mast meme output as bed

Question

[varsha619]

Hi could someone please help me output my mast results in a .bed format? Right now I can only get the matrix format xml and txt files but I would like the genomic locations of the matches with chr start and stop. Thank you!

[WouterDeCoster]

I have no idea what a mast meme result looks like, so perhaps you could add an example of what you have and an example of what you would like to obtain.

[varsha619]

Hi could someone please help me output my mast results in a .bed format? Right now I can only get the matrix format xml and txt files but I would like the genomic locations of the matches with chr start and stop. Thank you!

The meme mast command I used is - mast mast_miniMEME.txt genome.fa -o mastout

The output file contains sections -

SECTION: MOTIF DIAGRAMS 
SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM
-------------                      --------  -------------
chr4                                      8  3381_[+1]_933_[-1]_12892_[-1]_
SECTION: ANNOTATED SEQUENCES
3376 TTCGC......
4276 GCAAA.....

The format I wanted is of the format -

chr start stop
chr4 3376 3390....

I was wondering if there is a command line option to get this format directly.

[WouterDeCoster]

And those sections look always the same? Multiple sections per file, always the same number of lines with information in the same locations?

[varsha619]

Yes, multiple sections and same number of columns. http://meme-suite.org/doc/mast.html

[WouterDeCoster]

Can you show some more output to make it completely clear? Perhaps in a github gist

[varsha619]

@WouterDeCoster, I just found out the command to get the bed format was -hit_list, thank you anyways!