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jhkorhonen / MOODS

MOODS: Motif Occurrence Detection Suite
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Input file format #17

Closed sudhirjadhao closed 7 years ago

sudhirjadhao commented 7 years ago

Hi, I am trying to run MOODS with pwm file,. It gives below error

moods_dna.py: error: could not parse matrix file HNF6_MOUSE.H11MO.0.A.pwm

Command used:

~/Tools/MOODS-python-1.9.3/scripts/moods_dna.py -S HNF6_MOUSE.H11MO.0.A.pwm -s ~/Database/Mouse/mm10/mm10.fasta -p 0.0001

Input file format:

0.007870731351891107 -0.5026745162600582 -0.6426579251897485 0.6212723643415664 -0.8233170879861396 -0.22997490888551764 -0.10839091463378318 0.6255086957304884 -1.770121075237143 -0.3458284352918658 -0.43940523421984795 0.9073041393368604 1.3690370491215165 -3.324736791140142 -4.400058040447161 -3.903141843818025 -3.572690530904845 -4.400058040447161 -2.9606438896517475 1.362989297771286 -2.9606438896517475 -0.4642346826548472 -3.572690530904845 1.191348924768384 -3.572690530904845 -4.400058040447161 1.3730486588530793 -4.400058040447161 1.371044865612529 -3.903141843818025 -4.400058040447161 -3.572690530904845 -3.324736791140142 -2.4841943814369576 -3.572690530904845 1.3487339948893322 -3.9031418438180254 0.2503417686541541 -2.8186351867496584 0.9691373831245766 -0.55634002882743 -0.598567918596995 0.18027335610535977 0.518528091684519

Can you please tell me where I am going wrong ?

jhkorhonen commented 7 years ago

The files should follow the JASPAR format conventions, as explained in the wiki (https://github.com/jhkorhonen/MOODS/wiki/Getting-Started).

Specifically, you'll need to transpose your input files, i.e. each row corresponds to the scores of single nucleotide (in the order A, C, G, T).

sudhirjadhao commented 7 years ago

I transpose my input, but still its showing same error.

Update Input:

0.007870731 -0.823317088 -1.770121075 1.369037049 -3.572690531 -2.96064389 -3.572690531 1.371044866 -3.324736791 -3.903141844 -0.556340029 -0.502674516 -0.229974909 -0.345828435 -3.324736791 -4.40005804 -0.464234683 -4.40005804 -3.903141844 -2.484194381 0.250341769 -0.598567919 -0.642657925 -0.108390915 -0.439405234 -4.40005804 -2.96064389 -3.572690531 1.373048659 -4.40005804 -3.572690531 -2.818635187 0.180273356 0.621272364 0.625508696 0.907304139 -3.903141844 1.362989298 1.191348925 -4.40005804 -3.572690531 1.348733995 0.969137383 0.518528092

Note: Motif name HNF6 Source of matrix: http://hocomoco11.autosome.ru/motif/HNF6_MOUSE.H11MO.0.A

jhkorhonen commented 7 years ago

Copy-pasting that into a file definitely works for me. Can you attach the actual file?

(Looks like parser may not like it if there are too many newlines after the data, so that may be the issue. I'm making a note to myself to fix this in future releases.)

sudhirjadhao commented 7 years ago

Thank you for your time.

Please find attached file for your reference hnf6_motif3.zip

Best Regards, Sudhir

jhkorhonen commented 7 years ago

Please include an unzipped version of the file, my unzip doesn't like whatever version of zip you are using.