Introduction To Perl Exercises

Day 1

(A) String manipulation.

Write a program which takes two strings as arguments to the program.

On newlines print each argument.

On a newline print the 5^th->10^th characters of each argument.

            Exit with a warning if either of the arguments is < 10 characters in length.

Print each argument in reverse.

If the first argument begins with the word “hello”, print the message “The first arg

starts with hello!”

(B) Simple Calculator

Write a program which prompts the user for a number.

Next prompt the user to choose [+ - / *].

Next prompt the user for a second integer.

Print the operation which was just specified as well as the result.

Day 3

(A)Parsing and Reporting
Using the file fasta.fofn(fofn=File of File Names), open the three fasta files listed.
Write a text file report with a line for each fasta file which contains:

• the sequence ID
• the full length of the sequence
• and a count of how many As Cs Ts and Gs are in the sequence.

• ie:EGFR,130,10,50,60,10

(B) Sets!

From two lists of entrez gene IDs (listA and listB), identify the following four sets: all IDs which are shared between the two lists, all IDs which are unique to list A, all IDs which are unique to list B, the combination of all IDs. Write each of these four new lists to its own file.

**Don’t worry about maximum efficency or elegance just yet!

Day ?? 

() mRNA Reconstruction From Genomic Sequence

Using the geneInfo.log file, and the associated genomic GENE.fasta files, generate the mRNA sequence and write a new text file with the mRNA sequence for each gene.

*Hint- the fasta files are all in 5’->3’ orientation, so coordinates on negative strand genes will need to be handled separately from + strand genes. The resulting mRNA will need to be reverse complemented as well.