Using Libraries

1
Using Libraries
2
To or not to Function(perldoc perlsub)

• A subroutine may be called using an explicit ""
  prefix. The "" is
• optional in modern Perl, as are
  parentheses if the subroutine has been
• predeclared. The "" is not optional when
  just naming the subroutine,
• such as when its used as an argument to
  defined() or undef(). Nor is
• it optional when you want to do an
  indirect subroutine call with a
• subroutine name or reference using the
  "subref()" or "subref()"
• constructs, although the "subref-gt()"
  notation solves that problem.
• See perlref for more about all that.
• Subroutines may be called recursively. If
  a subroutine is called using
• the "" form, the argument list is
  optional, and if omitted, no _at__
• array is set up for the subroutine the _at__
  array at the time of the
• call is visible to subroutine instead.
  This is an efficiency mechanism
• that new users may wish to avoid.

3
-- continued

• foo(1,2,3) pass three
  arguments
• foo(1,2,3) the same
• foo() pass a null list
• foo() the same
• foo foo() get
  current args, like foo(_at__) !!
• foo like foo() IFF
  sub foo predeclared, else "foo"
• Not only does the "" form make the
  argument list optional, it also
• disables any prototype checking on
  arguments you do provide. This is
• partly for historical reasons, and partly
  for having a convenient way
• to cheat if you know what youre doing.
  See Prototypes below.

4
Sharing Code

• Another advantage is that programmers can reuse
  my subroutines, and vice-versa.
• "Bob" writes a subroutine called
  "reverse_complement", and some other subroutines,
  and stores these in a file called
  "BseqProcess.pl"
• I can use "reverse_complement" with
• do "BseqProcess.pl"
• Code is brought in from separate files
• 1) easier to maintain
• 2) permits inter-programmer cooperation

5
Using "do"

• Suppose that "Bob" used my "print_formatted_sequen
  ce" by using "do sequence_pro.pl" in
  "BseqProcess.pl"
• !/usr/bin/perl
• BseqProcess.pl
• do sequence_pro.pl
• sub reverse_complement
• Then I also use a "do sequence_pro.pl" -- these
  subroutines will be pulled in twice (and generate
  a warning with w)
• !/usr/bin/perl
• my_program
• do BseqProcess.pl
• do sequence_pro.pl done twice, since done in
  BseqProcess.pl too

6
require

• "require" is a mechanism that tracks what files
  have been brought in and brings them in only
  once.
• require "sequence_pro.pl"
• require "BseqProcess.pl"
• Note last expression evaluated in the file must
  return a true value thus most files evaluated
  for "require" have a cryptic "1" as the last
  line. This is simply an annoying relic that was
  never removed from the language.
• IS this in the module book????
• SHOW formated_seq.pl

7
formatted_seq.pl

• !/usr/bin/perl
• formatted_seq.pl
• require 'sequence_pro.pl'
• seq "ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAccc
  ccccccccccccccccccccccccccccccccccccccccccccccccgg
  gggggggggggggggggggggggggggggggggggggggggggggggggg
  ggggggggggggggggggggggggggggggggggggggggggggggggg"
  
• print_formatted_sequence(seq,50,10)

8
sequence_pro.pl

• sequence_pro.pl
• sub print_formatted_sequence
• if(_!2)
• die("Error in Seqprint_formatted_sequence.
  Expecting 3 parameters\n")
• my (seq,line_length,seq_length) _at__
• seq_length block length -- bad choice of
  variable name
• example line_length 20, seq_length 5
• AAAAA AAAAA AAAAA AAAAA
• my front 1
• my back line_length
• remainder seq

• while(length(remainder)gtline_length)
• _ remainder
• (format,remainder) m/(.line_length)(.)/
  match a line, then the rest
• format 1, and remainder 2
• format s/(.seq_length)/1 /g match for
  10, then insert a space
• print "front format back\n"
• front front line_length
• back back line_length
• format remainder
• format s/(.seq_length)/1 /g
• back front length(remainder)-1
• print "front format back\n"
• 1

