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ALLCools.sandbox.motif.utilities

ALLCools.sandbox.motif.utilities

Module Contents

meme_to_homer(meme_path, homer_path, score_power=0.85)[source]

Transfer MEME motif format into Homer motif format. Based on description here: http://homer.ucsd.edu/homer/motif/creatingCustomMotifs.html The score_power controls Log odds detection threshold by max_score ** score_power

Parameters

  • meme_path – Input path in meme format

  • homer_path – Output path in homer format

  • score_power – Log odds detection threshold = max_score ** score_power

meme_motif_file_to_dict(meme_motif_paths)[source]
single_meme_txt_to_pfm_df(text, bits_scale=True)[source]
meme_to_pfm_dict(meme_motif_paths, bits_scale=True)[source]
plot_pfm(pfm, ax=None, logo_kws=None)[source]
split_meme_motif_file(meme_motif_paths, output_dir)[source]

Given multi motif meme format file, split into single motif meme format file

Parameters

  • meme_motif_paths –

  • output_dir –

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