def computeAndWrite(reactor):
"""The per-step work of reading reactor state and computing figures of interest is done here."""
ens = reactor['ensemble']
mon = reactor['monomer']
numbers = [a.number for a in ens.assemblies]
numbers.sort(reverse=True)
if len(numbers)==0:
sizestr = '0'
else:
sizestr = ','.join(['{:d}'.format(n) for n in numbers])
largest_assembly = ens.largest()
if largest_assembly is None:
largest_radius = ens.monomer_radius
else:
largest_radius = largest_assembly.radius
mean_radius = options.monomer_radius_nm
if len(numbers)>0:
mean_assembly_radius = ens.statistic(lambda x: x.radius, stats.mean)
mean_radius = (mon.number * options.monomer_radius_nm + mean_assembly_radius * ens.number)/float(mon.number + ens.number)
intwt_radius = intensityWeightedRadius(mon.number, options.monomer_radius_nm, [a.radius for a in ens.assemblies])
prop_active = mon.getProportionActivated(reactor.temperature)
prop_assembled = 1.0 - float(mon.number)/n_monomers
line = ("{r.num_steps:d}\t{time:1.2f}\t{r.temperature}\t{prop_active:1.1E}\t{m.number:d}\t{prop_assembled:1.1E}\t{a.number:d}\t" + \
"{largest_radius:1.2f}\t{mean_radius:s}\t{intwt_radius:s}\t{sizes:s}\n").format(
r=reactor, time=min(options.simulation_time, reactor.time), prop_active=prop_active, m=mon, prop_assembled=prop_assembled, a=ens,
largest_radius=largest_radius, mean_radius=na.formatNA(mean_radius, '{:1.2f}'),
intwt_radius=na.formatNA(intwt_radius, '{:1.2f}'), sizes=sizestr)
data_outs.write(line)
def computeAndWrite(reactor):
"""The per-step work of reading reactor state and computing figures of interest is done here."""
ens = reactor['ensemble']
mon = reactor['monomer']
numbers = [a.number for a in ens.assemblies]
numbers.sort(reverse=True)
if len(numbers) == 0:
sizestr = '0'
else:
sizestr = ','.join(['{:d}'.format(n) for n in numbers])
largest_assembly = ens.largest()
if largest_assembly is None:
largest_radius = ens.monomer_radius
else:
largest_radius = largest_assembly.radius
mean_radius = options.monomer_radius_nm
if len(numbers) > 0:
mean_assembly_radius = ens.statistic(lambda x: x.radius,
stats.mean)
mean_radius = (mon.number * options.monomer_radius_nm +
mean_assembly_radius *
ens.number) / float(mon.number + ens.number)
intwt_radius = intensityWeightedRadius(
mon.number, options.monomer_radius_nm,
[a.radius for a in ens.assemblies])
prop_active = mon.getProportionActivated(reactor.temperature)
prop_assembled = 1.0 - float(mon.number) / n_monomers
line = ("{r.num_steps:d}\t{time:1.2f}\t{r.temperature}\t{prop_active:1.1E}\t{m.number:d}\t{prop_assembled:1.1E}\t{a.number:d}\t" + \
"{largest_radius:1.2f}\t{mean_radius:s}\t{intwt_radius:s}\t{sizes:s}\n").format(
r=reactor, time=min(options.simulation_time, reactor.time), prop_active=prop_active, m=mon, prop_assembled=prop_assembled, a=ens,
largest_radius=largest_radius, mean_radius=na.formatNA(mean_radius, '{:1.2f}'),
intwt_radius=na.formatNA(intwt_radius, '{:1.2f}'), sizes=sizestr)
data_outs.write(line)
def __str__(self):
line = self.key
floatformat = "{:1.4f}"
line += '\n\tH/L \t' + '\t'.join([na.formatNA(r,format=floatformat) for r in self.heavy_light_ratio_list]) + '\n'
line += '\tH/L Normal.\t' + '\t'.join([na.formatNA(r,format=floatformat) for r in self.heavy_light_normalized_ratio_list]) + '\n'
line += '\tIntensity H\t' + '\t'.join([na.formatNA(r,format=floatformat) for r in self.intensity_h_list]) + '\n'
line += '\tIntensity L\t' + '\t'.join([na.formatNA(r,format=floatformat) for r in self.intensity_l_list]) + '\n'
line += '\tMS/MS Count\t{0:d}\n'.format(self.msms_count)
return line
def formatLine(self, entry):
""" Format the entry by headers. """
line = ""
tab = '\t'
