def write_json(self,
directory,
color='index',
rndname=True,
model_num=None,
title=None,
filename=None,
**kwargs):
"""
Save a model in the json format, read by TADkit.
**Note:** If none of model_num, models or cluster parameter are set,
ALL the models will be written.
:param directory: location where the file will be written (note: the
name of the file will be model_1.cmm if model number is 1)
:param None model_num: the number of the model to save
:param True rndname: If True, file names will be formatted as:
model.RND.cmm, where RND is the random number feed used by IMP to
generate the corresponding model. If False, the format will be:
model_NUM_RND.cmm where NUM is the rank of the model in terms of
objective function value
:param None filename: overide the default file name writing
:param 'index' color: can be:
* a string as:
* '**index**' to color particles according to their position in the
model (:func:`pytadbit.utils.extraviews.color_residues`)
* '**tad**' to color particles according to the TAD they belong to
(:func:`pytadbit.utils.extraviews.tad_coloring`)
* '**border**' to color particles marking borders. Color according to
their score (:func:`pytadbit.utils.extraviews.tad_border_coloring`)
coloring function like.
* a function, that takes as argument a model and any other parameter
passed through the kwargs.
* a list of (r, g, b) tuples (as long as the number of particles).
Each r, g, b between 0 and 1.
:param kwargs: any extra argument will be passed to the coloring
function
"""
if isinstance(color, basestring):
if color == 'index':
color = color_residues(self, **kwargs)
elif color == 'tad':
if not 'tads' in kwargs:
raise Exception('ERROR: missing TADs\n ' +
'pass an Experiment.tads disctionary\n')
color = tad_coloring(self, **kwargs)
elif color == 'border':
if not 'tads' in kwargs:
raise Exception('ERROR: missing TADs\n ' +
'pass an Experiment.tads disctionary\n')
color = tad_border_coloring(self, **kwargs)
else:
raise NotImplementedError(
('%s type of coloring is not yet ' + 'implemeted\n') %
color)
elif hasattr(color, '__call__'): # it's a function
color = color(self, **kwargs)
elif not isinstance(color, list):
raise TypeError('one of function, list or string is required\n')
form = '''
{
"chromatin" : {
"id" : %(sha)s,
"title" : "%(title)s",
"source" : "TADbit %(version)s",
"metadata": {%(descr)s},
"type" : "tadbit",
"data": {
"models": [
{ %(xyz)s },
],
"clusters":[%(cluster)s],
"centroid":[%(centroid)s],
"restraints": [[][]],
"chromatinColor" : [ ]
}
}
}
'''
fil = {}
fil['sha'] = hashlib.new(fil['xyz']).hexdigest()
fil['title'] = title or "Sample TADbit data"
fil['version'] = version
fil['descr'] = ''.join(
'\n', ',\n'.join([
'"%s" : %s' % (k, ('"%s"' %
(v)) if isinstance(v, basestring) else v)
for k, v in list(self.get('description', {}).items())
]), '\n')
fil['xyz'] = ','.join([
'[%.4f,%.4f,%.4f]' % (self['x'][i], self['y'][i], self['z'][i])
for i in range(len(self['x']))
])
if filename:
out_f = open('%s/%s' % (directory, filename), 'w')
else:
if rndname:
out_f = open(
'%s/model.%s.cmm' % (directory, self['rand_init']), 'w')
else:
out_f = open(
'%s/model_%s_rnd%s.cmm' %
(directory, model_num, self['rand_init']), 'w')
out_f.write(out)
out_f.close()
def write_json(self, directory, color='index', rndname=True,
model_num=None, title=None, filename=None, **kwargs):
"""
Save a model in the json format, read by TADkit.
**Note:** If none of model_num, models or cluster parameter are set,
ALL the models will be written.
:param directory: location where the file will be written (note: the
name of the file will be model_1.cmm if model number is 1)
:param None model_num: the number of the model to save
:param True rndname: If True, file names will be formatted as:
model.RND.cmm, where RND is the random number feed used by IMP to
generate the corresponding model. If False, the format will be:
model_NUM_RND.cmm where NUM is the rank of the model in terms of
objective function value
:param None filename: overide the default file name writing
:param 'index' color: can be:
* a string as:
* '**index**' to color particles according to their position in the
model (:func:`pytadbit.utils.extraviews.color_residues`)
* '**tad**' to color particles according to the TAD they belong to
(:func:`pytadbit.utils.extraviews.tad_coloring`)
* '**border**' to color particles marking borders. Color according to
their score (:func:`pytadbit.utils.extraviews.tad_border_coloring`)
coloring function like.
* a function, that takes as argument a model and any other parameter
passed through the kwargs.
* a list of (r, g, b) tuples (as long as the number of particles).
Each r, g, b between 0 and 1.
