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)