def scan_to_table(input_table, genome, data_dir, scoring, pwmfile=None):
threshold = check_threshold(data_dir, genome, scoring)
config = MotifConfig()
if pwmfile is None:
pwmfile = config.get_default_params().get("motif_db", None)
if pwmfile is not None:
pwmfile = os.path.join(config.get_motif_dir(), pwmfile)
if pwmfile is None:
raise ValueError("no pwmfile given and no default database specified")
df = pd.read_table(input_table, index_col=0)
regions = list(df.index)
s = Scanner()
s.set_motifs(pwmfile)
s.set_genome(genome)
scores = []
if scoring == "count":
for row in s.count(regions, cutoff=threshold):
scores.append(row)
else:
for row in s.best_score(regions):
scores.append(row)
motif_names = [m.id for m in read_motifs(open(pwmfile))]
return pd.DataFrame(scores, index=df.index, columns=motif_names)
def threshold(args):
if args.fdr < 0 or args.fdr > 1:
print "Please specify a FDR between 0 and 1"
sys.exit(1)
motifs = pwmfile_to_motifs(args.pwmfile)
s = Scanner()
s.set_motifs(args.pwmfile)
score_table = []
for scores in s.best_score(args.inputfile):
score_table.append(scores)
print "Motif\tScore\tCutoff"
for i, scores in enumerate(np.array(score_table).transpose()):
motif = motifs[i]
pwm = motif.pwm
min_score = motif.pwm_min_score()
if len(scores) > 0:
opt_score = scoreatpercentile(scores, 100 - (100 * args.fdr))
cutoff = (opt_score - min_score) / (motif.pwm_max_score() -
min_score)
print "{0}\t{1}\t{2}".format(motif.id, opt_score, cutoff)
else:
sys.stderr.write("Warning: no matches for {0}\n".format(motif.id))
def scan_to_table(input_table, genome, data_dir, scoring, pwmfile=None):
threshold = check_threshold(data_dir, genome, scoring)
config = MotifConfig()
if pwmfile is None:
pwmfile = config.get_default_params().get("motif_db", None)
if pwmfile is not None:
pwmfile = os.path.join(config.get_motif_dir(), pwmfile)
if pwmfile is None:
raise ValueError("no pwmfile given and no default database specified")
df = pd.read_table(input_table, index_col=0)
regions = list(df.index)
s = Scanner()
s.set_motifs(pwmfile)
s.set_genome(genome)
scores = []
if scoring == "count":
for row in s.count(regions, cutoff=threshold):
scores.append(row)
else:
for row in s.best_score(regions):
scores.append(row)
motif_names = [m.id for m in read_motifs(open(pwmfile))]
return pd.DataFrame(scores, index=df.index, columns=motif_names)
def threshold(args):
if args.fdr < 0 or args.fdr > 1:
print "Please specify a FDR between 0 and 1"
sys.exit(1)
motifs = pwmfile_to_motifs(args.pwmfile)
s = Scanner()
s.set_motifs(args.pwmfile)
score_table = []
for scores in s.best_score(args.inputfile):
score_table.append(scores)
print "Motif\tScore\tCutoff"
for i,scores in enumerate(np.array(score_table).transpose()):
motif = motifs[i]
pwm = motif.pwm
min_score = motif.pwm_min_score()
if len(scores) > 0:
opt_score = scoreatpercentile(scores, 100 - (100 * args.fdr))
cutoff = (opt_score - min_score) / (
motif.pwm_max_score() - min_score)
print "{0}\t{1}\t{2}".format(
motif.id, opt_score , cutoff)
else:
sys.stderr.write("Warning: no matches for {0}\n".format(motif.id))
def command_scan(inputfile, pwmfile, nreport=1, fpr=0.01, cutoff=None,
bed=False, scan_rc=True, table=False, score_table=False, moods=False,
pvalue=None, bgfile=None, genome=None, ncpus=None, normalize=False):
motifs = read_motifs(pwmfile)
fa = as_fasta(inputfile, genome)
# initialize scanner
s = Scanner(ncpus=ncpus)
s.set_motifs(pwmfile)
if genome:
s.set_genome(genome=genome)
if genome or bgfile:
s.set_background(genome=genome, fname=bgfile, length=fa.median_length())
if not score_table:
s.set_threshold(fpr=fpr, threshold=cutoff)
if table:
it = scan_table(s, inputfile, fa, motifs, cutoff, bgfile, nreport, scan_rc, pvalue, moods)
elif score_table:
it = scan_score_table(s, fa, motifs, scan_rc, normalize=normalize)
else:
it = scan_normal(s, inputfile, fa, motifs, cutoff, bgfile, nreport, scan_rc, pvalue, moods, bed, normalize=normalize)
for row in it:
yield row
def roc(args):
""" Calculate ROC_AUC and other metrics and optionally plot ROC curve.
"""
pwmfile = args.pwmfile
fg_file = args.sample
bg_file = args.background
outputfile = args.outfile
# Default extension for image
if outputfile and not outputfile.endswith(".png"):
outputfile += ".png"
motifs = read_motifs(open(pwmfile), fmt="pwm")
s = Scanner()
s.set_motifs(pwmfile)
ids = []
if args.ids:
ids = args.ids.split(",")
else:
ids = [m.id for m in motifs]
fg_total = dict([(m.id, []) for m in motifs])
for scores in s.best_score(fg_file):
for motif,score in zip(motifs, scores):
fg_total[motif.id].append(score)
bg_total = dict([(m.id, []) for m in motifs])
for scores in s.best_score(bg_file):
for motif,score in zip(motifs, scores):
bg_total[motif.id].append(score)
plot_x = []
plot_y = []
# Print the metrics
print "Motif\tROC AUC\tMNCP\tEnr. at 5% FDR\tMax enr.\tRecall at 10% FDR"
for motif_id in ids:
fg_vals = fg_total[motif_id]
bg_vals = bg_total[motif_id]
(x, y) = ROC_values(fg_vals, bg_vals)
plot_x.append(x)
plot_y.append(y)
auc = ROC_AUC(fg_vals, bg_vals)
mncp = MNCP(fg_vals, bg_vals)
enr_fdr = enr_at_fdr(fg_vals, bg_vals)
max_enr,score = max_enrichment(fg_vals, bg_vals)
recall = recall_at_fdr(fg_vals, bg_vals, 0.1)
print "%s\t%0.3f\t%03f\t%0.2f\t%0.2f\t%0.4f" % (
motif_id, auc, mncp, enr_fdr, max_enr, recall)
# Plot the ROC curve
if outputfile:
roc_plot(outputfile, plot_x, plot_y, ids=ids)
def roc(args):
""" Calculate ROC_AUC and other metrics and optionally plot ROC curve.
