Description
Write a program that reads a pair of strings from stdin (which may be
re-directed from a file). Each string will be on a single line by itself.
Be sure to strip off whitespace at each end of the strings, including
newlines.
The program should align the pair of strings using the Needleman-Wunsch
algorithm as discussed in class (link on the Software Design and Development
web page). When there are choices in the traceback step, choose diagonal,
then left, and finally up. Note there is a special case in which you may get
to the leftmost column before top row in which you merely keep the remaining
chars from the top string matched with ‘-‘; similarly for getting to top
row before left column.
Run the program as follows:
./p5 match_value mismatch_penalty gap_penalty ## strs entered at keybd
./p5 match_value mismatch_penalty gap_penalty < filename
For example:
./p5 +5 -4 -8 < file_containing_a_pair_of_strs
Print the alignment to stdout with the first string in the input printed
first on the output.
Sample input:
ACGT
ACT
Sample output for the above input:
ACGT
AC-T
Use turnin to submit a tar file containing your program file(s) and a makefile.
The makefile should have the default target build an executable which MUST
be named p5, so that I can merely type “make”, and it will build. If you use
python, have the default target copy your python program to a file named p5,
and use chmod +x to make it executable; this also implies that you would
have the magic #! line as the first line in the python code.
To build the project, I will type:
rm -rf p5
rm -f *.o
make
