Transcript Writing queries in Lisp, Perl, and Java

Introduction to LISP
Programming of Pathway Tools
Queries and Updates
Myths and Facts About Lisp
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 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
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LISP and GFP References
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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-resources.html
 http://www.ai.sri.com/pkarp/loop.html
 http://bioinformatics.ai.sri.com/ptools/debugger.html
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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) -> “Ltryptophan”
 Invoking
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(eco)
the Navigator from Lisp:
LISP Syntax
 Prefix
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notation
 Simple
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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)
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LISP Expressions and Evaluation
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(+ 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
 (+) ---> 0
 (+ 1) ---> 1
 (+ 2 3 1 3 4 5 6) ----> 24
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(+ (* 3 4) 6) --> 18
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Turning off evaluation with Quote
 ’(+ 1 3) ----> (+ 1 3)
LISP Listener
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Also called “top level” and “read-eval-print loop”
Expressions typed in listener are evaluated interactively
Uses a three-step process
 Read
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Reader converts elements outside “” and || to uppercase
Evaluate
Print
Useful forms in listener:
 Previous Results: *, **, ***
 DO NOT use in programs
(+ 1 2)
-> 3
(+ 3 *)
-> 6
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
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Lists - (1 2 3)
(“a” “b” “c”) (“a” 2 “X”)
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Lisp Variables
 Global
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variable values can be set and used during
a session
 Declarations not needed
(setq x 5)
-> 5
x
-> 5
(+ 3 x)
-> 8
(setq y “atgc”)
-> “atgc”
Examples
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(select-organism :org-id ‘ecoli)
-> ECOLI
(setq genes (get-class-all-instances ‘|Genes|))
-> (……………)
(setq monomers (get-class-all-instances
‘|Polypeptides|))
-> (…………….)
(setq genes2 genes)
-> (…………….)
LISP Lists
 Fundamental
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to LISP ::: LISt Processing
 Zero or more elements enclosed by parentheses
 Typing
a list to the listener:
 ’(this is a list) => (THIS IS A LIST)
 Creating a list with functions :
 (list ’so ’is ’this) => (SO IS THIS)
 Examples:
(1 3 5 7), ((2 4 6) 10 (0 8)), ’(1 this T NIL “that”)
 The empty list: nil ()
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List Examples
(length genes)
-> 4316
(first genes)
-> XXX
(subseq genes 0 50)
-> (……………)
(nth 3 genes)
-> XXX
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Functions for Operating on Lists
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Length
 (length x)
 Returns the number of elements in the list X
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First
 (first x)
 Returns the first element in the list X
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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
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Nth
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(nth j x)
Returns the Jth element of list X (element 0 is the first element)
Defining Functions
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Put function definitions in a file
Reload the file when definitions change
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(defun <name> (<arguments>)
… code for function …)
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Creates a new operation called <name>
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Examples:
 (defun square (x)
(* x x))
 (defun message ()
(print “Hello”))
 (defun test-fn ()
1 2 3 4)
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Arglist Keywords
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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) ==> 8
(plus5 4 4) ==> 8
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(defun embed (x &key (y “<<<“) (z “>>>”)) (concatenate ‘string y x z) )
(embed “foo” :z “]]]”) ==> “<<<foo]]]”
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(defun listall (&rest rest-of-args) (sort (copy-seq rest-of-args) #’<))
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Problems
 all-substrates
 enzymes-of-reaction
 genes-of-reaction
 genes-of-pathway
 monomers-of-protein
 genes-of-enzyme
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Example Session
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(setq x ‘trp)
=> trp
(get-slot-value x ‘common-name)
=> “L-tryptophan”
(setq aas (get-class-all-instances ‘|Amino-Acids|))
=> (……..)
(loop for x in aas count x)
=> 20
Example Session
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(loop for x in genes
for name = (get-slot-value x ‘common-name)
when (and name (search “trp” name))
collect x))
-> (…)
(setq rxns (get-class-all-instances ‘|Reactions|))
-> (…)
(loop for x in rxns
when (member-slot-value-p x ‘substrates ‘trp)
collect x)
-> (…)
(replace-answer-list *)