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QUESTIONS ON SCRIPT EXAMPLE 7—PERL: PATTERN SUBSTITUTION AND INCREMENTAL DEVELOPMENT OF SCRIPTS (p. 600)
  1. In the "Usage" error message, why is it better to use $0 to identify the script than putting the actual script file name in the message?
  2. Huntington's disease is characterized by the presence of 39 or more tandem CAG repeats in a gene on Chromosome 4. Does this script provide a valid method of screening for such occurrences? Why or why not?
  3. Replace the three lines inside the "if(!defined $infil)" loop with a single line that accomplishes the same thing. Change the pattern-matching and substitution expressions so that the call to uc is no longer needed. Add code to look for a second command line argument, "-s, for silent mode", and, if present, change the output of the definition line to omit the doctor's name. Hint: Use split, then use the string operator "." to concatenate together only the pieces you want to output.
  4. Replace the call to chomp with a pattern substitution to remove newlines from the sequence.
  5. Rewrite the script to use the Bio::SeqIO module. What advantages are provided by Bio::SeqIO?




 

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