I'm trying to write a program that takes information from a text file and uses it to provide arguments to another executable file.
I want to use a BLAST executable to compare several DNA sequence files with each other and this would be much more convenient to accomplish if I could put the executable's mode operators (the dashed things -mode etc.) and the filenames into a text file and write a program that just feeds all the different permutations of comparisons into the BLAST EXE.
I haven't yet determined how the blast program returns its outputs or how to use it properly, so i'm not even sure how to handle what it will send back, but i'm sure its possible, as web servers interpret the results to post on screen when you run blasts on the science websites that host these services.
At the moment I just want to write the skeleton of the C code that will read the text file and set itself up to execute the permutations of comparisons.
This is not a homework assignment, I'm working in a lab for the summer for a summer internship, and I will have to use this process several times with different parameters to compare many different DNA sequences with each other to determine if there are any signifcant similarities between them. (comparing each with all the others once).
Can anybody give me advice on this?
I forgot to mention this, but either the file will also include the name for a text output file or I will construct names for seperate outputs for each comparison, if these are even possible to create with this software.