def write(motifs, format):
"""Return a string representation of motifs in the given format.
Currently supported formats (case is ignored):
- clusterbuster: Cluster Buster position frequency matrix format
- pfm : JASPAR simple single Position Frequency Matrix
- jaspar : JASPAR multiple PFM format
- transfac : TRANSFAC like files
"""
format = format.lower()
if format in ("pfm", "jaspar"):
from Bio.motifs import jaspar
return jaspar.write(motifs, format)
elif format == "transfac":
from Bio.motifs import transfac
return transfac.write(motifs)
elif format == "clusterbuster":
from Bio.motifs import clusterbuster
return clusterbuster.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
def __format__(self, format_spec):
"""Return a string representation of the Motif in the given format.
Currently supported formats:
- clusterbuster: Cluster Buster position frequency matrix format
- pfm : JASPAR single Position Frequency Matrix
- jaspar : JASPAR multiple Position Frequency Matrix
- transfac : TRANSFAC like files
"""
if format_spec in ("pfm", "jaspar"):
from Bio.motifs import jaspar
motifs = [self]
return jaspar.write(motifs, format_spec)
elif format_spec == "transfac":
from Bio.motifs import transfac
motifs = [self]
return transfac.write(motifs)
elif format_spec == "clusterbuster":
from Bio.motifs import clusterbuster
motifs = [self]
return clusterbuster.write(motifs)
else:
raise ValueError("Unknown format type %s" % format_spec)
def _PSSM_model_to_jaspar(self, filename):
"""Writes the PSSM to the given file in jaspar format."""
header = self.strain_name
jaspar_motif = jaspar.Motif(matrix_id='', name=header,
counts=self.TF_binding_model.pwm)
with open(filename, 'w') as f:
f.write(jaspar.write([jaspar_motif], 'jaspar'))
def to_jaspar(self, filename):
"""Writes the PWM to the given file in JASPAR format."""
jaspar_motif = jaspar.Motif(matrix_id=self.TF.accession_number,
name=self.name,
instances=self._motif.instances)
with open(filename, 'w') as f:
f.write(jaspar.write([jaspar_motif], 'jaspar'))
def _PSSM_model_to_jaspar(self, filename):
"""Writes the PSSM to the given file in jaspar format."""
header = self.strain_name
jaspar_motif = jaspar.Motif(matrix_id='',
name=header,
counts=self.TF_binding_model.pwm)
with open(filename, 'w') as f:
f.write(jaspar.write([jaspar_motif], 'jaspar'))
def format(self, format):
"""Returns a string representation of the Motif in a given format
Currently supported fromats:
- pfm : JASPAR Position Frequency Matrix
- transfac : TRANSFAC like files
"""
if format=="pfm":
from Bio.motifs import jaspar
return jaspar.write(self)
elif format=="transfac":
from Bio.motifs import transfac
motifs = [self]
return transfac.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
def write(motifs, format):
"""Returns a string representation of motifs in a given format
Currently supported formats (case is ignored):
- pfm : JASPAR simple single Position Frequency Matrix
- jaspar : JASPAR multiple PFM format
- transfac : TRANSFAC like files
"""
format = format.lower()
if format in ("pfm", "jaspar"):
from Bio.motifs import jaspar
return jaspar.write(motifs, format)
elif format == "transfac":
from Bio.motifs import transfac
return transfac.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
def format(self, format):
"""Return a string representation of the Motif in the given format.
Currently supported fromats:
- pfm : JASPAR single Position Frequency Matrix
- jaspar : JASPAR multiple Position Frequency Matrix
- transfac : TRANSFAC like files
"""
if format in ('pfm', 'jaspar'):
from Bio.motifs import jaspar
motifs = [self]
return jaspar.write(motifs, format)
elif format == "transfac":
from Bio.motifs import transfac
motifs = [self]
return transfac.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
def format(self, format):
"""Return a string representation of the Motif in the given format.
Currently supported fromats:
- pfm : JASPAR single Position Frequency Matrix
- jaspar : JASPAR multiple Position Frequency Matrix
- transfac : TRANSFAC like files
"""
if format in ('pfm', 'jaspar'):
from Bio.motifs import jaspar
motifs = [self]
return jaspar.write(motifs, format)
elif format == "transfac":
from Bio.motifs import transfac
motifs = [self]
return transfac.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
def write(motifs, format):
"""Returns a string representation of motifs in a given format
Currently supported fromats (case is ignored):
- pfm : JASPAR Position Frequency Matrix
[only if len(motifs)==1]
- transfac : TRANSFAC like files
"""
format = format.lower()
if format=="pfm":
from Bio.motifs import jaspar
if len(motifs)!=1:
raise Exception("Only a single motif can be written in the JASPAR Position Frequency Matrix (pfm) format")
motif = motifs[0]
return jaspar.write(motif)
elif format=="transfac":
from Bio.motifs import transfac
return transfac.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