:param kwargs: any extra argument will be passed to the coloring
function
"""
if isinstance(color, str):
if color == 'index':
color = color_residues(self, **kwargs)
elif color == 'tad':
if not 'tads' in kwargs:
raise Exception('ERROR: missing TADs\n ' +
'pass an Experiment.tads disctionary\n')
color = tad_coloring(self, **kwargs)
elif color == 'border':
if not 'tads' in kwargs:
raise Exception('ERROR: missing TADs\n ' +
'pass an Experiment.tads disctionary\n')
color = tad_border_coloring(self, **kwargs)
else:
raise NotImplementedError(('%s type of coloring is not yet ' +
'implemeted\n') % color)
elif hasattr(color, '__call__'): # it's a function
color = color(self, **kwargs)
elif not isinstance(color, list):
raise TypeError('one of function, list or string is required\n')
form = '''
{
"chromatin" : {
"id" : %(sha)s,
"title" : "%(title)s",
"source" : "TADbit %(version)s",
"metadata": {%(descr)s},
"type" : "tadbit",
"data": {
"models": [
{ %(xyz)s },
],
"clusters":[%(cluster)s],
"centroid":[%(centroid)s],
"restraints": [[][]],
"chromatinColor" : [ ]
}
}
}
'''
fil = {}
fil['sha'] = sha.new(fil['xyz']).hexdigest()
fil['title'] = title or "Sample TADbit data"
fil['version'] = version
fil['descr'] = ''.join('\n', ',\n'.join([
'"%s" : %s' % (k, ('"%s"' % (v)) if isinstance(v, str) else v)
for k, v in self['description'].items()]), '\n')
fil['xyz'] = ','.join(['[%.4f,%.4f,%.4f]' % (self['x'][i], self['y'][i],
self['z'][i])
for i in xrange(len(self['x']))])
if filename:
out_f = open('%s/%s' % (directory, filename), 'w')
else:
if rndname:
out_f = open('%s/model.%s.cmm' % (directory,
self['rand_init']), 'w')
else:
out_f = open('%s/model_%s_rnd%s.cmm' % (
directory, model_num, self['rand_init']), 'w')
out_f.write(out)
out_f.close()
def write_cmm(self,
directory,
color='index',
rndname=True,
model_num=None,
filename=None,
**kwargs):
"""
Save a model in the cmm format, read by Chimera
(http://www.cgl.ucsf.edu/chimera).
**Note:** If none of model_num, models or cluster parameter are set,
ALL the models will be written.
:param directory: location where the file will be written (note: the
name of the file will be model_1.cmm if model number is 1)
:param None model_num: the number of the model to save
:param True rndname: If True, file names will be formatted as:
model.RND.cmm, where RND is the random number feed used by IMP to
generate the corresponding model. If False, the format will be:
model_NUM_RND.cmm where NUM is the rank of the model in terms of
objective function value
:param None filename: overide the default file name writing
:param 'index' color: can be:
* a string as:
* '**index**' to color particles according to their position in the
model (:func:`pytadbit.utils.extraviews.color_residues`)
* '**tad**' to color particles according to the TAD they belong to
(:func:`pytadbit.utils.extraviews.tad_coloring`)
* '**border**' to color particles marking borders. Color according to
their score (:func:`pytadbit.utils.extraviews.tad_border_coloring`)
coloring function like.
* a function, that takes as argument a model and any other parameter
passed through the kwargs.
* a list of (r, g, b) tuples (as long as the number of particles).
Each r, g, b between 0 and 1.
