daquang
commented
10 years ago It appears that the latest version of weblogo is causing problems. For some reason, they changed the number of arguments in its png_formatter function. Please install weblogo3.3: https://weblogo.googlecode.com/files/weblogo-3.3.tar.gz
Sorry about the confusion. Will update the README right now.
margaret@Margaret-Cylon:~/Programs/EXTREME-2.0.0/ExampleFiles$ python ../src/EXTREME.py GM12878_NRSF_ChIP.fasta GM12878_NRSF_ChIP_shuffled.fasta GM12878_NRSF_ChIP.wm 1 Started at: Thu Jun 19 18:53:27 2014 Using initial motif guess cluster1 Adding 0.0 pseudocounts and normalizing Getting background model Getting subsequences Getting indicator matrices Scanning sequence with current PWM guess Guessing 752 sites Maximum number of sites not specified, so setting it to 3760 Try 1 Using a fudge factor of 1.0 Initial step size of 0.05 Running Online EM algorithm... KLD: 0.000734412151199 KLD threshold not met. Doing another pass KLD: 1.85297210012e-06 KLD threshold not met. Doing another pass KLD: 6.90740024157e-08 KLD threshold met on pass 3 Finding number of motif sites Found 1419 sites Motif has an acceptable number of sites Calculating log E-value Log E-value: -11589.8017606 Using PWM with log EV: -11589.8017606 Erasing motif from positive sequences Erased 1393 sites from the positive sequences Erasing motif from negative sequences Erased 36 sites from the negative sequences Motif 1 had a fraction of 7.8e-003 Motif 1 had an E-value of 4.1e-5034 Saving motif as a png... Traceback (most recent call last): File "../src/EXTREME.py", line 801, in
main()
File "../src/EXTREME.py", line 774, in main
outputMotif(theta_motif, theta_background_matrix, lambda_motif, logev, k, outpre)
File "../src/EXTREME.py", line 654, in outputMotif
png_formatter(data, forma, fout)
TypeError: png_formatter() takes exactly 2 arguments (3 given)
Looks like with a problem with calling Weblogo. I am using the provided datasets and instructions (https://github.com/uci-cbcl/EXTREME)