def create_validation_content(self, page, job_paths, key = "", title = ""):
wrangler = FileWrangler(job_paths, key)
page.div(id = "validation_table")
#Table header.
page.table()
page.tr()
page.th()#Empty one to offset run_names below it.
for job_id in wrangler.job_ids:
page.th(job_id.capitalize(), class_ = "validation_table", colspan = 3)
page.th()
page.tr.close()
page.tr()
page.th("Name")
for i in wrangler.job_ids:
page.th("TP")
page.th("FN")
page.th("FP")
page.th("Files")
page.tr.close()
#Table data.
is_alt = False
for run_id in wrangler.run_ids:
if is_alt:
page.tr(class_ = "alternate_row")
else:
page.tr()
is_alt = False if is_alt else True
page.th(run_id)
file_anchors = list()
for job_id in wrangler.job_ids:
if wrangler.file_exists(job_id, run_id):
path = wrangler.get_file(job_id, run_id)
gd = GenomeDiff(path, header_only = True)
header_info = gd.header_info()
assert "TP|FN|FP" in header_info.other
validation = header_info.other["TP|FN|FP"].split('|')
tp = validation[0]
fn = validation[1]
fp = validation[2]
page.td(tp, class_ = "validation_table_column")
page.td(fn, class_ = "validation_table_column")
page.td(fp, class_ = "validation_table_last_column")
href = os.path.relpath(path, self.settings.job_dir)
file_anchors.append(e.a(job_id.capitalize(), href = href))
else:
page.td('-', class_ = "validation_table_column")
page.td('-', class_ = "validation_table_column")
page.td('-', class_ = "validation_table_last_column")
page.th("/".join(file_anchors))
page.tr.close()
page.table.close()
page.div.close()
return page
def write_mutation_rates_table(self, job_paths):
verbose = True
print "***Writing {}".format(self.settings.job_mutation_rates_table_path)
table = open(self.settings.job_mutation_rates_table_path, 'w')
mut_types = [type for type in DiffEntry.line_specs if len(type) == 3]
table.write("run_id\tjob_id\t{}\n".format("\t".join(mut_types)))
wrangler = FileWrangler(job_paths, "comp.gd")
for run_id in wrangler.run_ids:
for job_id in wrangler.job_ids:
table.write("{}\t{}".format(run_id, job_id))
if wrangler.file_exists(job_id, run_id):
path = wrangler.get_file(job_id, run_id)
gd = GenomeDiff(path)
header_info = gd.header_info()
assert "TP|FN|FP" in header_info.other
for mut_type in mut_types:
n_tp = float(len([mut for mut in gd[mut_type] if "validation" in mut and mut["validation"] == "TP"]))
n_fn = float(len([mut for mut in gd[mut_type] if "validation" in mut and mut["validation"] == "FN"]))
n_fp = float(len([mut for mut in gd[mut_type] if "validation" in mut and mut["validation"] == "FP"]))
total = float(n_tp + n_fn + n_fp)
value = ""
if total:
value = "{}|{}|{}".format(n_tp, n_fn, n_fp)
else:
value = "-"
table.write("\t{}".format(value))
if verbose:
print "\t\t[mut_type]:", mut_type
print "\t\t[tdr]:", value
print ""
else:
for i in mut_types:
table.write("\t-")
table.write("\n")
table.close()
def write_validation_table(self, job_paths):
print "***Writing {}".format(self.settings.job_validation_table_path)
table = open(self.settings.job_validation_table_path, 'w')
table.write("run_id\tjob_id\tTP\tFN\tFP\n")
wrangler = FileWrangler(job_paths, "comp.gd")
for job_id, run_id, path in wrangler:
if wrangler.file_exists(job_id, run_id):
gd = GenomeDiff(path, header_only = True)
header_info = gd.header_info()
assert "TP|FN|FP" in header_info.other
validation = header_info.other["TP|FN|FP"].split('|')
tp = validation[0]
fn = validation[1]
fp = validation[2]
table.write("{}\t{}\t{}\t{}\t{}\n".format(run_id, job_id, tp, fn, fp))
else:
table.write("{}\t{}\t'-'\t'-'\t'-'\n".format(run_id, job_id))
table.close()