"""
pwmfile = args.pwmfile
fg_file = args.sample
bg_file = args.background
outputfile = args.outfile
# Default extension for image
if outputfile and not outputfile.endswith(".png"):
outputfile += ".png"
motifs = read_motifs(open(pwmfile), fmt="pwm")
s = Scanner()
s.set_motifs(pwmfile)
ids = []
if args.ids:
ids = args.ids.split(",")
else:
ids = [m.id for m in motifs]
fg_total = dict([(m.id, []) for m in motifs])
for scores in s.best_score(fg_file):
for motif, score in zip(motifs, scores):
fg_total[motif.id].append(score)
bg_total = dict([(m.id, []) for m in motifs])
for scores in s.best_score(bg_file):
for motif, score in zip(motifs, scores):
bg_total[motif.id].append(score)
plot_x = []
plot_y = []
# Print the metrics
print "Motif\tROC AUC\tMNCP\tEnr. at 5% FDR\tMax enr."
for motif_id in ids:
fg_vals = fg_total[motif_id]
bg_vals = bg_total[motif_id]
(x, y) = ROC_values(fg_vals, bg_vals)
plot_x.append(x)
plot_y.append(y)
auc = ROC_AUC(fg_vals, bg_vals)
mncp = MNCP(fg_vals, bg_vals)
enr_fdr = enr_at_fdr(fg_vals, bg_vals)
max_enr, score = max_enrichment(fg_vals, bg_vals)
print "%s\t%0.3f\t%03f\t%0.2f\t%0.2f" % (motif_id, auc, mncp, enr_fdr,
max_enr)
# Plot the ROC curve
if outputfile:
roc_plot(outputfile, plot_x, plot_y, ids=ids)
def get_PWMScore(self, fin_regions_fa):
""" Scan motif in every peak.
Arguments:
fin_regions_fa {[type]} -- [input fasta file]
Returns:
[type] -- [pfmscorefile]
"""
pfmscorefile = NamedTemporaryFile(mode="w", dir=mytmpdir(), delete=False)
seqs = [s.split(" ")[0] for s in as_fasta(fin_regions_fa, genome=self.genome).ids]
s = Scanner(ncpus=self.ncore)
s.set_motifs(self.pfmfile)
s.set_threshold(threshold=0.0)
s.set_genome(self.genome)
with open(self.pfmfile) as f:
motifs = read_motifs(f)
chunksize = 10000
# Run 10k peaks one time.
with tqdm(total=len(seqs)) as pbar:
for chunk in range(0, len(seqs), chunksize):
chunk_seqs = seqs[chunk : chunk + chunksize]
# print(chunk, "-", chunk + chunksize, "enhancers")
pfm_score = []
it = s.best_score(chunk_seqs, zscore=True, gc=True)
# We are using GC-normalization for motif scan because many sequence is GC-enriched.
# GimmeMotif develop branch already include GC-normalization option now.
for seq, scores in zip(chunk_seqs, it):
for motif, score in zip(motifs, scores):
pfm_score.append([motif.id, seq, score])
pbar.update(1)
pfm_score = pd.DataFrame(pfm_score, columns=["motif", "enhancer", "zscore"])
pfm_score = pfm_score.set_index("motif")
# print("\tCombine")
pfm_score["zscoreRank"] = minmax_scale(rankdata(pfm_score["zscore"]))
# When we built model, rank and minmax normalization was used.
cols = ["enhancer", "zscore", "zscoreRank"]
write_header = False
if chunk == 0:
write_header = True
pfm_score[cols].to_csv(pfmscorefile, sep="\t", header=write_header)
# pbar.update(chunk + chunksize)
return pfmscorefile.name
def scan_to_table(input_table,
genome,
data_dir,
scoring,
pwmfile=None,
ncpus=None):
config = MotifConfig()
if pwmfile is None:
pwmfile = config.get_default_params().get("motif_db", None)
if pwmfile is not None:
pwmfile = os.path.join(config.get_motif_dir(), pwmfile)
if pwmfile is None:
raise ValueError("no pwmfile given and no default database specified")
logger.info("reading table")
if input_table.endswith("feather"):
df = pd.read_feather(input_table)
idx = df.iloc[:, 0].values
else:
df = pd.read_table(input_table, index_col=0, comment="#")
idx = df.index
regions = list(idx)
s = Scanner(ncpus=ncpus)
s.set_motifs(pwmfile)
s.set_genome(genome)
nregions = len(regions)
scores = []
if scoring == "count":
logger.info("setting threshold")
s.set_threshold(fpr=FPR, genome=genome)
logger.info("creating count table")
for row in s.count(regions):
scores.append(row)
logger.info("done")
else:
s.set_threshold(threshold=0.0)
logger.info("creating score table")
for row in s.best_score(regions):
scores.append(row)
logger.info("done")
motif_names = [m.id for m in read_motifs(open(pwmfile))]
logger.info("creating dataframe")
return pd.DataFrame(scores, index=idx, columns=motif_names)
def get_motif_scores(fa, motifs):
s = Scanner()
s.set_motifs(motifs)
s.set_threshold(threshold=0.0)
seqs = Fasta(fa.seqfn)
for i, result in enumerate(s.scan(seqs, nreport=1)):
intron_id = seqs.ids[i]
for m, matches in enumerate(result):
motif = motifs[m]
for score, pos, strand in matches:
if score < 0:
score_rescaled = rescale(score,
orig_range=[motif.min_score, 0],
new_range=[0, 50])
else:
score_rescaled = rescale(score,
orig_range=[0, motif.max_score],
new_range=[50, 100])
yield (intron_id, motif.id, score_rescaled)
def threshold(args):
"""Calculate motif score threshold for a given FPR."""
if args.fpr < 0 or args.fpr > 1:
print("Please specify a FPR between 0 and 1")
sys.exit(1)
motifs = read_motifs(args.pwmfile)
s = Scanner()
s.set_motifs(args.pwmfile)
s.set_threshold(args.fpr, filename=args.inputfile)
print("Motif\tScore\tCutoff")
for motif in motifs:
min_score = motif.pwm_min_score()
max_score = motif.pwm_max_score()
opt_score = s.threshold[motif.id]
if opt_score is None:
opt_score = motif.pwm_max_score()
threshold = (opt_score - min_score) / (max_score - min_score)
print("{0}\t{1}\t{2}".format(motif.id, opt_score, threshold))
def scan(self, background_length=200, fpr=0.02, n_cpus=-1, verbose=True):
"""
Scan DNA sequences searching for TF binding motifs.