9
Libraries and Programs
It just works
A better way to organize code.
/home/tabraun/proj
/home/tabraun/proj
tlate.pl
sequence_pro.pl tlate.pl Seq.pm SeqIO.pm BPlite.p
m
/home/tabraun/perl/local/lib sequence_pro.pl
/home/tabraun/perl/bioperl-0.7.1/ Seq.pm SeqIO.pm
BPlite.pm
How will perl know to look in /local/lib and
bioperl-0.7.1 ????
10
_at_INC

• Terminology
• main code (program) the program that calls
  subroutines
• included files (library) collection of shared
  subroutines, software library
• What is the directory structure of the "main
  code" and the "included files"?
• It "just works" for the simplest case, in which
  the program and the "libraries" are in the same
  directory, and you run the program from that
  directory.
• Its not practical to have all shared libraries in
  the "current working directory" ideally these
  would be organized into specific subdirectories.
• Perl, searches for libraries along a "library
  search path", similar to what UNIX "shells" do
  with the PATH environment variable.
• The current directory is included in this "search
  path", so as long as your libraries are in the
  current working directory, it "just works."

11
_at_INC

• the "search path" is given in a special variable
  called _at_INC
• perl V
• (lots of stuff)
• _at_INC
• /home/tabraun/perl/bioperl-live//ensembl/modul
  es
• /home/tabraun/perl/bioperl-live//bioperl-0.7
• /home/tabraun/perl/bioperl-live//ensembl-exter
  nal/modules
• /home/tabraun/perl/bioperl-live//ensembl-lite/
  modules
• /usr/lib/perl5/5.8.0/i386-linux-thread-multi
• /usr/lib/perl5/5.8.0
• /usr/lib/perl5/site_perl/5.8.0/i386-linux-thre
  ad-multi
• /usr/lib/perl5/site_perl/5.8.0
• /usr/lib/perl5/site_perl
• /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-th
  read-multi
• /usr/lib/perl5/vendor_perl/5.8.0
• /usr/lib/perl5/vendor_perl
• /usr/lib/perl5/5.8.0/i386-linux-thread-multi
• /usr/lib/perl5/5.8.0

12
Extending _at_INC Programatically

• typically, users cannot alter the content of
  default directories in _at_INC
• _at_INC is an ordinary array
• may add libraries by modifying _at_INC
• unshift _at_INC, "/home/tabraun/perl/local/lib"
• For this program, perl will search (first) in
  this directory -- Why?

13
Extending _at_INC on the System

• Recall my "100" programs that used
  "sequence_pro.pl"
• To programatically add "/home/tabraun/perl/local/l
  ib" to each one would be 100 different edits
• Alternatively, a system variable may be set to
  tell perl where to look (so 100 programs don't
  have to be changed).
• env (tells me what my shell is)
• csh
• setenv PERL5LIB /home/tabraun/perl/local/lib
• BASH
• PERL5LIB/home/tabraun/perl/local/lib export
  PERL5LIB
• Advantage set it once, and forget it
• Disadvantage
• someone else wanting to use your library would
  need the same variable set

14
-I (Include)

• Yet another way
• perl I/home/tabraun/perl/local/lib
  /home/bob/perl-program

15
Namespace Collisions

• Terry has created sequence_pro.pl
• Bob has created BseqProcess.pl that has
  incorporated sequence_pro.pl
• !/usr/bin/perl
• BseqProcess.pl
• require "sequence_pro.pl"
• sub reverse_complement
• print_formatted_sequence(seq,50) Terry's sub
• Everything works fine.
• Now I modify sequence_pro.pl, and add a
  subroutine called reverse_complement (which is
  already in BseqProcess.pl Bob's)

