Where are .motif files from homer knownResults?

Question

I have been using homer's findMotifsGenome.pl, but with my new version (v4.9.1) of homer I don't get .motif files in the knownResults folder. I do get them in the homerResults (de novo) folder, though. With my previous version of homer I did get them and used them to find which peaks are in which motif. Which is what I would like to do

Does anyone know why there are no .motif files? I have only .svg files. I have seen that for the homerResults the .motif files are concatenated already into a file called homerMotifs.all.motifs, but no such file for knownResults.

PS. I tried to call Chuck for help, but he was not answering his phone...

PS2. I will ask this question on Biostars to hopefully get more response than here.

Answer 1

I have provided a solution in Biostars:

If you edit the file findKnownMotifs.pl and move the call to printMotif to come before testing $svgFlag you will find that .motif files are printed again.

In the following I have commented out the call from where it need not be, and introduced it as the first line, right before the if block:

   printMotif($_, $directory . "/$knownDir/$matrixFile"); # this should be done regardless of $svgFlag                                                                                                        
    if ($svgFlag) {
        my $str = HomerSVGLogo::motif2svg($_,$bitFlag,$rnaFlag2);
            open SVG, ">$directory/$knownDir/$logoFile.svg";
            print SVG $str;
            close SVG;
            print MAIN "$str\n";
    } else {
		#printMotif($_, $directory . "/$knownDir/$matrixFile"); # this should be done regardless of $svgFlag                                                                                               
            `profile2seq.pl "$directory/$knownDir/$matrixFile" 100 > "$tmpFile"`;
            my $width = $widthFactor * $_->{'len'};
            `seqlogo -a $bits -f "$tmpFile" -F PNG -S -c -o "$directory/$knownDir/$logoFile" -h $height -w $width`;
		`seqlogo -a $bits -f "$tmpFile" -F PDF -S -c -o "$directory/$knownDir/$logoFile" -h $height -w $width 2> /dev/null`;
		print MAIN "<IMG src=\"$knownDir/$logoFile.png\"/>";
}

I expect this change was mistakenly introduced while refactoring the code to support svg as alternate output format for logos.

I have reported this to the author of this code.

Answer 2

The relevant help page of homer seems to be this one.

On section 13 it says:

An HTML page is created in the output directory named homerResults.html along with a directory named "homerResults/" that contains all of the image and other support files to create the page. These pages are explicitly created by running a subprogram called "compareMotifs.pl".

You seeem to have this images on the expected folder.
Also on section 12 it says:

They [The *.motifs files] are reported in the output directories from findMotifs.pl and findMotifsGenome.pl

So you'll need to specify the output directory for findMotifsGenome.pl.