# If entry is a dictionary...
for h in self._header_list:
try:
fmt = "{:" + h.format + '}'
if line != '':
line += tab
line += fmt.format(entry[h.name])
except ValueError as ve:
if h.format == 's': # string
line += fmt.format(naStringParser(entry[h.name]))
else:
raise ve
except TypeError as te:
# This will occur if entry[h.name] is None. Format as NA.
val = entry[h.name]
res = na.formatNA(val)
fmt = "{:s}"
line += fmt.format(res)
return line + '\n'
def formatLine(self, entry):
""" Format the entry by headers. """
line = ""
tab = '\t'
# If entry is a dictionary...
for h in self._header_list:
try:
fmt = "{:"+h.format+'}'
if line != '':
line += tab
line += fmt.format(entry[h.name])
except ValueError as ve:
if h.format=='s': # string
line += fmt.format(naStringParser(entry[h.name]))
else:
raise ve
except TypeError as te:
# This will occur if entry[h.name] is None. Format as NA.
val = entry[h.name]
res = na.formatNA(val)
fmt = "{:s}"
line += fmt.format(res)
return line + '\n'
# Write output
n_written = 0
# Tack sequence on the end, for better readability
columns = headers[:]
columns.remove("sequence")
data_outs.write("\t".join(columns) + "\tp.value\tp.value.adj\tsequence\n")
for key in keys:
flds = data[key]
# entropy = flds['entropy']
# length = flds['length'] # length of the region
pval = p_value_dict[key]
adj_pval = None
if options.adjust:
adj_pval = adjusted_p_value_dict[key]
line = "\t".join(["{}".format(flds[col]) for col in columns])
line += "\t{pval}\t{adj_pval}".format(
pval=na.formatNA(pval, format="{:1.3E}"), adj_pval=na.formatNA(adj_pval, format="{:1.3E}")
)
line += "\t" + flds["sequence"] + "\n"
data_outs.write(line)
n_written += 1
# Write out stopping time
data_outs.write("# Run finished {}\n".format(util.timestamp()))
# Shut down output
if not options.out_fname is None:
info_outs.write("# Wrote {} lines to {}\n".format(n_written, options.out_fname))
outf.close()
#adjusted_p_value_dict = dict([(k, v) for (k,v) in zip(keys, adjusted_p_values)])
# Write output
n_written = 0
# Tack sequence on the end, for better readability
columns = headers[:]
columns.remove('sequence')
data_outs.write('\t'.join(columns) + "\tp.value\tp.value.adj\tsequence\n")
for key in keys:
flds = data[key]
#entropy = flds['entropy']
#length = flds['length'] # length of the region
pval = p_value_dict[key]
adj_pval = None
if options.adjust:
adj_pval = adjusted_p_value_dict[key]
line = '\t'.join(['{}'.format(flds[col]) for col in columns])
line += "\t{pval}\t{adj_pval}".format(pval=na.formatNA(pval, format="{:1.3E}"), adj_pval=na.formatNA(adj_pval, format="{:1.3E}"))
line += '\t' + flds['sequence'] + '\n'
data_outs.write(line)
n_written += 1
# Write out stopping time
data_outs.write("# Run finished {}\n".format(util.timestamp()))
# Shut down output
if not options.out_fname is None:
info_outs.write("# Wrote {} lines to {}\n".format(n_written, options.out_fname))
outf.close()
for (pos, pep) in pep_list:
n_peps += 1
pepid = "{}-{}".format(options.target_orf, n_peps)
line = gap*pos + pep.sequence + gap*(len_prot-(len(pep.sequence)+pos))
outs.write(">{}\n{}\n".format(pepid, line))
elif options.output_type == 'ratio':
outs.write("seq\tmod.seq\tbegin\tend\tratio\tint.ratio\tintensity\tintensity.h\tintensity.l\n")
n_written = 0
for (pos, pep) in pep_list:
#ratio_stats = pep.getHeavyLightRatioSummary()
for (ri,ratio) in enumerate(pep.heavy_light_ratio_list):
inth = pep.intensity_h_list[ri]
intl = pep.intensity_l_list[ri]
inten = None
# Ratio of intensities
int_ratio = None
if not (na.isNA(inth) or na.isNA(intl)):
inten = inth+intl
if intl>0:
int_ratio = inth/float(intl)
outs.write("{seq}\t{modseq}\t{begin}\t{end}\t{ratio}\t{intratio}\t{inten}\t{inth}\t{intl}\n".format(
