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 mutation_rate_table(output, union_table):
print "***Writing {}".format(output)
page = markup.page()
css = """
#wrapper {
margin:0px auto;
width:800px;
}
body {
text-size:16px;
}
table {
border:3px solid #0B5FA5;
border-collapse:collapse;
font-family:"Trebuchet MS", Arial, Helvetica, sans-serif;
width:800px;
}
th {
background-color:#25547B;
padding:2px 7px 2px 7px;
color:#ffffff;
}
td {
border:1px solid black;
padding:2px 7px 2px 7px;
text-align:center;
}
#third_column_border {
border-right:3px solid #0B5FA5;
}
#alternate_row_color {
background-color:#BCDEFF;
color:#000000;
}
"""
page.init(css_string = css)
page.div(id = "wrapper")
page.table()
for test_name in union_table.keys():
mut_types = [type for type in DiffEntry.line_specs if len(type) == 3]
#Header
#First Row
page.tr()
page.th(test_name.replace('_', '').capitalize(), style = "font-size:1.3em", rowspan = 2)
for mut_type in mut_types:
page.th(mut_type, colspan = 3)
page.th()
page.tr.close()
#Second Row
page.tr()
for mut_type in mut_types:
page.th("TP", style = "font-size:.8em")
page.th("FN", style = "font-size:.8em")
page.th("FP", style = "font-size:.8em")
page.th("Files")
page.tr.close()
#Data Rows
is_alt = False
for pipeline, path in union_table[test_name].iteritems():
gd = GenomeDiff(path)
if is_alt:
page.tr(id = "alternate_row_color")
else:
page.tr()
is_alt = False if is_alt else True
page.th(pipeline.capitalize())
for mut_type in mut_types:
n_tp = len([mut for mut in gd[mut_type] if "compare" in mut and mut["compare"] == "TP"])
n_fn = len([mut for mut in gd[mut_type] if "compare" in mut and mut["compare"] == "FN"])
n_fp = len([mut for mut in gd[mut_type] if "compare" in mut and mut["compare"] == "FP"])
total = n_tp + n_fn + n_fp
if total:
page.td(n_tp)
page.td(n_fn)
page.td(n_fp, id = "third_column_border")
else:
page.td('-')
page.td('-')
page.td('-', id = "third_column_border")
href = os.path.relpath(path, os.path.split(output)[0])
page.td(e.a("union.gd", href = href))
page.tr.close()
page.br()
page.table.close()
page.div.close()
open(output, 'w').write(str(page) + '\n')