RSAT, meme to transfac conversion problem

Question

[boczniak767]

RSAT doesn't work well, for example I have matrices in meme format. Consider the example

MOTIF ID0001

letter-probability matrix: alength= 4 w= 12 nsites= 1 E= 0
  0.000000  0.000000  1.000000  0.000000
  0.000000  0.500000  0.500000  0.000000
  0.428571  0.142857  0.142857  0.285714
  0.000000  0.000000  1.000000  0.000000
  0.000000  0.714286  0.285714  0.000000
  0.000000  0.000000  0.571429  0.428571
  0.214286  0.000000  0.785714  0.000000
  0.000000  0.000000  1.000000  0.000000
  0.857143  0.000000  0.142857  0.000000
  0.571429  0.428571  0.000000  0.000000
  0.642857  0.000000  0.285714  0.071429
  0.000000  0.214286  0.785714  0.000000

and it is converted to transfac as follows:

AC  ID0001
XX
ID  ID0001
XX
DE  gsngcgggaaag
P0           A         C         G         T
1         0.00      0.00      1.00      0.00
2         0.00      1.00      1.00      0.00
3         0.00      0.00      0.00      0.00
4         0.00      0.00      1.00      0.00
5         0.00      1.00      0.00      0.00
6         0.00      0.00      1.00      0.00
7         0.00      0.00      1.00      0.00
8         0.00      0.00      1.00      0.00
9         1.00      0.00      0.00      0.00
10        1.00      0.00      0.00      0.00
11        1.00      0.00      0.00      0.00
12        0.00      0.00      1.00      0.00

I've used default settings. Please, look at the third row, why there are zeroes? Also, why there only ones and zeroes?

Is there any other conversion tool? RSAT is really complicated - has many options.

Answer 1

[boczniak767]

For future reference, universalmotif package from Bioconductor works like a charm.

I needed two commands:

read_meme("filename", skip = 0, readsites = FALSE, readsites.meta = FALSE)

and

write_transfac(motifs, "filename", overwrite = FALSE, append = FALSE)