コード例 #1
0
ファイル: html_factory.py プロジェクト: GeoffColburn/pydcamp
    def write_index_page(self, job_paths):
        print "***Writing {}".format(self.settings.job_index_path)
        page = markup.page()
        css_path = self.copy_css_style(self.settings.job_index_path)
        css = [css_path]
        page.init(css = css_path)
        page = self.create_validation_content(page, job_paths, key = "comp.gd")

        open(self.settings.job_index_path, 'w').write(str(page) + '\n')
コード例 #2
0
ファイル: html_factory.py プロジェクト: GeoffColburn/pydcamp
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')