diff options
| -rwxr-xr-x[-rw-r--r--] | select_mers.py | 30 |
1 files changed, 15 insertions, 15 deletions
diff --git a/select_mers.py b/select_mers.py index ef3e8e1..a3fce06 100644..100755 --- a/select_mers.py +++ b/select_mers.py @@ -10,27 +10,27 @@ import pdb fg_mers = {} bg_mers = {} -fg_count_fn = sys.argv[1] -fg_fasta_fn = sys.argv[2] - -bg_count_fn = sys.argv[3] -bg_fasta_fn = sys.argv[4] +if(len(sys.argv) != 5): + fg_count_fn = sys.argv[1] + fg_fasta_fn = sys.argv[2] + bg_count_fn = sys.argv[3] + bg_fasta_fn = sys.argv[4] + output_file = sys.argv[5] +else: + print "please specify your inputs" + print "ex: select_mers.py fg_counts_file fg_fasta_file bg_counts_file bg_fasta_file output_file" + exit() # empty class to fill up mer information with class Mer: pass -class Score: - pass - # import our variables -min_mer_range = int(os.getenv("min_mer_range")); -max_mer_range = int(os.getenv("max_mer_range")); -min_mer_count = int(os.getenv("min_mer_count")); -max_select = int(os.getenv("max_select")); -max_mer_distance = int(os.getenv("max_mer_distance")); - -def populate_locations(input_fn, mers, mer): +min_mer_range = int(os.environ.get("min_mer_range", 6)); +max_mer_range = int(os.environ.get("max_mer_range", 10)); +min_mer_count = int(os.environ.get("min_mer_count", 0)); +max_select = int(os.environ.get("max_select", 15)); +max_mer_distance = int(os.environ.get("max_mer_distance", 5000)); |