def create_denovo_motif_report(inputfile,
pfmfile,
fgfa,
background,
locfa,
outdir,
params,
stats=None):
"""Create text and graphical (.html) motif reports."""
logger.info("creating de novo reports")
motifs = read_motifs(pfmfile, fmt="pwm")
# ROC plots
create_roc_plots(pfmfile, fgfa, background, outdir, params["genome"])
# Closest match in database
mc = MotifComparer()
closest_match = mc.get_closest_match(motifs)
if stats is None:
stats = {}
for bg, bgfa in background.items():
for m, s in calc_stats(fg_file=fgfa, bg_file=bgfa,
motifs=motifs).items():
if m not in stats:
stats[m] = {}
stats[m][bg] = s
stats = add_star(stats)
if not params:
params = {}
cutoff_fpr = params.get("cutoff_fpr", 0.9)
lsize = np.median([len(seq) for seq in Fasta(locfa).seqs])
# Location plots
logger.debug("Creating localization plots")
for motif in motifs:
logger.debug(" {} {}".format(motif.id, motif))
outfile = os.path.join(outdir,
"images/{}_histogram.svg".format(motif.id))
motif_localization(locfa, motif, lsize, outfile, cutoff=cutoff_fpr)
# Create reports
_create_text_report(inputfile, motifs, closest_match, stats, outdir)
_create_graphical_report(inputfile, pfmfile, background, closest_match,
outdir, stats)
def create_denovo_motif_report(inputfile, pwmfile, fgfa, background, locfa, outdir, params, stats=None):
"""Create text and graphical (.html) motif reports."""
logger.info("creating reports")
motifs = read_motifs(pwmfile, fmt="pwm")
# ROC plots
create_roc_plots(pwmfile, fgfa, background, outdir)
# Closest match in database
mc = MotifComparer()
closest_match = mc.get_closest_match(motifs)
if stats is None:
stats = {}
for bg, bgfa in background.items():
for m, s in calc_stats(motifs, fgfa, bgfa).items():
if m not in stats:
stats[m] = {}
stats[m][bg] = s
stats = add_star(stats)
if not params:
params = {}
cutoff_fpr = params.get('cutoff_fpr', 0.9)
lwidth = np.median([len(seq) for seq in Fasta(locfa).seqs])
# Location plots
logger.debug("Creating localization plots")
for motif in motifs:
logger.debug(" {} {}".format(motif.id, motif))
outfile = os.path.join(outdir, "images/{}_histogram.svg".format(motif.id))
motif_localization(locfa, motif, lwidth, outfile, cutoff=cutoff_fpr)
# Create reports
_create_text_report(inputfile, motifs, closest_match, stats, outdir)
_create_graphical_report(inputfile, pwmfile, background, closest_match, outdir, stats)