Perl Programming 2
Perl Programming 2
Bioinformatics: Issues and Algorithms
CSE 308-408 ? Fall 2007 ? Lecture 5
CSE 308-408 ? Bioinformatics: Issues and Algorithms Lopresti ? Fall 2007 ? Lecture 5
- 1 -
Administrative notes
? Homework #1 is due on Tuesday, Sept. 11 at 5:00 pm. Submit your work using Blackboard Assignment function.
? Homework #2 will be available on Blackboard on Thursday, Sept. 13 at 9:00 am.
CSE Department Ice Cream Social (yum!) Location: Packard Lab 360 Date: Tues., Sept. 11, 4:10 pm ? 5:00 pm
CSE 308-408 ? Bioinformatics: Issues and Algorithms Lopresti ? Fall 2007 ? Lecture 5
- 2 -
Arrays
As we know, in bioinformatics, much of the data we care about consists of collections of genetic sequences. Simple scalar variables won't suffice ...
#! /usr/bin/perl -w
A perl list data structure
# The 'arrays1' program.
@list_of_sequences = ( 'TTATTATGTT', 'GCTCAGTTCT', 'GACCTCTTAA' );
print "$list_of_sequences[1]\n";
Perl array variables start with "@"
metis:~/CSE308/Chapter4% arrays1 GCTCAGTTCT metis:~/CSE308/Chapter4%
Why did this print GCTCAGTTCT and not TTATTATGTT?
CSE 308-408 ? Bioinformatics: Issues and Algorithms Lopresti ? Fall 2007 ? Lecture 5
- 3 -
Arrays
Arrays in Perl (and many other languages) start at index [0]:
#! /usr/bin/perl -w # The 'arrays1' program. @list_of_sequences = ( 'TTATTATGTT', 'GCTCAGTTCT', 'GACCTCTTAA' ); print "$list_of_sequences[1]\n";
TTATTATGTT
[0]
GCTCAGTTCT
[1]
GACCTCTTAA
[2]
metis:~/CSE308/Chapter4% arrays1 GCTCAGTTCT metis:~/CSE308/Chapter4%
CSE 308-408 ? Bioinformatics: Issues and Algorithms Lopresti ? Fall 2007 ? Lecture 5
- 4 -
Manipulating arrays
#! /usr/bin/perl -w # The 'arrays2' program. @list_of_sequences = ( 'TTATTATGTT', 'GCTCAGTTCT', 'GACCTCTTAA' ); print "$list_of_sequences[1]\n"; $list_of_sequences[1] = 'CTATGCGGTA'; $list_of_sequences[3] = 'GGTCCATGAA'; print "$list_of_sequences[1]\n";
TTATTATGTT
[0]
GCTCAGTTCT
[1]
GACCTCTTAA
[2]
TTATTATGTT
[0]
CTATGCGGTA
[1]
GACCTCTTAA
[2]
GGTCCATGAA
[3]
CSE 308-408 ? Bioinformatics: Issues and Algorithms Lopresti ? Fall 2007 ? Lecture 5
- 5 -
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