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 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 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 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 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 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 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 moap(inputfile,
method="hypergeom",
scoring=None,
outfile=None,
motiffile=None,
pwmfile=None,
genome=None,
fpr=0.01,
ncpus=None,
subsample=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()
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")
pwmfile = pwmfile_location(pwmfile)
try:
motifs = read_motifs(pwmfile)
except:
sys.stderr.write("can't read motifs from {}".format(pwmfile))
raise
# initialize scanner
s = Scanner(ncpus=ncpus)
sys.stderr.write(pwmfile + "\n")
s.set_motifs(pwmfile)
s.set_genome(genome)
s.set_background(genome=genome)
# scan for motifs
sys.stderr.write("scanning for motifs\n")
motif_names = [m.id for m in read_motifs(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), normalize=True):
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
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 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_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 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)
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_