Args:
background_length (int): background length. This is used for the calculation of the binding score.
fpr (float): False positive rate for motif identification.
n_cpus (int): number of CPUs for parallel calculation.
verbose (bool): Whether to show a progress bar.
"""
self.fpr = fpr
self.background_length = background_length
print("initiating scanner ...")
## 1. initialilze scanner ##
# load motif
motifs = default_motifs()
# initialize scanner
s = Scanner(ncpus=n_cpus)
# set parameters
s.set_motifs(motifs)
s.set_background(genome=self.ref_genome, length=background_length)
#s.set_background(genome="mm9", length=400)
s.set_threshold(fpr=fpr)
## 2. motif scan ##
print("getting DNA sequences ...")
target_sequences = peak2fasta(self.all_peaks, self.ref_genome)
print("scanning motifs ...")
self.scanned_df = scan_dna_for_motifs(s, motifs, target_sequences,
verbose)
self.__addLog("scanMotifs")
def threshold(args):
"""Calculate motif score threshold for a given FPR."""
if args.fpr < 0 or args.fpr > 1:
print("Please specify a FPR between 0 and 1")
sys.exit(1)
motifs = read_motifs(args.pwmfile)
s = Scanner()
s.set_motifs(args.pwmfile)
s.set_threshold(args.fpr, filename=args.inputfile)
print("Motif\tScore\tCutoff")
for motif in motifs:
min_score = motif.pwm_min_score()
max_score = motif.pwm_max_score()
opt_score = s.threshold[motif.id]
if opt_score is None:
opt_score = motif.pwm_max_score()
threshold = (opt_score - min_score) / (max_score - min_score)
print("{0}\t{1}\t{2}".format(
motif.id, opt_score, threshold))
def scan_to_table(input_table, genome, scoring, pwmfile=None, ncpus=None):
"""Scan regions in input table with motifs.
Parameters
----------
input_table : str
Filename of input table. Can be either a text-separated tab file or a
feather file.
genome : str
Genome name. Can be either the name of a FASTA-formatted file or a
genomepy genome name.
scoring : str
"count" or "score"
pwmfile : str, optional
Specify a PFM file for scanning.
ncpus : int, optional
If defined this specifies the number of cores to use.
Returns
-------
table : pandas.DataFrame
DataFrame with motif ids as column names and regions as index. Values
are either counts or scores depending on the 'scoring' parameter.s
"""
config = MotifConfig()
if pwmfile is None:
pwmfile = config.get_default_params().get("motif_db", None)
if pwmfile is not None:
pwmfile = os.path.join(config.get_motif_dir(), pwmfile)
if pwmfile is None:
raise ValueError("no pwmfile given and no default database specified")
logger.info("reading table")
if input_table.endswith("feather"):
df = pd.read_feather(input_table)
idx = df.iloc[:,0].values
else:
df = pd.read_table(input_table, index_col=0, comment="#")
idx = df.index
regions = list(idx)
s = Scanner(ncpus=ncpus)
s.set_motifs(pwmfile)
s.set_genome(genome)
s.set_background(genome=genome)
nregions = len(regions)
scores = []
if scoring == "count":
logger.info("setting threshold")
s.set_threshold(fpr=FPR)
logger.info("creating count table")
for row in s.count(regions):
scores.append(row)
logger.info("done")
else:
s.set_threshold(threshold=0.0)
logger.info("creating score table")
for row in s.best_score(regions, normalize=True):
scores.append(row)
logger.info("done")
motif_names = [m.id for m in read_motifs(pwmfile)]
logger.info("creating dataframe")
return pd.DataFrame(scores, index=idx, columns=motif_names)
def moap(
inputfile,
method="hypergeom",
scoring=None,
outfile=None,
motiffile=None,
pfmfile=None,
genome=None,
fpr=0.01,
ncpus=None,
subsample=None,
zscore=True,
gc=True,
):
"""Run a single motif activity prediction algorithm.
Parameters
----------
inputfile : str
:1File with regions (chr:start-end) in first column and either cluster
name in second column or a table with values.
method : str, optional
Motif activity method to use. Any of 'hypergeom', 'lasso',
'lightningclassification', 'lightningregressor', 'bayesianridge',
'rf', 'xgboost'. Default is 'hypergeom'.
scoring: str, optional
Either 'score' or 'count'
outfile : str, optional
Name of outputfile to save the fitted activity values.
motiffile : str, optional
Table with motif scan results. First column should be exactly the same
regions as in the inputfile.
pfmfile : str, optional
File with motifs in pwm format. Required when motiffile is not
supplied.
genome : str, optional
Genome name, as indexed by gimme. Required when motiffile is not
supplied
fpr : float, optional
FPR for motif scanning
ncpus : int, optional
Number of threads to use. Default is the number specified in the config.
zscore : bool, optional
Use z-score normalized motif scores.
gc : bool optional
Use GC% bins for z-score.
Returns
-------
pandas DataFrame with motif activity
"""
if scoring and scoring not in ["score", "count"]:
raise ValueError("valid values are 'score' and 'count'")
if inputfile.endswith("feather"):
df = pd.read_feather(inputfile)
df = df.set_index(df.columns[0])
else:
# read data
df = pd.read_table(inputfile, index_col=0, comment="#")
clf = Moap.create(method, ncpus=ncpus)
if clf.ptype == "classification":
if df.shape[1] != 1:
raise ValueError("1 column expected for {}".format(method))
else:
if np.dtype("object") in set(df.dtypes):
raise ValueError("columns should all be numeric for {}".format(method))
if motiffile is None:
if genome is None:
raise ValueError("need a genome")
pfmfile = pfmfile_location(pfmfile)
try:
motifs = read_motifs(pfmfile)
except Exception:
sys.stderr.write("can't read motifs from {}".format(pfmfile))
raise
# initialize scanner
s = Scanner(ncpus=ncpus)
s.set_motifs(pfmfile)
s.set_genome(genome)
s.set_background(genome=genome)
# scan for motifs
motif_names = [m.id for m in read_motifs(pfmfile)]
scores = []
if method == "classic" or scoring == "count":
logger.info("motif scanning (scores)")
scores = scan_to_table(
inputfile,
genome,
"count",
pfmfile=pfmfile,
ncpus=ncpus,
zscore=zscore,
gc=gc,
)
else:
logger.info("motif scanning (scores)")
scores = scan_to_table(
inputfile,
genome,
"score",
pfmfile=pfmfile,
ncpus=ncpus,
zscore=zscore,
gc=gc,
)
motifs = pd.DataFrame(scores, index=df.index, columns=motif_names)
elif isinstance(motiffile, pd.DataFrame):
motifs = motiffile
else:
motifs = pd.read_table(motiffile, index_col=0, comment="#")
if outfile and os.path.exists(outfile):
out = pd.read_table(outfile, index_col=0, comment="#")
ncols = df.shape[1]
if ncols == 1:
ncols = len(df.iloc[:, 0].unique())
if out.shape[0] == motifs.shape[1] and out.shape[1] == ncols:
logger.warn("%s output already exists... skipping", method)
return out
if subsample is not None:
n = int(subsample * df.shape[0])
logger.debug("Subsampling %d regions", n)
df = df.sample(n)
motifs = motifs.loc[df.index]
if method == "lightningregressor":
outdir = os.path.dirname(outfile)
tmpname = os.path.join(outdir, ".lightning.tmp")
clf.fit(motifs, df, tmpdir=tmpname)
shutil.rmtree(tmpname)
else:
clf.fit(motifs, df)
if outfile:
with open(outfile, "w") as f:
f.write("# maelstrom - GimmeMotifs version {}\n".format(__version__))
f.write("# method: {} with motif {}\n".format(method, scoring))
if genome:
f.write("# genome: {}\n".format(genome))
if isinstance(motiffile, str):
f.write("# motif table: {}\n".format(motiffile))
f.write("# {}\n".format(clf.act_description))
with open(outfile, "a") as f:
clf.act_.to_csv(f, sep="\t")
return clf.act_
def scan_to_table(
input_table, genome, scoring, pfmfile=None, ncpus=None, zscore=True, gc=True
):
"""Scan regions in input table with motifs.
