Textbook

reading assignments

Class for discussion and problem solving not frontal lectures

SP accounts

Send programs and assignments to
bioinf@carrot.mcb.uconn.edu  

Basic UNIX commands
ls, cd, chmod, cp, rm, mkdir, more (or) less, vi, ps, kill –9,

http://carrot.mcb.uconn.edu/mcb372/old/UNIXCOMM.htm

Where to get Perl.  http://cpan.org/

Basic Perl Punctuation line ends with “;”

Files from Windows to UNIX and return: End of Line characters are a problem

IN windows Don't use notepad, it does not understand UNIX newline symbols

best write your programs under UNIX

2nd best remove end of line symbols in UNIX editor or use sed (Stream EDitor):
sed s/.$// infilename > outfilename

empty lines in program are ignored

comments start with #

first line points to path to interpreter

#! /usr/bin/perl

keep one command per line for readability

operators for basic arithmetic (Tab2.2, page 17)

Variables start with $calars, @rrays, or %ashes

Scalars: types on page 14

Data Types: Intergers, strings, floating points, arrays

Special characters \n newline 

Print function (example)

Variable interpolation

Assignments:

• Read chapter 1 and 2
• Create first Perl Program- “hello, world!” [make file executable using chmod 755]
• Ex. 1,2,3 p. 24