def prepare_denovo_input_fa(inputfile, params, outdir):
"""Create all the FASTA files for de novo motif prediction and validation.
Parameters
----------
"""
fraction = float(params["fraction"])
abs_max = int(params["abs_max"])
logger.info("preparing input (FASTA)")
pred_fa = os.path.join(outdir, "prediction.fa")
val_fa = os.path.join(outdir, "validation.fa")
loc_fa = os.path.join(outdir, "localization.fa")
# Split inputfile in prediction and validation set
logger.debug(
"Splitting %s into prediction set (%s) and validation set (%s)",
inputfile,
pred_fa,
val_fa,
)
divide_fa_file(inputfile, pred_fa, val_fa, fraction, abs_max)
# File for location plots
shutil.copy(val_fa, loc_fa)
seqs = Fasta(loc_fa).seqs
lsize = len(seqs[0])
all_same_size = not (False in [len(seq) == lsize for seq in seqs])
if not all_same_size:
logger.warn(
"PLEASE NOTE: FASTA file contains sequences of different sizes. "
"Positional preference plots might be incorrect!")
def prepare_denovo_input_fa(inputfile, params, outdir):
"""Create all the FASTA files for de novo motif prediction and validation.
Parameters
----------
"""
fraction = float(params["fraction"])
abs_max = int(params["abs_max"])
logger.info("preparing input (FASTA)")
pred_fa = os.path.join(outdir, "prediction.fa")
val_fa = os.path.join(outdir, "validation.fa")
loc_fa = os.path.join(outdir, "localization.fa")
# Split inputfile in prediction and validation set
logger.debug(
"Splitting %s into prediction set (%s) and validation set (%s)",
inputfile, pred_fa, val_fa)
divide_fa_file(inputfile, pred_fa, val_fa, fraction, abs_max)
# File for location plots
shutil.copy(val_fa, loc_fa)
seqs = Fasta(loc_fa).seqs
lwidth = len(seqs[0])
all_same_width = not(False in [len(seq) == lwidth for seq in seqs])
if not all_same_width:
logger.warn(
"PLEASE NOTE: FASTA file contains sequences of different lengths. "
"Positional preference plots might be incorrect!")
def prepare_input_fa(self, inputfile, width=200, fraction=0.2, abs_max=1000):
""" Create all the bed- and fasta-files necessary for motif prediction and validation """
self.inputfile = inputfile
width = int(width)
fraction = float(fraction)
abs_max = int(abs_max)
self.logger.info("preparing input (FASTA)")
# Split inputfile in prediction and validation set
self.logger.debug(
"Splitting %s into prediction set (%s) and validation set (%s)",
self.inputfile, self.prediction_fa, self.validation_fa)
self.prediction_num, self.validation_num = divide_fa_file(self.inputfile, self.prediction_fa, self.validation_fa, fraction, abs_max)
def prepare_input_fa(self,
inputfile,
width=200,
fraction=0.2,
abs_max=1000):
""" Create all the bed- and fasta-files necessary for motif prediction and validation """
self.inputfile = inputfile
width = int(width)
fraction = float(fraction)
abs_max = int(abs_max)
self.logger.info("preparing input (FASTA)")
# Split inputfile in prediction and validation set
self.logger.debug(
"Splitting %s into prediction set (%s) and validation set (%s)",
self.inputfile, self.prediction_fa, self.validation_fa)
self.prediction_num, self.validation_num = divide_fa_file(
self.inputfile, self.prediction_fa, self.validation_fa, fraction,
abs_max)