Parameters
----------
input_table : str
Filename of input table. Can be either a text-separated tab file or a
feather file.
genome : str
Genome name. Can be either the name of a FASTA-formatted file or a
genomepy genome name.
scoring : str
"count" or "score"
pfmfile : str, optional
Specify a PFM file for scanning.
ncpus : int, optional
If defined this specifies the number of cores to use.
Returns
-------
table : pandas.DataFrame
DataFrame with motif ids as column names and regions as index. Values
are either counts or scores depending on the 'scoring' parameter.s
"""
config = MotifConfig()
if pfmfile is None:
pfmfile = config.get_default_params().get("motif_db", None)
if pfmfile is not None:
pfmfile = os.path.join(config.get_motif_dir(), pfmfile)
if pfmfile is None:
raise ValueError("no pfmfile given and no default database specified")
logger.info("reading table")
if input_table.endswith("feather"):
df = pd.read_feather(input_table)
idx = df.iloc[:, 0].values
else:
df = pd.read_table(input_table, index_col=0, comment="#")
idx = df.index
regions = list(idx)
if len(regions) >= 1000:
check_regions = np.random.choice(regions, size=1000, replace=False)
else:
check_regions = regions
size = int(
np.median([len(seq) for seq in as_fasta(check_regions, genome=genome).seqs])
)
s = Scanner(ncpus=ncpus)
s.set_motifs(pfmfile)
s.set_genome(genome)
s.set_background(genome=genome, gc=gc, size=size)
scores = []
if scoring == "count":
logger.info("setting threshold")
s.set_threshold(fpr=FPR)
logger.info("creating count table")
for row in s.count(regions):
scores.append(row)
logger.info("done")
else:
s.set_threshold(threshold=0.0)
msg = "creating score table"
if zscore:
msg += " (z-score"
if gc:
msg += ", GC%"
msg += ")"
else:
msg += " (logodds)"
logger.info(msg)
for row in s.best_score(regions, zscore=zscore, gc=gc):
scores.append(row)
logger.info("done")
motif_names = [m.id for m in read_motifs(pfmfile)]
logger.info("creating dataframe")
return pd.DataFrame(scores, index=idx, columns=motif_names)
def diff(args):
infiles = args.inputfiles.split(",")
bgfile = args.bgfile
outfile = args.outputfile
pwmfile = args.pwmfile
cutoff = args.cutoff
genome = args.genome
minenr = float(args.minenr)
minfreq = float(args.minfreq)
tmpdir = mkdtemp()
# Retrieve FASTA clusters from BED file
if len(infiles) == 1 and infiles[0].endswith("bed"):
if not args.genome:
sys.stderr.write("Can't convert BED file without genome!\n")
sys.exit(1)
clusters = {}
for line in open(infiles[0]):
vals = line.strip().split("\t")
clusters.setdefault(vals[4], []).append(vals[:3])
infiles = []
for cluster, regions in clusters.items():
sys.stderr.write("Creating FASTA file for {0}\n".format(cluster))
inbed = os.path.join(tmpdir, "{0}.bed".format(cluster))
outfa = os.path.join(tmpdir, "{0}.fa".format(cluster))
with open(inbed, "w") as f:
for vals in regions:
f.write("{0}\t{1}\t{2}\n".format(*vals))
Genome(genome).track2fasta(inbed, outfa)
infiles.append(outfa)
pwms = dict([(m.id, m) for m in pwmfile_to_motifs(pwmfile)])
motifs = [m for m in pwms.keys()]
names = [os.path.basename(os.path.splitext(fname)[0]) for fname in infiles]
s = Scanner()
s.set_motifs(pwmfile)
s.set_threshold(threshold=cutoff)
# Get background frequencies
nbg = float(len(Fasta(bgfile).seqs))
bgcounts = s.total_count(bgfile, nreport=1)
bgfreq = [(c + 0.01) / nbg for c in bgcounts]
# Get frequences in input files
freq = {}
counts = {}
for fname in infiles:
mcounts = s.total_count(fname, nreport=1)
n = float(len(Fasta(fname).seqs))
counts[fname] = mcounts
freq[fname] = [(c + 0.01) / n for c in mcounts]
freq = np.array([freq[fname] for fname in infiles]).transpose()
counts = np.array([counts[fname] for fname in infiles]).transpose()
#for row in freq:
# print freq
diff_plot(motifs,
pwms,
names,
freq,
counts,
bgfreq,
bgcounts,
outfile,
minenr=minenr,
minfreq=minfreq)
shutil.rmtree(tmpdir)
def command_scan(inputfile, pwmfile, nreport=1, cutoff=0.9, bed=False,
scan_rc=True, table=False, score_table=False, moods=False,
pvalue=None, bgfile=None, genome=None):
motifs = pwmfile_to_motifs(pwmfile)
index_dir = None
if genome is not None:
index_dir = os.path.join(MotifConfig().get_index_dir(), genome)
# initialize scanner
s = Scanner()
s.set_motifs(pwmfile)
fa = as_fasta(inputfile, index_dir)
if moods:
result_it = scan_it_moods(inputfile, motifs, cutoff, bgfile, nreport, scan_rc, pvalue, table)
else:
result_it = s.scan(fa, nreport, scan_rc, cutoff)
if table:
# header
yield "\t{}".format("\t".join([m.id for m in motifs]))
if moods:
result_it = scan_it_moods(inputfile, motifs, cutoff, bgfile, nreport, scan_rc, pvalue, table)
for seq_id, counts in result_it:
yield "{}\t{}".format(seq_id, "\t".join([str(x) for x in counts]))
else:
# get iterator
result_it = s.count(fa, nreport, scan_rc, cutoff)
# counts table
for i, counts in enumerate(result_it):
yield "{}\t{}".format(
fa.ids[i],
"\t".join([str(x) for x in counts])
)
elif score_table:
# get iterator
result_it = s.best_score(fa, scan_rc)
# header
yield "\t{}".format("\t".join([m.id for m in motifs]))
# score table
for i,scores in enumerate(result_it):
yield "{}\t{}".format(
fa.ids[i],
"\t".join([str(x) for x in scores])
)
else:
if moods:
for motif, d in result_it:
for seq_id,matches in d.items():
for pos,score,strand in matches:
yield format_line(fa, seq_id, motif,
score, pos, strand, bed=bed)
else:
for i, result in enumerate(result_it):
seq_id = fa.ids[i]
for motif, matches in zip(motifs, result):
for (score, pos, strand) in matches:
yield format_line(fa, seq_id, motif,
score, pos, strand, bed=bed)
def moap(inputfile, method="classic", scoring="score", outfile=None, motiffile=None, pwmfile=None, genome=None, cutoff=0.95):
""" Run a single motif activity prediction algorithm.
