PART1. LEARNING BASICS OF PERL |
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Class
1 |
Basic
UNIX commands. Where to get Perl. Basic Perl Punctuation. Variables and Data
Types. Basic I/O. Chapters 1,2. Assignments: Read
chapter 1 and 2 ·
Create first Perl Program- “hello, world!” [make file executable
using chmod 755] ·
Ex. 1,2,3 p. 24 |
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Class
2 |
Discussion
of assignments and problems Interpolation
Assignments: ·
Read chapter 3 ·
exercise 5 / challenge 3 (p24/25) |
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Class
3 |
Arrays
and Hashes. Chapter 3. Assignments: ·
Read chapter 3 ·
Write a program that calculates GC content of a sequence. |
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Class
4 |
Control
Structures. Boolean Operators. Chapter 4. |
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Class
5 |
Input
and Output. Chapter 7. Assignments: ·
Ex. 2, p. 103. Modification: Make FASTA-formatted file to have
customized definition line |
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Class
6 |
String
Manipulation. Pattern Matching. Chapter 6. Assignments: ·
Write a program that takes as input sequence file & file with
known restriction enzymes and saves a report of which enzymes cut/do not cut
the sequence. |
PART 2. MAKING USE OF PERL FOR DAILY TASKS |
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Count
how many sequences/trees in a file |
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Remove
identical strings in a file (sequences, gi #s, whatever) |
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Add
names to the deflines in FASTA files |
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Work
with many files in a batch |
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Run
external programs in a batch |
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Parse
output of programs such PHYLIP, TREE-PUZZLE, BLAST |
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