meme ouput in either .pfm or .adm format

[Matthew McC]

Is there a way I can get MEME to output in either .pfm, JASPAR format, or .adm format. I need to put the output into MOODS 1.9.1, https://github.com/jhkorhonen/MOODS/wiki/Getting-started

[cegrant]

The MEME Suite includes several scripts for translating other formats like pfm/JASPAR into MEME  format, but we don't have any for going the other direction.

The closest we provide to a pfm/JASPAR format is a count matrix. In the MEME HTML output, if you click on the right pointing arrow in the Submit/Download column for your motif of interest, you'll get a pop-up window. In the pop-up window select the "Download Motif" tab. For the format choose "Count Matrix". Then click on the download button. However, this matrix is N by 4, N being the width of the motif. pfm/JASPAR wants 4 by N. You'll have to write your own script to convert the matrix into the needed form or do it by hand.