Programming Challenge: Freestyle textual analysis.

I wanted to make something that I could actually use. I'm a biologist and something that's really boring is making PCR primers. It's boring because it's super mundane and because I'm always second guessing myself making sure that I picked the right pair, that they fit all the criteria, and that I'm not making primers for the same strand.

So I built a primer designer in Python. Just paste your sequence in FASTA format. It will convert it from multi-line to single-line, it will scan the sequence at designated lengths, and seek out stretches that contain the desired GC content, and having found stretches that fit that criteria the code will print: the sequence, the reverse complement, the location of the primer, the GC%, and the melting temperature of the primer.

I'm sure this has been done before, but I'm super proud that I was able to build this from scratch:

print("Paste FASTA sequence, then hit 'enter'...")

fastaSL=[]
while True:
    fasta=input()
    fastaSL.append(fasta)
    if fasta=='':
        break

gene=''.join(fastaSL)

size=int(input('Primer length:\n'))
GCmax=int(input('Max GC%:\n'))
GCmin=int(input('Min GC%:\n'))

seq=[]
base=[]

for i in range(0,len(gene)-size+1):
    fragS=str(gene[i:i+size])
    seq.append(fragS)
    base.append(i)

for j in range(0,len(seq)):
    GC=[]
    frag=seq[j]
    loc=base[j]
    GCcount=[]
    for i in range(0,len(frag)):
        if frag[i]=='G':
            GCcount.append(i)
        if frag[i]=='C':
            GCcount.append(i)
    if GCmax > 100 * len(GCcount) / len(frag) > GCmin:
        GC.append((100*len(GCcount))//len(frag))
        rc=frag[::-1]
        rcseq=[]
        for h in range(0, len(rc)):
            if rc[h] == 'A':
                rcseq.append('T')
            elif rc[h] == 'T':
                rcseq.append('A')
            elif rc[h] == 'C':
                rcseq.append('G')
            elif rc[h] == 'G':
                rcseq.append('C')
        rcprim = ''.join(rcseq)
        print("......Coding Sequence...", frag)
        print("...Reverse Complement...", rcprim)
        print("......Primer Location...", j, '-', j+len(frag), 'bases')
        print("..................GC%...", (GC)[0])
        print("...................Tm...", 4*(len(GCcount))+2*(len(frag)-len(GCcount)),'C \n')

Sorry I’m late to this party, but do you have an intro to programming somewhere? I’m really interested in learning this skill, but I don’t even know where to start :(

I have a simple thing to submit this week; I may come back with something more complex if I have time. I have started working on a program to solve sudoku puzzles. To that end, I devised a way to represent the starting state of the board in a text file. Here is a sample one I made for testing.

0,0,0,1
1,3,1,2
2,6,2,3
3,1,3,4
4,4,4,5
5,7,5,6
6,2,6,7
7,5,7,8
8,8,8,9

The first number is the sector on the board, the next two are the column and row of the number, and last number is the number to place in that square. Here is the relevant code section for processing the file into the structs I am using to store the information:

int main(int argc, char const *argv[])
{
  BOARD gameBoard = newBoard();

  // TODO prompt for file name instead
  FILE *fp = fopen("testboard.txt", "r");


  while(!feof(fp))
  {
    int value, row, column, sector;
    fscanf(fp, "%d,%d,%d,%d", &sector,&column,&row,&value);
    free(gameBoard.squares[column][row]);
    gameBoard.squares[column][row] = newSquare(value, row, column, sector);
  }

  printBoard(gameBoard);

  return 0;
}

And lastly, here's the output from the test file I showed above:

 1       |          |          
         |  4       |          
         |          |  7       
------------------------------
    2    |          |          
         |     5    |          
         |          |     8    
------------------------------
       3 |          |          
         |        6 |          
         |          |        9

I'm not sure if it will quite come out here but it looks good in the terminal!