Parameters
----------
inputfile : str
File with regions (chr:start-end) in first column and either cluster
name in second column or a table with values.
method : str, optional
Motif activity method to use. Any of 'classic', 'ks', 'lasso',
'lightning', 'mara', 'rf'. Default is 'classic'.
scoring: str, optional
Either 'score' or 'count'
outfile : str, optional
Name of outputfile to save the fitted activity values.
motiffile : str, optional
Table with motif scan results. First column should be exactly the same
regions as in the inputfile.
pwmfile : str, optional
File with motifs in pwm format. Required when motiffile is not
supplied.
genome : str, optional
Genome name, as indexed by gimme. Required when motiffile is not
supplied
cutoff : float, optional
Cutoff for motif scanning
Returns
-------
pandas DataFrame with motif activity
"""
if scoring not in ['score', 'count']:
raise ValueError("valid values are 'score' and 'count'")
config = MotifConfig()
m2f = None
# read data
df = pd.read_table(inputfile, index_col=0)
if method in CLUSTER_METHODS:
if df.shape[1] != 1:
raise ValueError("1 column expected for {}".format(method))
else:
if np.dtype('object') in set(df.dtypes):
raise ValueError(
"columns should all be numeric for {}".format(method))
if method not in VALUE_METHODS:
raise ValueError("method {} not valid".format(method))
if motiffile is None:
if genome is None:
raise ValueError("need a genome")
# check pwmfile
if pwmfile is None:
pwmfile = config.get_default_params().get("motif_db", None)
if pwmfile is not None:
pwmfile = os.path.join(config.get_motif_dir(), pwmfile)
if pwmfile is None:
raise ValueError("no pwmfile given and no default database specified")
if not os.path.exists(pwmfile):
raise ValueError("{} does not exist".format(pwmfile))
try:
motifs = read_motifs(open(pwmfile))
except:
sys.stderr.write("can't read motifs from {}".format(pwmfile))
raise
base = os.path.splitext(pwmfile)[0]
map_file = base + ".motif2factors.txt"
if os.path.exists(map_file):
m2f = pd.read_table(map_file, index_col=0)
# initialize scanner
s = Scanner()
sys.stderr.write(pwmfile + "\n")
s.set_motifs(pwmfile)
s.set_genome(genome)
# scan for motifs
sys.stderr.write("scanning for motifs\n")
motif_names = [m.id for m in read_motifs(open(pwmfile))]
scores = []
if method == 'classic' or scoring == "count":
for row in s.count(list(df.index), cutoff=cutoff):
scores.append(row)
else:
for row in s.best_score(list(df.index)):
scores.append(row)
motifs = pd.DataFrame(scores, index=df.index, columns=motif_names)
else:
motifs = pd.read_table(motiffile, index_col=0)
motifs = motifs.loc[df.index]
clf = None
if method == "ks":
clf = KSMoap()
if method == "mwu":
clf = MWMoap()
if method == "rf":
clf = RFMoap()
if method == "lasso":
clf = LassoMoap()
if method == "lightning":
clf = LightningMoap()
if method == "mara":
clf = MaraMoap()
if method == "more":
clf = MoreMoap()
if method == "classic":
clf = ClassicMoap()
clf.fit(motifs, df)
if outfile:
with open(outfile, "w") as f:
f.write("# maelstrom - GimmeMotifs version {}\n".format(GM_VERSION))
f.write("# method: {} with motif {}\n".format(method, scoring))
if genome:
f.write("# genome: {}\n".format(genome))
if motiffile:
f.write("# motif table: {}\n".format(motiffile))
f.write("# {}\n".format(clf.act_description))
with open(outfile, "a") as f:
clf.act_.to_csv(f, sep="\t")
return clf.act_
def diff(args):
infiles = args.inputfiles.split(",")
bgfile = args.bgfile
outfile = args.outputfile
pwmfile = args.pwmfile
cutoff = args.cutoff
genome = args.genome
minenr = float(args.minenr)
minfreq = float(args.minfreq)
tmpdir = mkdtemp()
# Retrieve FASTA clusters from BED file
if len(infiles) == 1 and infiles[0].endswith("bed"):
if not args.genome:
sys.stderr.write("Can't convert BED file without genome!\n")
sys.exit(1)
clusters = {}
for line in open(infiles[0]):
vals = line.strip().split("\t")
clusters.setdefault(vals[4], []).append(vals[:3])
infiles = []
for cluster,regions in clusters.items():
sys.stderr.write("Creating FASTA file for {0}\n".format(cluster))
inbed = os.path.join(tmpdir, "{0}.bed".format(cluster))
outfa = os.path.join(tmpdir, "{0}.fa".format(cluster))
with open(inbed, "w") as f:
for vals in regions:
f.write("{0}\t{1}\t{2}\n".format(*vals))
Genome(genome).track2fasta(inbed, outfa)
infiles.append(outfa)
pwms = dict([(m.id, m) for m in pwmfile_to_motifs(pwmfile)])
motifs = [m for m in pwms.keys()]
names = [os.path.basename(os.path.splitext(fname)[0]) for fname in infiles]
s = Scanner()
s.set_motifs(pwmfile)
s.set_threshold(threshold=cutoff)
# Get background frequencies
nbg = float(len(Fasta(bgfile).seqs))
bgcounts = s.total_count(bgfile, nreport=1)
bgfreq = [(c + 0.01) / nbg for c in bgcounts]
# Get frequences in input files
freq = {}
counts = {}
for fname in infiles:
mcounts = s.total_count(fname, nreport=1)
n = float(len(Fasta(fname).seqs))
counts[fname] = mcounts
freq[fname] = [(c + 0.01) / n for c in mcounts]
freq = np.array([freq[fname] for fname in infiles]).transpose()
counts = np.array([counts[fname] for fname in infiles]).transpose()
#for row in freq:
# print freq
diff_plot(motifs, pwms, names, freq, counts, bgfreq, bgcounts, outfile, minenr=minenr, minfreq=minfreq)
shutil.rmtree(tmpdir)
def calc_stats_iterator(
fg_file=None,
bg_file=None,
fg_table=None,
bg_table=None,
motifs=None,
stats=None,
genome=None,
zscore=True,
gc=True,
ncpus=None,
):
"""Calculate motif enrichment metrics.
