motif mapping not correct?

[YichaoOU]

Input: test.fa

>test
ARGRGGAAGTGAATG
>test2
AAGAGGAAGTGAATG

Input: motif matrix (PWM)

0.562501	0.461538	0.206731	0.576922	0.139423	0.072115	0.985577	0.975962	0.149038	0.048077	0.028846	0.817307	0.572115	0.711539	0.269231
0.086538	0.033654	0.139423	0.067308	0.0	0.0	0.0	0.0	0.365385	0.024038	0.0	0.004808	0.091346	0.091346	0.350962
0.182692	0.235577	0.600961	0.302885	0.798077	0.913462	0.0	0.0	0.485577	0.024038	0.971154	0.177885	0.269231	0.076923	0.283654
0.168269	0.269231	0.052885	0.052885	0.0625	0.014423	0.014423	0.024038	0.0	0.903847	0.0	0.0	0.067308	0.120192	0.096154

command

python ../moods_dna.py -S M4453_1.02_BCL11A.pfm -s test.fa -t 0

output

test,M4453_1.02_BCL11A.pfm,0,+,9.802885,ARGRGGAAGTGAATG,aGgAggaagtgaatg
test,M4453_1.02_BCL11A.pfm,0,+,9.528848,ARGRGGAAGTGAATG,aGgGggaagtgaatg
test,M4453_1.02_BCL11A.pfm,0,-,1.052883,ARGRGGAAGTGAATG,aGgAggaagtgaatg
test,M4453_1.02_BCL11A.pfm,0,-,1.057691,ARGRGGAAGTGAATG,aGgGggaagtgaatg
test2,M4453_1.02_BCL11A.pfm,0,+,10.028846,AAGAGGAAGTGAATG,
test2,M4453_1.02_BCL11A.pfm,0,-,1.081729,AAGAGGAAGTGAATG,

question

MOODS is supposed to give me all combinations of the input SNPs, right?

Clearly, the 5th row, where the score is 10, is not captured in test sequence.

So there is a bug somewhere in MOODS?

Thanks,
Yichao

[jhkorhonen]

Looks like a bug. Thanks, I'll have to figure this out.

[jhkorhonen]

Fixed in 19e9e11.

[YichaoOU]

Hi,

It did work for the example I gave but seems it doesn't work for more general sequences, such as ARRRRGAAGTGAATG

[YichaoOU]

OK, found the bug, if I include more than 2 SNPs in one TFBS, then your program won't work.

[jhkorhonen]

Right, I'm now somewhat amazed that I've never managed to hit any of these cases myself earlier. More fixes in 90cfb54; I'll do more thorough testing in the near future.

[YichaoOU]

Thank you so much! As far as I can tell, my problem is fixed.