extended read me file
[pid.git] / configFile_454_run1.py
1 ###
2 # Configuration parameters for: p1_trim_and_filter
3 ###
4
5 #######
6 # 454 #
7 #######
8 cfg={
9 'runid':'PID_454_run1',
10 'p5_virus_match':'GTAGCATGACAAAAATCTTAGAGCC',
11 'p3_virus_match':'CATTRCTTTGGATGGGTATGAA',
12 'barcodes':['ACG','CAG','GTA', 'GTC'],
13 'input_data_file':'/ebio/ag-neher/share/data/PID_454/rawdata_reg1.fsa',
14 'p5_cutoff': 21,#=len(p5_virus_match)-4
15 'p3_cutoff': 18,#=len(p3_virus_match)-4
16 'min_occ_same_pid':1,
17 'min_length_pid':10,
18 'reverse':True,
19 'barcode_length_range':range(3,5)
20 }
21