def color_by_change(libraries, out_prefix, nucleotides_to_count='ATCG', exclude_constitutive=False, subtract_background=False):
for library in libraries:
log_fold_changes = {}
maxval = 0.0
minval = 0.0
for rRNA_name in library.rRNA_mutation_data:
log_fold_changes[rRNA_name] = {}
for nucleotide in library.rRNA_mutation_data[rRNA_name].nucleotides:
if library.rRNA_mutation_data[rRNA_name].nucleotides[nucleotide].identity in nucleotides_to_count and \
library.rRNA_mutation_data[rRNA_name].nucleotides[nucleotide].\
get_control_fold_change_in_mutation_rate(subtract_background=subtract_background) not in [0.0, float('inf'), float('-inf')]:
if exclude_constitutive and library.rRNA_mutation_data[rRNA_name].nucleotides[nucleotide].exclude_constitutive:
pass
else:
log_fold_changes[rRNA_name][nucleotide] = math.log(library.rRNA_mutation_data[rRNA_name].nucleotides[nucleotide].get_control_fold_change_in_mutation_rate(subtract_background=subtract_background), 10)
maxval = max(maxval, log_fold_changes[rRNA_name][nucleotide])
minval = min(minval, log_fold_changes[rRNA_name][nucleotide])
else:
pass
absmax = max(abs(maxval), abs(minval))
output_file = open(os.path.join(out_prefix, "%s.txt" % (library.lib_settings.sample_name)), 'w')
reference_pymol_script_file = open(library.experiment_settings.get_property('pymol_base_script_colorchange'), 'rU')
for line in reference_pymol_script_file:
if line.startswith('#<insert b-factors>'):
output_file.write('python\n')
output_file.write('cmd.alter(\'all\', \'b=0.0\')\n')
for rRNA_name in log_fold_changes:
for nucleotide in log_fold_changes[rRNA_name]:
output_file.write('cmd.alter(\''+rRNA_name+' and resi '+str(nucleotide)+'\', \'b=float("'+str(log_fold_changes[rRNA_name][nucleotide])+'")\')\n')
output_file.write('python end\n')
elif line.startswith('#<insert spectrum>'):
output_file.write('spectrum b, bluish_green white vermillion, minimum='+str(-absmax)+', maximum='+str(absmax)+'\n')
output_file.write('ramp_new scale, S.c.25S__rRNA, ['+str(-absmax)+',0,'+str(absmax)+'], [bluish_green, white, vermillion]')
else:
output_file.write(line)
reference_pymol_script_file.close()
output_file.close()
def highlight_structure(libraries, out_prefix, nucleotides_to_count='ATCG', exclude_constitutive=False):
"""
:param libraries:
:param out_prefix:
:param nucleotides_to_count:
:param exclude_constitutive:
:return: for each library use bokeh to plot an interactive plot of magnitude of signal (experimental+control)/2
vs log10 fold change (experimental/control).
Protected and de-protected calls will be colored, based on a fold change cutoff and confidence interval.
All nucleotides will be labelled on mouseover.
"""
for library in libraries:
protected_nucleotides = library.get_changed_nucleotides('protected', confidence_interval=library.experiment_settings.get_property('confidence_interval_cutoff'),
fold_change_cutoff=library.experiment_settings.get_property('fold_change_cutoff'))
num_protected = 0
for rRNA in protected_nucleotides:
num_protected += len(protected_nucleotides[rRNA])
deprotected_nucleotides = library.get_changed_nucleotides('deprotected', confidence_interval=library.experiment_settings.get_property('confidence_interval_cutoff'),
fold_change_cutoff=library.experiment_settings.get_property('fold_change_cutoff'))
num_deprotected = 0
for rRNA in deprotected_nucleotides:
num_deprotected += len(deprotected_nucleotides[rRNA])
if num_protected>0 or num_deprotected>0:
output_file = open(os.path.join(out_prefix, "%s.txt" % (library.lib_settings.sample_name)), 'w')
reference_pymol_script_file = open(library.experiment_settings.get_property('pymol_base_script'), 'rU')
for line in reference_pymol_script_file:
if line.startswith('#<insert nucleotide highlighting here>'):
if num_protected>0:
rRNA_selections = []
for rRNA in protected_nucleotides:
if len(protected_nucleotides[rRNA])>0:
rRNA_selections.append('%s and resi %s' % (rRNA, '+'.join([str(nucleotide.position) for
nucleotide in protected_nucleotides[rRNA]])))
outline = 'create protected_nucleotides, %s\n' % (' or '.join(rRNA_selections))
output_file.write(outline)
if num_deprotected>0:
rRNA_selections = []
for rRNA in deprotected_nucleotides:
if len(deprotected_nucleotides[rRNA])>0:
rRNA_selections.append('%s and resi %s' % (rRNA, '+'.join([str(nucleotide.position) for
nucleotide in deprotected_nucleotides[rRNA]])))
outline = 'create deprotected_nucleotides, %s\n' % (' or '.join(rRNA_selections))
output_file.write(outline)
elif line.startswith('#<color groups here>'):
if num_protected>0:
output_file.write('color vermillion, protected_nucleotides\n')
if num_deprotected>0:
output_file.write('color bluish_green, deprotected_nucleotides\n')
elif line.startswith('#<show spheres for changing nucleotides here>'):
if num_protected>0:
output_file.write('show spheres, protected_nucleotides\n')
if num_deprotected>0:
output_file.write('deprotected_nucleotides\n')
else:
output_file.write(line)
reference_pymol_script_file.close()
output_file.close()