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,
sample2gc,
sample2median_depth,
sampls2cumulated_size,
sample2n_contigs,
sample2scientific_name,
undetermined_snps_files=undetermined_snp_tables,
core_genome_size=core_size)
snp_heatmap_str = ""
for n, snp_table in enumerate(snp_tables):
snp_heatmap_str += '''
%s
sampls2cumulated_size,
sampls2cumulated_size_filtered,
sample2n_contigs,
sample2scientific_name,
low_cov_detail=low_cov_detail)
table_virulence = report.virulence_table(virulence_reports, blast_files,
ordered_samples)
mash_table = report.get_mash_table(mash_results, mash_detail,
sample2scientific_name)
centrifuge_table = report.get_centrifuge_table(centrifuge_tables,
sample2scientific_name)
multiqc_table = report.get_multiqc_table(assembly_multiqc=multiqc_assembly)
qualimap_table = report.qualimap_table(qualimap_reports, self_mapping=True)
report_str = f"""
.. raw:: html
{SCRIPT}
{STYLE}
=============================================================
Diag Pipeline - Virulence report
=============================================================
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(mapping_multiqc=multiqc_mapping_list)
qualimap_table = report.qualimap_table(qualimap_reports)
snp_heatmap_str = ""
for n, snp_table in enumerate(snp_tables):
snp_heatmap_str += '''
%s
******************************************************
.. raw:: html
%s