Parameters
----------
fg_file : str, optional
Filename of a FASTA, BED or region file with positive sequences.
bg_file : str, optional
Filename of a FASTA, BED or region file with negative sequences.
fg_table : str, optional
Filename of a table with motif scan results of positive sequences.
bg_table : str, optional
Filename of a table with motif scan results of negative sequences.
motifs : str, list or Motif instance, optional
A file with motifs in pfm format, a list of Motif instances or a
single Motif instance. If motifs is `None`, the default motif
database is used.
genome : str, optional
Genome or index directory in case of BED/regions.
stats : list, optional
Names of metrics to calculate. See gimmemotifs.rocmetrics.__all__
for available metrics.
ncpus : int, optional
Number of cores to use.
Returns
-------
result : dict
Dictionary with results where keys are motif ids and the values are
dictionary with metric name and value pairs.
"""
if not stats:
stats = rocmetrics.__all__
if fg_table is None:
if fg_file is None:
raise ValueError("Need either fg_table or fg_file argument")
elif fg_file is not None:
raise ValueError("Need either fg_table or fg_file argument, not both")
if bg_table is None:
if bg_file is None:
raise ValueError("Need either bg_table or bg_file argument")
elif bg_file is not None:
raise ValueError("Need either bg_table or bg_file argument, not both")
if fg_table is not None or bg_table is not None:
remove_stats = []
for s in stats:
func = getattr(rocmetrics, s)
if func.input_type == "pos":
remove_stats.append(s)
if len(remove_stats) != 0:
logger.warn(
"Cannot calculate stats that require position from table of motif scores."
)
logger.warn(f"Skipping the following statistics: {', '.join(remove_stats)}")
stats = [s for s in stats if s not in remove_stats]
if isinstance(motifs, Motif):
all_motifs = [motifs]
else:
if type([]) == type(motifs):
all_motifs = motifs
else:
motifs = pfmfile_location(motifs)
all_motifs = read_motifs(motifs, fmt="pwm")
if fg_table is not None or bg_table is not None:
filtered_motifs = pd.read_csv(
fg_table, sep="\t", index_col=0, nrows=1, comment="#"
).columns
filtered_motifs = filtered_motifs.intersection(
pd.read_csv(bg_table, sep="\t", index_col=0, nrows=1, comment="#").columns
)
all_motifs = [m for m in all_motifs if m.id in filtered_motifs]
if ncpus is None:
ncpus = int(MotifConfig().get_default_params()["ncpus"])
if fg_file is not None or bg_file is not None:
if zscore or gc:
# Precalculate mean and stddev for z-score calculation
s = Scanner(ncpus=ncpus)
s.set_motifs(all_motifs)
s.set_genome(genome)
s.set_meanstd(gc=gc)
chunksize = 240
for i in range(0, len(all_motifs), chunksize):
result = {}
logger.debug(
"chunk %s of %s", (i / chunksize) + 1, len(all_motifs) // chunksize + 1
)
motifs = all_motifs[i : i + chunksize]
if fg_table is None:
fg_total = scan_to_best_match(
fg_file, motifs, ncpus=ncpus, genome=genome, zscore=zscore, gc=gc
)
else:
fg_total = pd.read_csv(
fg_table, sep="\t", usecols=[m.id for m in motifs], comment="#"
).to_dict(orient="list")
for m in fg_total:
fg_total[m] = [(x, None) for x in fg_total[m]]
if bg_table is None:
bg_total = scan_to_best_match(
bg_file, motifs, ncpus=ncpus, genome=genome, zscore=zscore, gc=gc
)
else:
bg_total = pd.read_csv(
bg_table, sep="\t", usecols=[m.id for m in motifs], comment="#"
).to_dict(orient="list")
for m in bg_total:
bg_total[m] = [(x, None) for x in bg_total[m]]
logger.debug("calculating statistics")
if ncpus == 1:
it = _single_stats(motifs, stats, fg_total, bg_total)
else:
it = _mp_stats(motifs, stats, fg_total, bg_total, ncpus)
for motif_id, s, ret in it:
if motif_id not in result:
result[motif_id] = {}
result[motif_id][s] = ret
yield result
def moap(inputfile,
method="hypergeom",
scoring=None,
outfile=None,
motiffile=None,
pwmfile=None,
genome=None,
fpr=0.01,
ncpus=None):
"""Run a single motif activity prediction algorithm.
Parameters
----------
inputfile : str
:1File with regions (chr:start-end) in first column and either cluster
name in second column or a table with values.
method : str, optional
Motif activity method to use. Any of 'hypergeom', 'lasso',
'lightningclassification', 'lightningregressor', 'bayesianridge',
'rf', 'xgboost'. Default is 'hypergeom'.
scoring: str, optional
Either 'score' or 'count'
outfile : str, optional
Name of outputfile to save the fitted activity values.
motiffile : str, optional
Table with motif scan results. First column should be exactly the same
regions as in the inputfile.
pwmfile : str, optional
File with motifs in pwm format. Required when motiffile is not
supplied.
genome : str, optional
Genome name, as indexed by gimme. Required when motiffile is not
supplied
fpr : float, optional
FPR for motif scanning
ncpus : int, optional
Number of threads to use. Default is the number specified in the config.
