"searching": true,
"bLengthChange": false,
"paging": true,
"info": false
} );
} );
</script>
"""
if core_genome_bed:
core_size = get_core_genome_size(core_genome_bed)
for i in reference_genomes:
if "cgMLST" in i:
ref_size = get_reference_genome_size(i)
fraction_core = round(float(core_size) / float(ref_size) * 100, 2)
core_str = """
- Size of the reference genome: %s
- Size of the core genome: %s (%s %% of the reference)
""" % (ref_size,
core_size,
fraction_core)
else:
core_size = False
core_str = ""
multiqc_table = report.get_multiqc_table(multiqc_assembly,
multiqc_mapping_list)
table_lowcoverage_contigs = quality_table(low_cov_fastas,
********
.. raw:: html
{table_virulence}
Resistance (RGI/CARD)
----------------------
.. raw:: html
{table_resistance}
"""
with open(output_file, "w") as fh:
publish_file(
source=io.StringIO(report_str),
destination=fh,
writer_name="html",
settings_overrides={"stylesheet_path": ""},
)
net = convert2cytoscapeJSON(get_MN_tree(snp_table), leaf2mlst)
write_report(output_file, STYLE, SCRIPT % net, virulence_reports, blast_files,
resistance_reports, spanning_tree_core, low_cov_fastas,
ete_figure_counts, mlst_tree, snp_table,
get_core_genome_size(core_genome_bed),
get_reference_genome_size(reference_genome), virulence_table)