Description
Write a program that designs primers from bacterial
genomic DNA for PCR. Yippie!
Your program requires 4 command-line arguments:
A. The name of the DNA file (a string).
B. The name of the FASTA file (a string).
C. The size of the forward primer (integer).
D. The size of the reverse primer (integer).
If the user does not include the 4 required arguments
your program must display a help message, then exit:
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* HW4 ? provides help menu. *
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If the command-line argument is a “?” your program must
display the following menu, then exit:
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* HW4 Help Menu. *
* *
* HW4 will fail to start if no command line arguments are *
* provided. To get this help menu start AADS as follows: *
* ./HW4 ? *
* *
* Required command line arguments include: *
* ./HW4 DNA_file FASTA_file Forward_count Reverse_count *
* *
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If the required command-line arguments are provided, your
program must include 4 functions that perform the following:
A. Load the DNA file.
B. Load the FASTA file.
C. Find the location in the DNA data where the FASTA data is.
D. Determine and display the forward primer.
E. Determine and display the reverse primer.
Notes on A and B:
1) A and B can be done with the same function.
2) As both the DNA and FASTA files have a bunch of garbage characters
in them, I highly suggest you open these files for reading binary
(rb). The only characters we care about are the ‘A’, ‘C’, ‘G’, and
‘T’. You can skip over any/all other characters.
3) Your code MUST store the resulting characters in dynamic arrays.
one array for each file.
4) Don’t forget to trap errors, such as the DNA or FASTA file could
not be opened.
Notes on C:
1) To find where the FASTA data is in the DNA simply search character
by character, if you find a difference, your search failed.
2) You probably want to record the starting location (and maybe the
ending location) of any match.
3) Don’t forget to trap errors, such as the case where no match was
made (maybe return a -1).
Notes on D:
1) Let’s say the forward primer size (count) is 10. Then the forward
primer will be the 5 letters BEFORE the match BEGIN and the 5 letters AFTER
the match BEGIN.
2) Display the forward primer as “Foward Primer : ACTACT…”
Notes on E:
1) Let’s say the reverse primer size (count) is 10. Then the reverse
primer will be the 5 letters BEFORE the match END and the 5 letters
AFTER the match END.
2) The reverse primer requires that the complement be made. The complement
is simply the letters swapped with their complement. The complement of
A is T (and vice versa) and the complement of C is G (and vice versa).
So the complement of GATCGTA is CTAGCAT
3) The reverse primer also requires that the complement be reversed. To
do this you will need to have stored the complement in a dynamic
array and then print out the array in reverse order (don’t forget to
free the array!). So the reverse of 12345 is 54321.
4) Display the reverse primer as “Reverse Primer: ACTACT…”
REQUIREMENTS:
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1. Your program must run in Streibel 115/109 or on shell.aero.und.edu.
2. Your full name must appear as a comment at the beginning of your
program.
3. Your source code must be named hw4-yourname.c
3. Email your source (subject hw4-yourname) to rmarsh@cs.und.edu
