Perl Lab 13

							                                          Perl Lab 13 
 

On the Menu Today: 
Let’s review! 
 

Links: 
Sorting: http://www.perlfect.com/articles/sorting.shtml 
More Sorting: http://perlhowto.com/sort_ordering_by_multiple_columns 
Printing a tab‐delimited array to a CSV file: http://www.perlmonks.org/?node_id=46529 
Perl special variables ‐ as used for printing delimited fields: 
http://www.kichwa.com/quik_ref/spec_variables.html 
 

Assignments: 
    1. Read a blast results file in tabular format into a 2 dimensional array and sort it by two
       columns, one containing the hit length, the other the e-value:
           a. Use split to split the columns in a row into an array @rowArray and push the array
              into a 2 dimensional array @twoDimArray

                 push @twoDimArray,[@rowArray];

           b. To sort by columns 0 and 1 use the following code:

       my @orderedlist = sort { $b->[0] <=> $a->[0] || $a->[1] <=> $b->[1] }
       @twoDimArray;

    1. Given a list of genotype markers containing the amino acid position in a gene of interest
       and the letter indicating the amino acid that is associated with a particular disease, parse a
       list of sequences and for each sequence report if the sequence has the marker or not.
            a. Pick one file from the patients DNA sequences from lab 7. Write a script to open
                that file and convert the DNA sequences to protein sequence
            b. As before but now read a file that contains the following list of markers into an
                array:

                 3L,27R,29N,32R,62I,65N\S,70I,146V\I,177Y\D\F,181E\Q

           c. As before, but now loop though all the sequences, and search for only the 3L
              markers in each protein sequence. If present write the name of the sequence and
              number 1 to a file.




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    d. As before, but now look for 27R in each protein sequence (in addition to looking
       for 3L). If present write the name of the sequence and number 2 to a file. If a
       sequence has both marker the result for that sequence should be:

               037.Rc49,1 2

       Where 037.Rc49 is the sequence id and 1 refers to amino acid 3L, and 2 to amino
       acid 27R.

    e. As before, but now write a subroutine hasMarker which accepts as input:
           i. A protein sequence
          ii. A marker (for example 177Y\D\F)

       The output of the program should be:

          iii. True or False depending if the marker is present or not



    f. As before, but now loop though all the sequences, and search for the markers in the
       protein sequence by looping through the 10 markers and calling the subroutine
       hasMarker.




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