seq=pep.sequence, modseq=pep.modified_sequence, begin=pos+1, end=pos+len(pep.sequence),
ratio=na.formatNA(ratio), intratio=na.formatNA(int_ratio), inten=na.formatNA(inten), inth=na.formatNA(inth), intl=na.formatNA(intl)))
n_written += 1
info_outs.write("# Wrote {} peptide records\n".format(n_written))
#outs.write("{seq}\t{begin}\t{end}\t{ratio}\t{ratio_n}\n".format(
# seq=pep.sequence, begin=pos+1, end=pos+len(pep.sequence), ratio=na.formatNA(ratio_stats.median), ratio_n=na.formatNA(ratio_stats.n)))
# Write output
n_written = 0
# Tack sequence on the end, for better readability
columns = headers[:]
columns.remove('sequence')
data_outs.write('\t'.join(columns) + "\tp.value\tp.value.adj\tsequence\n")
for key in keys:
flds = data[key]
#entropy = flds['entropy']
#length = flds['length'] # length of the region
pval = p_value_dict[key]
adj_pval = None
if options.adjust:
adj_pval = adjusted_p_value_dict[key]
line = '\t'.join(['{}'.format(flds[col]) for col in columns])
line += "\t{pval}\t{adj_pval}".format(
pval=na.formatNA(pval, format="{:1.3E}"),
adj_pval=na.formatNA(adj_pval, format="{:1.3E}"))
line += '\t' + flds['sequence'] + '\n'
data_outs.write(line)
n_written += 1
# Write out stopping time
data_outs.write("# Run finished {}\n".format(util.timestamp()))
# Shut down output
if not options.out_fname is None:
info_outs.write("# Wrote {} lines to {}\n".format(
n_written, options.out_fname))
outf.close()
if not options.sequence is None:
seq = options.sequence
if options.degap and not seq is None:
seq = seq.replace('-','')
if options.write_report and not seq is None:
score_res = motif.score(seq, matrix, return_windows=True)
header = 'pos\tresidue\tscore\tabove.threshold\twindow\n'
outs.write(header)
for sentry in score_res.results:
resthresh_out = ' '
if sentry.score >= options.score_threshold and sentry.residue != '-':
resthresh_out = "*"
line = "{pos}\t{aa}\t{resscore}\t{resthresh}\t{win}\n".format(
pos=sentry.pos+1, aa=sentry.residue, resscore=na.formatNA(sentry.score,"{:1.2f}"), resthresh=resthresh_out, win=sentry.window)
outs.write(line)
sys.exit()
if options.write_report and not orf_dict is None:
header = "orf\tnum.sites\tnum.motifs\tprop.sites\tmax.score\t" + \
'\t'.join(['num.motifs.{:d}'.format(i+1) for i in range(options.maximum_frequency_bin)]) + '\tnum.motifs.longer\n'
outs.write(header)
for (hdr,rawseq) in zip(headers,sequences):
orf = biofile.firstField(hdr)
if options.translate:
seq = translate.translate(rawseq)
if seq is None:
outs.write("# Skipping {} -- bad translation\n".format(orf))
continue
else:
"seq\tmod.seq\tbegin\tend\tratio\tint.ratio\tintensity\tintensity.h\tintensity.l\n"
)
n_written = 0
for (pos, pep) in pep_list:
#ratio_stats = pep.getHeavyLightRatioSummary()
for (ri, ratio) in enumerate(pep.heavy_light_ratio_list):
inth = pep.intensity_h_list[ri]
intl = pep.intensity_l_list[ri]
inten = None
# Ratio of intensities
int_ratio = None
if not (na.isNA(inth) or na.isNA(intl)):
inten = inth + intl
if intl > 0:
int_ratio = inth / float(intl)
outs.write(
"{seq}\t{modseq}\t{begin}\t{end}\t{ratio}\t{intratio}\t{inten}\t{inth}\t{intl}\n"
.format(seq=pep.sequence,
modseq=pep.modified_sequence,
begin=pos + 1,
end=pos + len(pep.sequence),
ratio=na.formatNA(ratio),
intratio=na.formatNA(int_ratio),
inten=na.formatNA(inten),
inth=na.formatNA(inth),
intl=na.formatNA(intl)))
n_written += 1
info_outs.write("# Wrote {} peptide records\n".format(n_written))
#outs.write("{seq}\t{begin}\t{end}\t{ratio}\t{ratio_n}\n".format(
# seq=pep.sequence, begin=pos+1, end=pos+len(pep.sequence), ratio=na.formatNA(ratio_stats.median), ratio_n=na.formatNA(ratio_stats.n)))