Estimating the q from the data

[croth1]

Todo

• write write q value into meme file in shoot-peng (Christian)
• change q-value in BaMM such that it reads it from meme, if not defined, use it from the command line argument.

[croth1]

I will add the q as an extra occur field to the MEME output format of shoot_peng. BaMM can then read it from there.

MOTIF CGRACGAA
letter-probability matrix: alength= 4 w= 8 nsites= 5912 bg_prob= 0.00358952 opt_bg_order= 2 log(Pval)= -590.93200684 zoops_score= 0.04408185237682 occur= 0.314159265
0.2833 0.3249 0.2578 0.1341
0.2287 0.2181 0.3500 0.2032
0.3044 0.1791 0.3372 0.1793
0.2897 0.2459 0.2880 0.1764
0.2842 0.3248 0.2606 0.1304
0.2226 0.2333 0.3543 0.1898
0.3174 0.2722 0.2644 0.1460
0.2825 0.2389 0.2665 0.2121

[wge11]

BaMM is now able to parse q value from "occur=" in the MEME output.
Still need to test if the q is helpful for distinguishing different PWM seeds.

[croth1]

looks good.