:param kwargs: any extra argument will be passed to the coloring
function
"""
if isinstance(color, basestring):
if color == 'index':
color = color_residues(self, **kwargs)
elif color == 'tad':
if not 'tads' in kwargs:
raise Exception('ERROR: missing TADs\n ' +
'pass an Experiment.tads disctionary\n')
color = tad_coloring(self, **kwargs)
elif color == 'border':
if not 'tads' in kwargs:
raise Exception('ERROR: missing TADs\n ' +
'pass an Experiment.tads disctionary\n')
color = tad_border_coloring(self, **kwargs)
else:
raise NotImplementedError(
('%s type of coloring is not yet ' + 'implemeted\n') %
color)
elif hasattr(color, '__call__'): # it's a function
color = color(self, **kwargs)
elif not isinstance(color, list):
raise TypeError('one of function, list or string is required\n')
out = '<marker_set name=\"%s\">\n' % (self['rand_init'])
form = (
'<marker id=\"%s\" x=\"%s\" y=\"%s\" z=\"%s\"' +
' r=\"%s\" g=\"%s\" b=\"%s\" ' + 'radius=\"' + #str(30) +
str(self['radius']) + '\" note=\"%s\"/>\n')
for i in range(len(self['x'])):
out += form % (i + 1, self['x'][i], self['y'][i], self['z'][i],
color[i][0], color[i][1], color[i][2], i + 1)
form = (
'<link id1=\"%s\" id2=\"%s\" r=\"1\" ' +
'g=\"1\" b=\"1\" radius=\"' + str(self['radius'] / 10.) +
# str(self['radius']/2) +
'\"/>\n')
break_chroms = [1]
try:
for beg, end in zip(self['description']['start'],
self['description']['end']):
break_chroms.append((end - beg) /
self['description']['resolution'] +
break_chroms[-1])
except:
pass
for i in range(1, len(self['x'])):
if i in break_chroms[1:]:
continue
out += form % (i, i + 1)
out += '</marker_set>\n'
if filename:
out_f = open('%s/%s' % (directory, filename), 'w')
else:
if rndname:
out_f = open(
'%s/model.%s.cmm' % (directory, self['rand_init']), 'w')
else:
out_f = open(
'%s/model_%s_rnd%s.cmm' %
(directory, model_num, self['rand_init']), 'w')
out_f.write(out)
out_f.close()
def write_cmm(self, directory, color='index', rndname=True,
model_num=None, filename=None, **kwargs):
"""
Save a model in the cmm format, read by Chimera
(http://www.cgl.ucsf.edu/chimera).
**Note:** If none of model_num, models or cluster parameter are set,
ALL the models will be written.
:param directory: location where the file will be written (note: the
name of the file will be model_1.cmm if model number is 1)
:param None model_num: the number of the model to save
:param True rndname: If True, file names will be formatted as:
model.RND.cmm, where RND is the random number feed used by IMP to
generate the corresponding model. If False, the format will be:
model_NUM_RND.cmm where NUM is the rank of the model in terms of
objective function value
:param None filename: overide the default file name writing
:param 'index' color: can be:
* a string as:
* '**index**' to color particles according to their position in the
model (:func:`pytadbit.utils.extraviews.color_residues`)
* '**tad**' to color particles according to the TAD they belong to
(:func:`pytadbit.utils.extraviews.tad_coloring`)
* '**border**' to color particles marking borders. Color according to
their score (:func:`pytadbit.utils.extraviews.tad_border_coloring`)
coloring function like.
* '**copy**' to color particles according to the copy they belong to
(:func:`pytadbit.utils.extraviews.copy_coloring`)
* a function, that takes as argument a model and any other parameter
passed through the kwargs.
* a list of (r, g, b) tuples (as long as the number of particles).
Each r, g, b between 0 and 1.
:param kwargs: any extra argument will be passed to the coloring
function
"""
if isinstance(color, str):
if color == 'index':
color = color_residues(self, **kwargs)
elif color == 'tad':
if not 'tads' in kwargs:
raise Exception('ERROR: missing TADs\n ' +
'pass an Experiment.tads dictionary\n')
color = tad_coloring(self, **kwargs)
elif color == 'border':
if not 'tads' in kwargs:
raise Exception('ERROR: missing TADs\n ' +
'pass an Experiment.tads dictionary\n')
color = tad_border_coloring(self, **kwargs)
elif color == 'copy':
color = copy_coloring(self, **kwargs)
else:
raise NotImplementedError(('%s type of coloring is not yet ' +
'implemeted\n') % color)
elif hasattr(color, '__call__'): # it's a function
color = color(self, **kwargs)
elif not isinstance(color, list):
raise TypeError('one of function, list or string is required\n')
out = '<marker_set name=\"%s\">\n' % (self['rand_init'])
form = ('<marker id=\"%s\" x=\"%s\" y=\"%s\" z=\"%s\"' +
' r=\"%s\" g=\"%s\" b=\"%s\" ' +
'radius=\"' +
str(self['radius']) +
'\" note=\"%s\"/>\n')
ncopy=0
for molecule in self['x']:
for i in xrange(len(self['x'][molecule])):
out += form % (i + 1,
self['x'][molecule][i], self['y'][molecule][i], self['z'][molecule][i],
color[ncopy][0], color[ncopy][1], color[ncopy][2], i + 1)
ncopy = ncopy + 1
form = ('<link id1=\"%s\" id2=\"%s\" r=\"1\" ' +
'g=\"1\" b=\"1\" radius=\"' + str(10) +
# str(self['radius']/2) +
'\"/>\n')
for i in xrange(1, len(self['x'])):
out += form % (i, i + 1)
out += '</marker_set>\n'
if filename:
out_f = open('%s/%s' % (directory, filename), 'w')
else:
if rndname:
out_f = open('%s/model.%s.cmm' % (directory,
self['rand_init']), 'w')
else:
out_f = open('%s/model_%s_rnd%s.cmm' % (
directory, model_num, self['rand_init']), 'w')
out_f.write(out)
out_f.close()