FormatMotifs

Background

Transcription factor motifs are often obtained from various databases with different motif formats such as JASPAR or MEME. It can therefore be necessary to convert or filter these motif files. TOBIAS FormatMotifs is a small utility to handle common operations such as "join" and "split" of motif files.

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Example commands

Join individual motif files to one:

$ TOBIAS FormatMotifs --input test_data/individual_motifs/* --task join --output joined_motifs.jaspar

~< 1 second

Split a motif file containing several motifs:

$ TOBIAS FormatMotifs --input test_data/motifs.jaspar --format meme --task split --output split_output

~< 1 second

Filter a larger motif file using TF names:

$ echo 'MAFK CTCF JUNB' > TF_names.txt
$ TOBIAS FormatMotifs --input test_data/motifs.jaspar --output filtered_motifs.jaspar --filter TF_names.txt

~< 1 second