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Dowell-Lab / TFEA

Transcription Factor Enrichment Analysis
GNU General Public License v3.0
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error with meme file format #28

Open archanabhardwaj opened 2 years ago

archanabhardwaj commented 2 years ago

Hello

TFEA is really nice method to explore the motifs in sequencing data. I would like to use TFEA on my ranked gene list. I tried test data and followed these steps :

With test data which I downloaded from

wget https://raw.githubusercontent.com/Dowell-Lab/TFEA/master/TFEA/test/test_files/test_ranked_file.bed wget https://raw.githubusercontent.com/Dowell-Lab/TFEA/master/TFEA/test/test_files/test_database.meme wget 'https://github.com/Dowell-Lab/TFEA/blob/master/TFEA/test/test_files/chr22.fa?raw=true' -O chr22.fa wget https://raw.githubusercontent.com/Dowell-Lab/TFEA/master/TFEA/test/test_files/chr22.fa.fai

> TFEA --output test_output --ranked_file test_ranked_file.bed --genomefasta chr22.fa --fimo_motifs test_database.meme User arguments verified, all required inputs present and not conflicting. TFEA start: Scanning regions using fimo... TFEA: Completed: 0/4 Traceback (most recent call last): File "/home/archana/.local/bin/TFEA", line 4, in main.run() File "/home/archana/.local/lib/python3.8/site-packages/TFEA/main.py", line 148, in run scanner.main() File "/home/archana/.local/lib/python3.8/site-packages/TFEA/scanner.py", line 220, in main motif_distances = multiprocess.main(function=fimo, args=motif_list, File "/home/archana/.local/lib/python3.8/site-packages/TFEA/multiprocess.py", line 74, in main x = function(arg, **kwargs) File "/home/archana/.local/lib/python3.8/site-packages/TFEA/scanner.py", line 594, in fimo distances = fimo_parse_stdout(fimo_stdout=fimo_out, File "/home/archana/.local/lib/python3.8/site-packages/TFEA/scanner.py", line 701, in fimo_parse_stdout name_index = header.index('sequence_name') ValueError: 'sequence_name' is not in list

Even, I also tried different meme database files, but always gives me same error. TFEA --output test_output --ranked_file test_ranked_file.bed --genomefasta chr22.fa --fimo_motifs HOCOMOCOv11_full_MOUSE_mono_meme_format.mem

I tried to fix the space issue by replacing special character as mentioned in https://github.com/Dowell-Lab/TFEA/issues/14 still can not fix this issue.

It would be great if you can help me to fix it.

biomaral commented 6 months ago

Hello, I know it is super late now to reply this question. You already analyzed all the data by now. But for the future for those they are facing this problem now: This error migh be related to the format of the Memes or how update it is. after using the version of 5.2.2 of the Meme package, I didnot have any problem