def generate_html(region_layer: RegionLayer, results: ModuleResults,
_record_layer: RecordLayer,
_options_layer: OptionsLayer) -> HTMLSections:
""" Generates the HTML sections for all sideloaded annotations """
assert isinstance(results, SideloadedResults)
template = FileTemplate(
path.get_full_path(__file__, "templates", "general.html"))
tooltip_content = (
"This annotation was made externally by %r and not by antiSMASH")
html = HTMLSections("sideloaded")
tools_by_name = {}
areas_by_tool_name = defaultdict(list)
for area in results.get_areas():
if not region_layer.location.start <= area.start <= region_layer.location.end:
continue
areas_by_tool_name[area.tool.name].append(area)
tools_by_name[area.tool.name] = area.tool
for tool_name, areas in areas_by_tool_name.items():
# avoid HTML class names containing spaces
html_name = tool_name.replace(" ", "-")
html.add_detail_section(
tool_name,
template.render(
tool=tools_by_name[tool_name],
areas=areas,
tooltip_content=tooltip_content % tool_name,
), html_name)
return html
def generate_html(region_layer: RegionLayer, results: T2PKSResults,
_record_layer: RecordLayer,
options_layer: OptionsLayer) -> HTMLSections:
""" Generate the sidepanel HTML with results from the type II PKS module """
html = HTMLSections("t2pks")
predictions = []
for cluster in region_layer.get_unique_clusters():
if cluster.product == "T2PKS":
predictions.append(
results.cluster_predictions[cluster.get_cluster_number()])
template = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel.html"))
docs_url = options_layer.urls.docs_baseurl + "modules/t2pks"
tooltip_content = (
"Predictions of starter units, elongations, product classes, "
"and potential molecular weights for type II PKS clusters.")
tooltip_content += "<br>More detailed information is available <a href='%s' target='_blank'>here</a>." % docs_url
html.add_sidepanel_section(
"Type II PKS",
template.render(predictions=predictions,
tooltip_content=tooltip_content))
return html
def generate_div(tag: str, region_layer: RegionLayer,
record_layer: RecordLayer, template_name: str, tooltip: str,
results: List[Tuple[ReferenceRegion, float]],
proto_results: ScoresByProtocluster, active: bool, label: str,
url: Optional[str]) -> Markup:
""" Generates a single div within the details body for different kinds of
comparisons against a particular database.
Arguments:
tag: the type of analysis
region_layer: the relevant RegionLayer
record_layer: the relevant RecordLayer
template_name: the name of the template file to use
tooltip: the tooltip to use for the section
results: a ranked list of ReferenceRegion and scores
proto_results: details usd in calculating the region ranking
active: whether this particular div should be the default drawn
label: the name of the database to use within the div
url: a optional URL to use for linking a reference region externally
Returns:
a Markup instance of the generated div
"""
template = FileTemplate(
path.get_full_path(__file__, "templates", f"{template_name}.html"))
return template.render(
tag=tag,
record=record_layer,
region=region_layer,
tooltip=tooltip,
results=results,
proto_results=proto_results,
extra_class="comparison-container-active" if active else "",
class_name=label,
url=url)
def generate_html(region_layer: RegionLayer, _results: ModuleResults,
_record_layer: RecordLayer, _options_layer: OptionsLayer
) -> HTMLSections:
""" Generate the details section of NRPS/PKS domains in the main HTML output """
template = FileTemplate(path.get_full_path(__file__, 'templates', 'details.html'))
section = template.render(has_domain_details=has_domain_details, region=region_layer)
html = HTMLSections("nrps_pks")
html.add_detail_section("NRPS/PKS domains", section)
return html
def generate_webpage(records: List[Record],
results: List[Dict[str, module_results.ModuleResults]],
options: ConfigType) -> None:
""" Generates and writes the HTML itself """
generate_searchgtr_htmls(records, options)