16
Namespace Collision Solutions

• One particularly BAD solution, is for Terry to
  add a prefix to every scalar, subroutine, array,
  and hash, such as "sequence_pro_"
• Every reference to a subroutine/variable in
  "sequence_pro" would have this prefix
  "sequence_pro_
• Now Bob's looks like
• !/usr/bin/perl
• BseqProcess.pl
• require "sequence_pro.pl"
• sub reverse_complement
• sequence_pro_print_formatted_sequence(seq,50)
  Terry's sub
• Awkward for Terry

17
Solution in Perl is Packages

• The problem with the previous solution is that
  "name prefix" had to be spelled out in every
  instance.
• Alternative is "Package"

18

• package Sequence_pro declaring a package
• sub print_formatted_sequence
• sub reverse_complement
• 1
• The package declaration tells Perl to insert
  "Sequence_pro in front of most names within the
  file.
• Essentially, the code behaves like this
• sub Sequence_proprint_formatted_sequence
• sub Sequence_proreverse_complement
• 1

19
Require'ing a Package

• Now Bob may use the Sequence_pro library, and
  simply adds Sequence_pro to subroutines defined
  in the library.
• !/usr/bin/perl
• require 'sequence_pro2.pl'
• sub reverse_complement
• Sequence_proprint_formatted_sequence(seq,50)
• The Sequence_pro prefix is left off for
  subroutines he wants to define on his own.
• (Look at formatted_seq2.pl and sequence_pro2.pl)

20
formatted_seq.pl

• !/usr/bin/perl
• require 'sequence_pro2.pl'
• seq "ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAccc
  ccccccccccccccccccccccccccccccccccccccccccccccccgg
  gggggggggggggggggggggggggggggggggggggggggggggggggg
  ggggggggggggggggggggggggggggggggggggggggggggggggg"
  
• print_formatted_sequence(seq,50,10)
• print_sequence(seq,50,10)
• sub print_sequence
• Sequence_proprint_formatted_sequence(_0,_
  1,_2)

21
sequence_pro2.pl

• package Sequence_pro
• sub print_formatted_sequence
• if(_!2)
• die("Error in Seqprint_formatted_sequence.
  Expecting 3 parameters\n")
• my (seq,line_length,seq_length) _at__
• my front 1
• my back line_length

• remainder seq
• while(length(remainder)gtline_length)
• _ remainder
• (format,remainder) m/(.line_length)(.)/
  match a line, then the res
• t
• format s/(.seq_length)/1 /g match for
  10, then insert a space
• print "front format back\n"
• front front line_length
• back back line_length
• format remainder
• format s/(.seq_length)/1 /g
• back front length(remainder)-1
• print "front format back\n"
• 1

22
Package Names

• similar to perl variable names
• alphanumerics and underscores
• no first digit
• convention
• to use capital letter as first letter
• do not use same name as existing modules (core
  and CPAN) comes with experience
• may contain multiple names/double colons
• UtilsSequenceAlignment
• Reference
• perldoc perlmodlib (description of included
  modules)
• man perlmodlib

23
Packages and Variables

• may access variables in a package
• package Sequence_pro
• sequence "ATG"
• sub print_formatted_sequence
• 1
• Then, in "main" program
• seq Sequence_prosequence

24
Perldoc perlmodlib

• Perl does not enforce private and public parts of
  its modules as you
• may have been used to in other languages
  like C, Ada, or Modula-17.
• Perl doesnt have an infatuation with
  enforced privacy. It would
• prefer that you stayed out of its living
  room because you werent
• invited, not because it has a shotgun.
• The module and its user have a contract,
  part of which is common law,
• and part of which is "written". Part of
  the common law contract is
• that a module doesnt pollute any
  namespace it wasnt asked to. The
• written contract for the module (A.K.A.
  documentation) may make other
• provisions. But then you know when you
  "use RedefineTheWorld" that
• youre redefining the world and willing to
  take the consequences.

25
End