon start, end
\s+(\d+)
# exon length!
/ox ) {
my ($genenum,$exonnum,$strand,$type,$start,$end,
$len) = ( $1,$2,$3,$4,$5,$6,$7);
}
}
90
90
Day II: assignment.
1. Modify one of your existing programs to do something useful
using a Regular Expression. (see the last lab)
2. Read about Perl DBI. (Safari on-line documentation is available.)
3. Read about BioPerl. (Safari and CPAN)
4. Write a paragraph describing what you hope to do with Perl in
your BSI project and email it to me. ([email protected])
91
If you remember nothing else
•Biology is hard and messy: better tools will help.
•The key problems are social.
•Together we are smarter than any one of us.
•Technology is easy by comparison.
92
Questions?
93
Thank You.
94