Introduction%20to%20LISP%20Programming%20of%20Pathway%20Tools%20Queries%20and%20Updates

1
Introduction to LISP Programming of Pathway
Tools Queries and Updates
2
Myths and Facts About Lisp

• Myth Lisp runs interpreted only
• Fact All major Lisp implementations have
  compilers
• Myth Lisp uses huge amounts of memory
• Fact Baseline Lisp installation requires 8-10MB
• Myth Lisp is complicated
• Fact Lisp is much simpler and more elegant than
  Perl

3
LISP and GFP References

• Lisp on the web ALU.org
• ANSI Common LISP
• Paul Graham
• Common LISP, the Language -- The standard
  reference
• Guy L. Steele
• On Common LISP
• Paul Graham
• The Art of the Metaobject Protocol
• Kiczales, Rivieres, Bobrow
• Information on writing Pathway Tools queries
• http//bioinformatics.ai.sri.com/ptools/ptools-res
  ources.html
• http//www.ai.sri.com/pkarp/loop.html
• http//bioinformatics.ai.sri.com/ptools/debugger.h
  tml

4
Accessing Lisp through the Pathway Tools

• Starting Pathway Tools for Lisp work
• pathway-tools lisp
• (select-organism org-id XXX)
• Lisp expressions can be typed at any time to the
  Pathway Tools listener
• Command (get-slot-value trp common-name) -gt
  L-tryptophan
• Invoking the Navigator from Lisp
• (eco)

5
LISP Syntax

• Prefix notation
• Simple and clean syntax
• Expressions are delimited by parentheses
• The same syntax is used for programs and for data
• (1 2 3 4 5 10 10)
• (a b c d e f)
• ( 1 2)
• (subseq abcdefg 0 2)

6
LISP Expressions and Evaluation

• ( 3 4 5)
• is a function
• ( 3 4 5) is a function call with 3 arguments
• Arguments are evaluated
• Numbers evaluate to themselves
• If any of the args are themselves expressions,
  they are evaled in the same way
• ( 1 ( 3 4))
• The values of the args are passed to the function
• Because of prefix notation, variable number of
  args
• () ---gt 0
• ( 1) ---gt 1
• ( 2 3 1 3 4 5 6) ----gt 24
• ( ( 3 4) 6) --gt 18
• Turning off evaluation with Quote
• ( 1 3) ----gt ( 1 3)

7
LISP Listener

• Also called top level and read-eval-print
  loop
• Expressions typed in listener are evaluated
  interactively
• Uses a three-step process
• Read
• Reader converts elements outside and to
  uppercase
• Evaluate
• Print
• Useful forms in listener
• Previous Results , ,
• DO NOT use in programs
• ( 1 2)
• -gt 3
• ( 3 )
• -gt 6
• -gt 3

8
LISP Data Types

• Usual types in other languages
• Numbers -- 2, 312, 1.45, -222e2
• Strings -- sky, this is a lisp intro
• Characters - \D, \space
• Hashtables
• True/False T / NIL
• Fundamental LISP data types
• Symbols - BLUE, CONT
• Lists - (1 2 3) (a b c) (a 2 X)

9
Lisp Variables

• Global variable values can be set and used during
  a session
• Declarations not needed
• (setq x 5)
• -gt 5
• x
• -gt 5
• ( 3 x)
• -gt 8
• (setq y atgc)
• -gt atgc

10
Examples

• (select-organism org-id ecoli)
• -gt ECOLI
• (setq genes (get-class-all-instances Genes))
• -gt ()
• (setq monomers (get-class-all-instances
  Polypeptides))
• -gt (.)
• (setq genes2 genes)
• -gt (.)

11
LISP Lists

• Fundamental to LISP LISt Processing
• Zero or more elements enclosed by parentheses
• Typing a list to the listener
• (this is a list) gt (THIS IS A LIST)
• Creating a list with functions
• (list so is this) gt (SO IS THIS)
• Examples
• (1 3 5 7), ((2 4 6) 10 (0 8)), (1 this T NIL
  that)
• The empty list nil ()

12
List Examples

• (length genes)
• -gt 4316
• (first genes)
• -gt XXX
• (subseq genes 0 50)
• -gt ()
• (nth 3 genes)
• -gt XXX

13
Functions for Operating on Lists

• Length
• (length x)
• Returns the number of elements in the list X
• First
• (first x)
• Returns the first element in the list X
• Subseq
• (subseq x j k)
• Returns a newly created list containing a
  subsequence of list X, starting at element number
  J and ending before element number K
• Nth
• (nth j x)
• Returns the Jth element of list X (element 0 is
  the first element)

14
Equality in LISP

• Internally LISP refers to objects via pointers
• Fundamental equality operation is EQ
• True if the two arguments point to the same
  object
• Very efficient
• Other comparison operators
• for numbers ( x 4)
• EQUAL for list structures or exact string
  matching (equal x abc)
• STRING-EQUAL for case-insensitive string
  matching (string-equal x AbC)
• EQL for characters (eql x \A)
• EQ for list structures or symbols (compares
  pointers) (eq x ABC)
• FEQUAL for frames (fequal x trp)
• Simple rule Use EQUAL for everything except
  frames

15
LISP Symbols

• Think of them as words in a dictionary, not
  strings
• Lisp looks to see if symbol already exists
• If so, it returns a pointer to that symbol,
  otherwise it creates a new one
• Similar to strings, but different
• Symbols live in packages, strings do not

16
Symbols vs Strings

• (setq x trp)
• -gt TRP
• (eq x trp)
• -gt T
• (setq y trp)
• -gt trp
• (eq y trp)
• -gt NIL
• (equal y trp)
• -gt T

17
Example Session

• (setq x (trp arg))
• gt (TRP ARG)
• (replace-answer-list x)
• gt (TRP ARG)
• (eco)

18
Defining Functions

• Put function definitions in a file
• Reload the file when definitions change
• (defun ltnamegt (ltargumentsgt)
• code for function )
• Creates a new operation called ltnamegt
• Examples
• (defun square (x)
• ( x x))
• (defun message ()
• (print Hello))
• (defun test-fn ()
• 1 2 3 4)

19
Arglist Keywords

• Are markers in arglist
• Not themselves argument names, but flag that
  following arguments are different somehow
• Most common are
• optional
• rest
• key
• Examples
• (defun plus5 (x optional (y 5)) ( x y) )
• (plus5 3) gt 8 (plus5 4 4) gt 8
• (defun embed (x key (y ltltlt) (z gtgtgt))
  (concatenate string y x z) )
• (embed foo z ) gt ltltltfoo
• (defun listall (rest rest-of-args) (sort
  (copy-seq rest-of-args) lt))

20
Problems

• all-substrates
• enzymes-of-reaction
• genes-of-reaction
• genes-of-pathway
• monomers-of-protein
• genes-of-enzyme

21
Example Session

• (setq x trp)
• gt trp
• (get-slot-value x common-name)
• gt L-tryptophan
• (setq aas (get-class-all-instances
  Amino-Acids))
• gt (..)
• (loop for x in aas count x)
• gt 20

22
Example Session

• (loop for x in genes
• for name (get-slot-value x
  common-name)
• when (and name (search trp name))
• collect x))
• -gt ()
• (setq rxns (get-class-all-instances
  Reactions))
• -gt ()
• (loop for x in rxns
• when (member-slot-value-p x substrates
  trp)
• collect x)
• -gt ()
• (replace-answer-list )