json_records, js_domains = build_json_data(records, results, options)
write_regions_js(json_records, options.output_dir, js_domains)
with open(os.path.join(options.output_dir, 'index.html'),
'w') as result_file:
template = FileTemplate(
path.get_full_path(__file__, "templates", "overview.html"))
options_layer = OptionsLayer(options)
record_layers_with_regions = []
record_layers_without_regions = []
results_by_record_id = {
} # type: Dict[str, Dict[str, module_results.ModuleResults]]
for record, record_results in zip(records, results):
if record.get_regions():
record_layers_with_regions.append(
RecordLayer(record, None, options_layer))
else:
record_layers_without_regions.append(
RecordLayer(record, None, options_layer))
results_by_record_id[record.id] = record_results
regions_written = sum(len(record.get_regions()) for record in records)
job_id = os.path.basename(options.output_dir)
page_title = ""
if options.html_title:
page_title = options.html_title
elif options.sequences:
page_title, _ = os.path.splitext(
os.path.basename(options.sequences[0]))
elif options.reuse_results:
page_title, _ = os.path.splitext(
os.path.basename(options.reuse_results))
html_sections = generate_html_sections(record_layers_with_regions,
results_by_record_id, options)
aux = template.render(
records=record_layers_with_regions,
options=options_layer,
version=options.version,
extra_data=js_domains,
regions_written=regions_written,
sections=html_sections,
results_by_record_id=results_by_record_id,
config=options,
job_id=job_id,
page_title=page_title,
records_without_regions=record_layers_without_regions)
result_file.write(aux)
def generate_div(region_layer: RegionLayer, record_layer: RecordLayer,
options_layer: OptionsLayer, search_type: str) -> Markup:
""" Generates the specific HTML section of the body for a given variant of
clusterblast
"""
template = FileTemplate(
path.get_full_path(__file__, "templates", "%s.html" % search_type))
return template.render(record=record_layer,
region=region_layer,
options=options_layer)
def generate_html(region_layer: RegionLayer, results: NRPS_PKS_Results,
record_layer: RecordLayer,
options_layer: OptionsLayer) -> HTMLSections:
""" Generate the sidepanel HTML with results from the NRPS/PKS module """
html = HTMLSections("nrps_pks")
nrps_layer = NrpspksLayer(results, region_layer.region_feature,
record_layer)
features_with_domain_predictions: Dict[str, List[str]] = {}
for domain_name, consensus in results.consensus.items():
if not consensus:
continue
domain = record_layer.get_domain_by_name(domain_name)
features_with_domain_predictions[domain.locus_tag] = []
for feature_name, monomers in features_with_domain_predictions.items():
for domain in record_layer.get_cds_by_name(
feature_name).nrps_pks.domains:
monomer = results.consensus.get(domain.feature_name)
if monomer:
monomers.append(monomer)
prod_tt = (
"Shows estimated product structure and polymer for each candidate cluster in the region. "
"To show the product, click on the expander or the candidate cluster feature drawn in the overview. "
)
mon_tt = (
"Shows the predicted monomers for each adynelation domain and acyltransferase within genes. "
"Each gene prediction can be expanded to view detailed predictions of each domain. "
"Each prediction can be expanded to view the predictions by tool "
" (and, for some tools, further expanded for extra details). ")
if not nrps_layer.has_any_polymer():
return html
for filename, name, class_name, tooltip in [
("products.html", "NRPS/PKS products", "nrps_pks_products", prod_tt),
("monomers.html", "NRPS/PKS monomers", "", mon_tt)
]:
template = FileTemplate(
path.get_full_path(__file__, "templates", filename))
section = template.render(
record=record_layer,
region=nrps_layer,
results=results,
relevant_features=features_with_domain_predictions,
options=options_layer,
tooltip=tooltip)
html.add_sidepanel_section(name, section, class_name)
return html
def generate_html_sections(
records: List[RecordLayer],
