Version 0.14.0

Changelog

Added

• The gimme motifs command supports new de novo motif prediction tools: DREME, ProSampler, YAMDA, DiNAMO and RPMCMC.
• A set of non-redundant motifs is selected using recursive feature elimination for gimme motifs.
• Motif scan results for non-redundant motifs are now included in the output.
• Plot motif logos using different styles of visualization (information content, frequency, energy or Ensembl).
• New scoring scheme that uses a z-score based on genomic sequences with a similar GC%.
• CIS-BP motif database version 2.0 (Lambert et al. 2019).
• JASPAR 2020 motif database.

Changed

• Only three motif prediction tools are selected by default for gimme motifs: BioProspector, Homer and MEME.
• The xl motif setting (motif width 6-20) is selected by default for gimme motifs.
• Output names for files and reports of gimme motifs are now more consistent.
• Command line tools gimme roc has been removed. This functionality has now been merged with gimme motifs. The gimme motifs command now scans for both known and de novo motifs.
• Replaced weblogo/seqlogo with logomaker.
• GC% background now uses a genomic index of GC% frequencies.
• GC% z-score is now the default score for all gimme tools.

Fixed

• FASTA files with > symbols in the header are now correctly parsed.
• Fixed GC% background. The GC% background is now correct for all input formats.
• factorial import for scipy >= 1.3.0.
• All output columns in HTML reports can now be sorted correctly.