def motif_enrichment_control(in_files, out_enrichment): """Determine a motif's enrichment vs. control data""" in_motifs, in_peaks, in_control_sample = in_files[0] for zscore in cfg.get('motifs', 'motif_zscores').split(','): args = shlex.split('''%s --motif_file=%s --bg_samples=%s --genome=%s --output_file=%s --zscore=%s''' % ( in_peaks, in_motifs, in_control_sample, cfg.get('DEFAULT', 'worldbase_genome'), out_enrichment, zscore)) motif_significance.main(args)
def motif_enrichment_control(in_files, out_enrichment): """Determine a motif's enrichment vs. control data""" in_motifs, in_peaks, in_control_sample = in_files[0] for zscore in cfg.get('motifs', 'motif_zscores').split(','): args = shlex.split( '''%s --motif_file=%s --bg_samples=%s --genome=%s --output_file=%s --zscore=%s''' % (in_peaks, in_motifs, in_control_sample, cfg.get('DEFAULT', 'worldbase_genome'), out_enrichment, zscore)) motif_significance.main(args)
def consensus_enrichment(in_files, out_enrichment): """Determine a consensus motif's enrichment vs. genomic samples""" in_samples, in_peaks = in_files[:2] in_consensuses = in_files[2:] for in_con in in_consensuses: args = shlex.split('''%s --consensus_file=%s --bg_samples=%s --genome=%s --output_file=%s ''' % ( in_peaks, in_con, in_samples, cfg.get('DEFAULT', 'worldbase_genome'), out_enrichment)) motif_significance.main(args)
def consensus_enrichment(in_files, out_enrichment): """Determine a consensus motif's enrichment vs. genomic samples""" in_samples, in_peaks = in_files[:2] in_consensuses = in_files[2:] for in_con in in_consensuses: args = shlex.split( '''%s --consensus_file=%s --bg_samples=%s --genome=%s --output_file=%s ''' % (in_peaks, in_con, in_samples, cfg.get('DEFAULT', 'worldbase_genome'), out_enrichment)) motif_significance.main(args)
def motif_enrichment_genomic(in_files, out_pattern, out_template): """Determine a motif's enrichment vs. genomic samples""" in_motifs = in_files[0] in_peaks = in_files[1][0] in_control_samples = filter(lambda x: x.endswith('sample'), in_files[1][1:]) for peak_file in in_peaks: # get the similar control data cur_control = filter(lambda x: x == (peak_file + '.similar.genomic.sample'), in_control_samples) for c in cur_control: short_control = c.split(peak_file)[1][1:] for zscore in cfg.get('motifs', 'motif_zscores').split(','): outfile = out_template % (zscore) args = shlex.split( '%s --motif_file=%s --bg_samples=%s ' '--genome=%s --output_file=%s --zscore=%s' % (peak_file, in_motifs, c, cfg.get('DEFAULT', 'worldbase_genome'), outfile, zscore)) print args motif_significance.main(args)
def motif_enrichment_genomic(in_files, out_pattern, out_template): """Determine a motif's enrichment vs. genomic samples""" in_motifs = in_files[0] in_peaks = in_files[1][0] in_control_samples = filter(lambda x: x.endswith('sample'), in_files[1][1:]) for peak_file in in_peaks: # get the similar control data cur_control = filter( lambda x: x == (peak_file + '.similar.genomic.sample'), in_control_samples) for c in cur_control: short_control = c.split(peak_file)[1][1:] for zscore in cfg.get('motifs', 'motif_zscores').split(','): outfile = out_template % (zscore) args = shlex.split( '%s --motif_file=%s --bg_samples=%s ' '--genome=%s --output_file=%s --zscore=%s' % (peak_file, in_motifs, c, cfg.get('DEFAULT', 'worldbase_genome'), outfile, zscore)) print args motif_significance.main(args)