cfljam/galaxy-pcr-markers — pull request #4 by cflszl (2013-01-10 03:40:07+00:00)
Title: design_primers_params.py added

Hi John, I'm assuming this is how to do a merge request. I have made a fork and added design_primers_params.py. It currently uses sys.argv for the Primer3 parameter settings. The sys.argv are as follows:

in_file = sys.argv[1]
gff_file = sys.argv[2]
target_file = sys.argv[3]
prod_min_size = int(sys.argv[4])
prod_max_size = int(sys.argv[5])
optimum_length = int(sys.argv[6])	## Recommended: 20
max_tm_diff = int(sys.argv[7]) ## Recommended: 1
optimum_tm = int(sys.argv[8])	## Recommended: 59-61
opt_GC_percent = int(sys.argv[9]) ## Recommended: 50
maxpolyx = int(sys.argv[10]) ## Recommended: less than 4
gc_clamp = int(sys.argv[11])	## Recommended: 2 G/Cs

I'm also trying to work on a getopt/function based parameter setter, however it is more difficult due to how the script is structured.

Cheers,
Scout