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Using Modules. Module Example. Next I will describe a very simple implementation of a perl module. This will be the minimum amount of information needed to use modules as intended.
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Module Example Next I will describe a very simple implementation of a perl module. This will be the minimum amount of information needed to use modules as intended. This is useful for when we attempt to use modules (such as File::Basename), we'll have a better understanding of what they are.
Exporting • require Exporter; # a package written to do symbol (variable) exporting • @ISA = qw(Exporter); # "is a" is simply an array that specifies to perl the classes/packages to search for methods/subroutines # mechanism for inheritance that we'll come back to # sufficient to know that if you omit this, perl modules will not work as described here # Note that on quoted words – you may define your own boundary chars • @EXPORT = qw(&say_hello $text); # lists the symbols that are exported • reference: perldoc Exporter
#!/usr/bin/perl # main.pl # #require "Silly.pm"; # Note no quotes, or .pm use Silly; my $name = "Terry"; #Silly::say_hello($name); # We don't know what this SR does yet &say_hello($name); # Don't know what the value of this is either print "The _text_ in Silly = $text\n"; #Hello Terry #The text in Silly = Terry # Silly.pm package Silly; #package statement require Exporter; #we now know what this means @ISA = qw(Exporter); #technically we know what is going on @EXPORT = qw(&say_hello $text); $text=""; # Note, I did not use "my" # "my" would make it local to this package # so even though it is "exported", it would # not be available to the "main" sub say_hello { $text = $_[0]; # Why don't I do $text = shift ???? print "Hello $text\n"; } 1; Example (use)
#!/usr/bin/perl # main.pl # require "Silly.pm"; #use Silly; my $name = "Terry"; Silly::say_hello($name); #&say_hello($name); print "The _text_ in Silly = $Silly::text\n"; package Silly; #package statement require Exporter; #we now know what this means #QUESTION: why no ".pm" here, # that is used in main.pl???? # Answer: could have done require Silly # (no quotes) @ISA = qw(Exporter); #technically we know what is going on @EXPORT = qw(&say_hello $text); $text=""; # Note, I did not use "my" # "my" would make it local to this package # so even though it is "exported", it would # not be available to the "main" sub say_hello { $text = $_[0]; # Why don't I do $text = shift ???? print "Hello $text\n"; } 1; Example (require)
POD perldoc perlpod • NAME • perlpod − the Plain Old Documentation format • DESCRIPTION • Pod is a simple‐to‐use markup language used for writing documentation for Perl, Perl programs, and Perl modules. • Allows you to intersperse codes and comments (if you like). • You can also put all of your documentation at the end of your code following a :__END__
POD All command paragraphs (which are typically only one line long) start with "=", followed by an identifier, followed by arbitrary text that the command can use however it pleases. Currently recognized commands are =head1 Heading Text =head2 Heading Text =head3 Heading Text =head4 Heading Text =over indentlevel =item stuff =back =cut =pod =begin format =end format =for format text...
Process • Markup your module • podchecker (can check syntax) • pod2text (to see your documentation) • perldoc NameOfYourModule.pm • perldoc Silly-doc.pm
Annoyance • The formatting markup requires blank spaces before/after each line (rather annoying).
Example =head1 NAME Silly -- example of a perl module =head1 SYNOPSIS use Silly; say_hello("any text"); print "The _text_ in Silly = $text\n"; =head1 DESRIPTION These routines have no useful function whatsoever. =cut This is all text that is displayed by perldoc Marks end of formatting, or the start of real code
package Silly; #package statement require Exporter; #we now know what this means @ISA = qw/Exporter/; #technically we know what is going on @EXPORT = qw(&say_hello $text); $text=""; # Note, I did not use "my" # "my" would make it local to this package # so even though it is "exported", it would # not be available to the "main" =over 4 =item say_hello($string) This function takes a string and simply prints it to the screen proceeded by the text 'Hello '. The string is also stored in local variable $text; =cut Start of itemized List – indented by 4 spaces Item tag – followed by description
sub say_hello { $text = $_[0]; # Why don't I do $text = shift ???? print "Hello $text\n"; } =back =cut 1; End of itemized list
Very Basic Intro to BLAST • Basic Local Alignment Search Tool • Application to search for 1 sequence against a database of sequences • Note, that the database of sequences may be a single sequence itself, so that BLAST may be used to compare 2 sequences • Nucleotide to nucleotide • Amino acid to amino acid (protein) • Nucelotide to aa • aa to nt • etc.
Example http://www.ncbi.nlm.nih.gov/BLAST/
Pairwise Sequence Alignment Example • Example: S1: TTACTTGCC (9 bases) S2: ATGACGAC (8 bases) • Scoring (1 possibility): +2 match 0 mismatch -1 gap in either sequence • One Possible alignment: T T - A C T T G C C A T G A C - - G A C 0 2-1 2 2-1-1 2 0 2 Score = 10 – 3 = 7
Cue to a Data Structure Gap in S2 Gap in S1 Alignment (match/mismatch)
How hard can this be? • Brute force approach: consider all possible alignments, and choose the one with best score • 3 choices at each internal branch point • Assume n x n comparison. 3n comparisons • n = 3 33 = 27 paths • n = 20 320 = 3.4 x 109 paths • n = 200 3200 = 2.6 x 1095 paths • If 1 path takes 1 nanosecond (10-9 secs) • 8.4 x 1078 years! • But, using data structures cleverly, this can be greatly sped up to O(n2)