Returns
-------
pandas DataFrame with motif activity
"""
if scoring and scoring not in ['score', 'count']:
raise ValueError("valid values are 'score' and 'count'")
config = MotifConfig()
m2f = None
if inputfile.endswith("feather"):
df = pd.read_feather(inputfile)
df = df.set_index(df.columns[0])
else:
# read data
df = pd.read_table(inputfile, index_col=0, comment="#")
clf = Moap.create(method, ncpus=ncpus)
if clf.ptype == "classification":
if df.shape[1] != 1:
raise ValueError("1 column expected for {}".format(method))
else:
if np.dtype('object') in set(df.dtypes):
raise ValueError(
"columns should all be numeric for {}".format(method))
if motiffile is None:
if genome is None:
raise ValueError("need a genome")
# check pwmfile
if pwmfile is None:
pwmfile = config.get_default_params().get("motif_db", None)
if pwmfile is not None:
pwmfile = os.path.join(config.get_motif_dir(), pwmfile)
if pwmfile is None:
raise ValueError(
"no pwmfile given and no default database specified")
if not os.path.exists(pwmfile):
raise ValueError("{} does not exist".format(pwmfile))
try:
motifs = read_motifs(open(pwmfile))
except:
sys.stderr.write("can't read motifs from {}".format(pwmfile))
raise
base = os.path.splitext(pwmfile)[0]
map_file = base + ".motif2factors.txt"
if os.path.exists(map_file):
m2f = pd.read_table(map_file, index_col=0, comment="#")
# initialize scanner
s = Scanner(ncpus=ncpus)
sys.stderr.write(pwmfile + "\n")
s.set_motifs(pwmfile)
s.set_genome(genome)
# scan for motifs
sys.stderr.write("scanning for motifs\n")
motif_names = [m.id for m in read_motifs(open(pwmfile))]
scores = []
if method == 'classic' or scoring == "count":
s.set_threshold(fpr=fpr)
for row in s.count(list(df.index)):
scores.append(row)
else:
for row in s.best_score(list(df.index)):
scores.append(row)
motifs = pd.DataFrame(scores, index=df.index, columns=motif_names)
else:
motifs = pd.read_table(motiffile, index_col=0, comment="#")
if outfile and os.path.exists(outfile):
out = pd.read_table(outfile, index_col=0, comment="#")
ncols = df.shape[1]
if ncols == 1:
ncols = len(df.iloc[:, 0].unique())
if out.shape[0] == motifs.shape[1] and out.shape[1] == ncols:
logger.warn("%s output already exists... skipping", method)
return out
motifs = motifs.loc[df.index]
if method == "lightningregressor":
outdir = os.path.dirname(outfile)
tmpname = os.path.join(outdir, ".lightning.tmp")
clf.fit(motifs, df, tmpdir=tmpname)
shutil.rmtree(tmpname)
else:
clf.fit(motifs, df)
if outfile:
with open(outfile, "w") as f:
f.write(
"# maelstrom - GimmeMotifs version {}\n".format(GM_VERSION))
f.write("# method: {} with motif {}\n".format(method, scoring))
if genome:
f.write("# genome: {}\n".format(genome))
if motiffile:
f.write("# motif table: {}\n".format(motiffile))
f.write("# {}\n".format(clf.act_description))
with open(outfile, "a") as f:
clf.act_.to_csv(f, sep="\t")
return clf.act_
def moap(inputfile,
method="classic",
scoring="score",
outfile=None,
motiffile=None,
pwmfile=None,
genome=None,
cutoff=0.95):
""" Run a single motif activity prediction algorithm.
Parameters
----------
inputfile : str
File with regions (chr:start-end) in first column and either cluster
name in second column or a table with values.
method : str, optional
Motif activity method to use. Any of 'classic', 'ks', 'lasso',
'lightning', 'mara', 'rf'. Default is 'classic'.
scoring: str, optional
Either 'score' or 'count'
outfile : str, optional
Name of outputfile to save the fitted activity values.
motiffile : str, optional
Table with motif scan results. First column should be exactly the same
regions as in the inputfile.
pwmfile : str, optional
File with motifs in pwm format. Required when motiffile is not
supplied.
genome : str, optional
Genome name, as indexed by gimme. Required when motiffile is not
supplied
cutoff : float, optional
Cutoff for motif scanning
Returns
-------
pandas DataFrame with motif activity
"""
if scoring not in ['score', 'count']:
raise ValueError("valid values are 'score' and 'count'")
config = MotifConfig()
m2f = None
# read data
df = pd.read_table(inputfile, index_col=0)
if method in CLUSTER_METHODS:
if df.shape[1] != 1:
raise ValueError("1 column expected for {}".format(method))
else:
if np.dtype('object') in set(df.dtypes):
raise ValueError(
"columns should all be numeric for {}".format(method))
if method not in VALUE_METHODS:
raise ValueError("method {} not valid".format(method))
if motiffile is None:
if genome is None:
raise ValueError("need a genome")
# check pwmfile
if pwmfile is None:
pwmfile = config.get_default_params().get("motif_db", None)
if pwmfile is not None:
pwmfile = os.path.join(config.get_motif_dir(), pwmfile)
if pwmfile is None:
raise ValueError(
"no pwmfile given and no default database specified")
if not os.path.exists(pwmfile):
raise ValueError("{} does not exist".format(pwmfile))
try:
motifs = read_motifs(open(pwmfile))
except:
sys.stderr.write("can't read motifs from {}".format(pwmfile))
raise
base = os.path.splitext(pwmfile)[0]
map_file = base + ".motif2factors.txt"
if os.path.exists(map_file):
m2f = pd.read_table(map_file, index_col=0)
# initialize scanner
s = Scanner()
sys.stderr.write(pwmfile + "\n")
s.set_motifs(pwmfile)
s.set_genome(genome)
# scan for motifs
sys.stderr.write("scanning for motifs\n")
motif_names = [m.id for m in read_motifs(open(pwmfile))]
scores = []
if method == 'classic' or scoring == "count":
for row in s.count(list(df.index), cutoff=cutoff):
scores.append(row)
else:
for row in s.best_score(list(df.index)):
scores.append(row)
motifs = pd.DataFrame(scores, index=df.index, columns=motif_names)
else:
motifs = pd.read_table(motiffile, index_col=0)
clf = None
if method == "ks":
clf = KSMoap()
if method == "mwu":
clf = MWMoap()
if method == "rf":
clf = RFMoap()
if method == "lasso":
clf = LassoMoap()
if method == "lightning":
clf = LightningMoap()
if method == "mara":
clf = MaraMoap()
if method == "more":
clf = MoreMoap()
if method == "classic":
clf = ClassicMoap()
clf.fit(motifs, df)
if outfile:
with open(outfile, "w") as f:
f.write(
"# maelstrom - GimmeMotifs version {}\n".format(GM_VERSION))
f.write("# method: {} with motif {}\n".format(method, scoring))
if genome:
f.write("# genome: {}\n".format(genome))
if motiffile:
f.write("# motif table: {}\n".format(motiffile))
f.write("# {}\n".format(clf.act_description))
with open(outfile, "a") as f:
clf.act_.to_csv(f, sep="\t")
return clf.act_
def scan(self,
background_length=200,
fpr=0.02,
n_cpus=-1,
verbose=True,
motifs=None,
TF_evidence_level="direct_and_indirect",
TF_formatting="auto"):
"""
Scan DNA sequences searching for TF binding motifs.
