search

loosolab / Datenanalyse-2021

2 stars 0 forks source link

Example Test: Test WP5´s new Motif´s for TF-co-occurences #9

Closed oKoch closed 2 years ago

oKoch commented 2 years ago

See WP6 Chat.

Related to Issue #6 new_example_motifs_wp5.zip .

oKoch commented 2 years ago

The single file motif file of WP5 is readable and could be used for the market basket analyses. One task has to be done possibility matrix for the new motif has to be added to the existing jaspar_file with all known motifs.

next step: merge new tf-motif to existing tf-motifs -> do market basket analyses -> and find significant rules of the tf-motif

oKoch commented 2 years ago

I have got a problem with merging the Jaspar file automatically with TOBIAS in python. On the command line it is working fine.

print(f'TOBIAS FormatMotifs --input {motif_path}{new_motif_file_name}{" "}{main_jaspar_file} --task join --output {merged_motif_path}joined_{new_motif_name}.jaspar')
    system(f'TOBIAS FormatMotifs --input {motif_path}{new_motif_file_name}{" "}{main_jaspar_file} --task join --output {merged_motif_path}joined_{new_motif_name}.jaspar')

I already tried to add the TOBIAS command to the PATH variable of my python environment, but it is still not working.

Another solution could be a bash script that is merging the files with TOBIAS, but i would like to do it in python.

oKoch commented 2 years ago

Found a solution for merging: In jupyter notebooks, use the full path to the command line tool. For example: Use TOBIAS with full path os.system("/home/stud6/.conda/envs/tfcomb_env/bin/TOBIAS FormatMotifs ...

oKoch commented 2 years ago

Example is working fine. So i close this ticket