def save_total_report(output_dirpath, min_contig, ref_fpath):
from quast_libs import reporting
asm_names = [
qutils.label_from_fpath(this) for this in reporting.assembly_fpaths
]
report = reporting.table(reporting.Fields.grouped_order)
subreports = []
ref_names = []
if qconfig.is_combined_ref and ref_labels_by_chromosomes:
ref_names = sorted(
list(set([ref for ref in ref_labels_by_chromosomes.values()])))
subreports = [
reporting.table(reporting.Fields.grouped_order, ref_name=ref_name)
for ref_name in ref_names
]
t = datetime.datetime.now()
return save(
join(output_dirpath, total_report_fname), {
'date': t.strftime('%d %B %Y, %A, %H:%M:%S'),
'assembliesNames': asm_names,
'referenceName':
qutils.name_from_fpath(ref_fpath) if ref_fpath else '',
'order': [i for i, _ in enumerate(asm_names)],
'report': report,
'subreferences': ref_names,
'subreports': subreports,
'minContig': min_contig
})
def save_total_report(output_dirpath, min_contig, ref_fpath):
from quast_libs import reporting
asm_names = [qutils.label_from_fpath(this) for this in reporting.assembly_fpaths]
report = reporting.table(reporting.Fields.grouped_order)
subreports = []
ref_names = []
if qconfig.is_combined_ref and ref_labels_by_chromosomes:
ref_names = sorted(list(set([ref for ref in ref_labels_by_chromosomes.values()])))
subreports = [reporting.table(reporting.Fields.grouped_order, ref_name=ref_name) for ref_name in ref_names]
t = datetime.datetime.now()
return save(join(output_dirpath, total_report_fname), {
'date': t.strftime('%d %B %Y, %A, %H:%M:%S'),
'assembliesNames': asm_names,
'referenceName': qutils.name_from_fpath(ref_fpath) if ref_fpath else '',
'order': [i for i, _ in enumerate(asm_names)],
'report': report,
'subreferences': ref_names,
'subreports': subreports,
'minContig': min_contig
})
def save_total_report(output_dirpath, min_contig, ref_fpath):
from quast_libs import reporting
asm_names = map(qutils.label_from_fpath, reporting.assembly_fpaths)
report = reporting.table(reporting.Fields.grouped_order)
t = datetime.datetime.now()
return save(join(output_dirpath, total_report_fname), {
'date': t.strftime('%d %B %Y, %A, %H:%M:%S'),
'assembliesNames': asm_names,
'referenceName': qutils.name_from_fpath(ref_fpath) if ref_fpath else '',
'order': [i for i, _ in enumerate(asm_names)],
'report': report,
'minContig': min_contig,
'assembliesWithNs': qconfig.potential_scaffolds_assemblies if qconfig.potential_scaffolds_assemblies else None
})
def save_total_report(output_dirpath, min_contig, ref_fpath):
from quast_libs import reporting
asm_names = [qutils.label_from_fpath(this) for this in reporting.assembly_fpaths]
report = reporting.table(reporting.Fields.grouped_order)
t = datetime.datetime.now()
return save(join(output_dirpath, total_report_fname), {
'date': t.strftime('%d %B %Y, %A, %H:%M:%S'),
'assembliesNames': asm_names,
'referenceName': qutils.name_from_fpath(ref_fpath) if ref_fpath else '',
'order': [i for i, _ in enumerate(asm_names)],
'report': report,
'minContig': min_contig,
'assembliesWithNs': qconfig.potential_scaffolds_assemblies if qconfig.potential_scaffolds_assemblies else None
})