Args:
background_length (int): background length. This is used for the calculation of the binding score.
fpr (float): False positive rate for motif identification.
n_cpus (int): number of CPUs for parallel calculation.
verbose (bool): Whether to show a progress bar.
motifs (list): a list of gimmemotifs motifs, will revert to default_motifs() if None
TF_evidence_level (str): Please select one from ["direct", "direct_and_indirect"]. If "direct" is selected, TFs that have a binding evidence were used.
If "direct_and_indirect" is selected, TFs with binding evidence and inferred TFs are used.
For more information, please read explanation of Motif class in gimmemotifs documentation (https://gimmemotifs.readthedocs.io/en/master/index.html)
"""
self.fpr = fpr
self.background_length = background_length
## 1. initialilze scanner ##
# load motif
if motifs is None:
if verbose:
print(
"No motif data entered. Loading default motifs for your species ..."
)
if self.species in [
"Mouse", "Human", "Rat"
]: # If species is vertebrate, we use gimmemotif default motifs as a default.
motifs = default_motifs()
self.motif_db_name = "gimme.vertebrate.v5.0"
self.TF_formatting = True
if verbose:
print(
" Default motif for vertebrate: gimme.vertebrate.v5.0. \n For more information, please go https://gimmemotifs.readthedocs.io/en/master/overview.html \n"
)
elif self.species in [
"Zebrafish"
]: # If species is Zebrafish, we use CisBP database.
self.motif_db_name = 'CisBP_ver2_Danio_rerio.pfm'
motifs = load_motifs(self.motif_db_name)
self.TF_formatting = False
if verbose:
print(
f" Default motif for {self.species}: {self.motif_db_name}. \n For more information, please go celloracle documentation. \n"
)
elif self.species in [
"S.cerevisiae"
]: # If species is S.cerevisiae, we use CisBP database.
self.motif_db_name = 'CisBP_ver2_Saccharomyces_cerevisiae.pfm'
motifs = load_motifs(self.motif_db_name)
self.TF_formatting = False
if verbose:
print(
f" Default motif for {self.species}: {self.motif_db_name}. \n For more information, please go celloracle documentation. \n"
)
elif self.species in [
"Xenopus"
]: # If species is S.cerevisiae, we use CisBP database.
self.motif_db_name = 'CisBP_ver2_Xenopus_tropicalis_and_Xenopus_laevis.pfm'
motifs = load_motifs(self.motif_db_name)
self.TF_formatting = False
if verbose:
print(
f" Default motif for {self.species}: {self.motif_db_name}. \n For more information, please go celloracle documentation. \n"
)
elif self.species in [
"Drosophila"
]: # If species is S.cerevisiae, we use CisBP database.
self.motif_db_name = 'CisBP_ver2_Drosophila_mix.pfm'
motifs = load_motifs(self.motif_db_name)
self.TF_formatting = False
if verbose:
print(
f" Default motif for {self.species}: {self.motif_db_name}. \n For more information, please go celloracle documentation. \n"
)
elif self.species in [
"C.elegans"
]: # If species is S.cerevisiae, we use CisBP database.
self.motif_db_name = 'CisBP_ver2_Caenorhabditis_elegans.pfm'
motifs = load_motifs(self.motif_db_name)
self.TF_formatting = False
if verbose:
print(
f" Default motif for {self.species}: {self.motif_db_name}. \n For more information, please go celloracle documentation. \n"
)
elif self.species in [
"Arabidopsis"
]: # If species is S.cerevisiae, we use CisBP database.
self.motif_db_name = 'CisBP_ver2_Arabidopsis_thaliana.pfm'
motifs = load_motifs(self.motif_db_name)
self.TF_formatting = False
if verbose:
print(
f" Default motif for {self.species}: {self.motif_db_name}. \n For more information, please go celloracle documentation. \n"
)
else:
raise ValueError(
f"We have no default motifs for your species, {self.species}. Please set motifs."
)
else:
# Check format
if isinstance(motifs, list):
if isinstance(motifs[0], Motif):
if verbose:
print(
"Checking your motifs... Motifs format looks good. \n"
)
else:
raise ValueError(f"Motif data type was invalid.")
else:
raise ValueError(
f"motifs should be a list of Motif object in gimmemotifs.")
self.motif_db_name = "custom_motifs"
if TF_formatting == "auto":
self.TF_formatting = False
else:
self.TF_formatting = TF_formatting
self.motifs = motifs
self.dic_motif2TFs = _get_dic_motif2TFs(
species=self.species,
motifs=motifs,
TF_evidence_level=TF_evidence_level,
formatting=self.TF_formatting)
self.TF_evidence_level = TF_evidence_level
# initialize scanner
if verbose:
print("Initiating scanner... \n")
s = Scanner(ncpus=n_cpus)
# set parameters
s.set_motifs(motifs)
try:
s.set_background(
genome=self.ref_genome,
size=background_length) # For gimmemotifs ver 14.4
except:
s.set_background(
genome=self.ref_genome,
length=background_length) # For old gimmemotifs ver 13
#s.set_background(genome="mm9", length=400)
if verbose:
print(
"Calculating FPR-based threshold. This step may take substantial time when you load a new ref-genome. It will be done quicker on the second time. \n"
)
s.set_threshold(fpr=fpr)
## 2. motif scan ##
print("Convert peak info into DNA sequences ... \n")
# Get DNA sequences
target_sequences = peak2fasta(self.all_peaks, self.ref_genome)
# Remove DNA sequence with zero length
target_sequences = remove_zero_seq(fasta_object=target_sequences)
print(
"Scanning motifs ... It may take several hours if you proccess many peaks. \n"
)
self.scanned_df = scan_dna_for_motifs(s, motifs, target_sequences,
verbose)
self.__addLog("scanMotifs")