results: Dict[str, Dict[str, module_results.ModuleResults]],
options: ConfigType) -> Dict[str, Dict[int, List[HTMLSections]]]:
""" Generates a mapping of record->region->HTMLSections for each record, region and module
Arguments:
records: a list of RecordLayers to pass through to the modules
results: a dictionary mapping record name to
a dictionary mapping each module name to its results object
options: the current antiSMASH config
Returns:
a dictionary mapping record id to
a dictionary mapping region number to
a list of HTMLSections, one for each module
"""
details = {}
for record in records:
record_details = {}
record_result = results[record.id]
for region in record.regions:
sections = []
for handler in region.handlers:
if handler.will_handle(region.products):
handler_results = record_result.get(handler.__name__)
if handler_results is None:
continue
sections.append(
handler.generate_html(region, handler_results, record,
options))
record_details[region.get_region_number()] = sections
if any(
record.get_pfam_domains_in_cds(cds)
for cds in region.cds_children):
html = HTMLSections("pfam-domains")
template = FileTemplate(
path.get_full_path(__file__, "templates",
"pfam_domains.html"))
tooltip = """Shows Pfam domains found in each gene within the region.
Click on each domain for more information about the domain's
accession, location, description, and any relevant Gene Ontology.
Domains with a bold border have Gene Ontology information. """
section = template.render(region=region,
record=record,
tooltip=tooltip)
html.add_detail_section("Pfam domains", section,
"pfam-details")
sections.append(html)
details[record.id] = record_details
return details
def generate_html(region_layer: RegionLayer, results: ClusterCompareResults,
record_layer: RecordLayer,
_options_layer: OptionsLayer) -> HTMLSections:
""" Generates the HTML sections for all variants
"""
html = HTMLSections("cluster-compare")
base_tooltip = (
"Shows careas that are similar to the current region to a reference database.<br>"
"Mouseover a score cell in the table to get a breakdown of how "
"the score was calculated.")
for label, db_results in results.by_database.items():
tooltip = base_tooltip
if db_results.description:
tooltip += f"{db_results.description}<br>"
if db_results.url:
tooltip += f"<br>Click on an accession to open that entry in the {db_results.name} database."
variant_results = db_results.by_region.get(
region_layer.get_region_number(), {})
divs: List[Tuple[str, str, Markup]] = []
for variant, result in sorted(variant_results.items()):
scores = result.scores_by_region[:DISPLAY_LIMIT]
scores_by_proto = result.details.details
tag = variant.replace(" ", "-")
search_type = "row"
kind = "Protocluster to Region"
if "ProtoToProto" in variant:
kind = "Protocluster to Protocluster"
search_type = "matrix"
elif "RegionToRegion" in variant:
kind = "Region to Region"
search_type = "single"
assert isinstance(scores_by_proto, list)
scores_by_proto = scores_by_proto[:DISPLAY_LIMIT]
div = generate_div(tag, region_layer, record_layer, search_type,
tooltip, scores, scores_by_proto,
len(divs) == 0, label, db_results.url)
divs.append((tag, kind, div))
template = FileTemplate(
path.get_full_path(__file__, "templates", "gathered.html"))
markup = template.render(variants=divs,
class_name=label,
description="Similar gene clusters",
tooltip=tooltip,
anchor=region_layer.anchor_id)
html.add_detail_section(f"{label} comparison", markup,
label + "-cluster-compare")
return html
def generate_html(region_layer: RegionLayer, results: RREFinderResults,
_record_layer: RecordLayer,
_options_layer: OptionsLayer) -> HTMLSections:
""" Generates HTML output for the module """
html = HTMLSections("rrefinder")
side_tooltip = ("RREfinder results sidepanel.")
template = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel.html"))
html.add_sidepanel_section(
"RREFinder",
template.render(results=results,
region=region_layer.region_feature,
tooltip=side_tooltip), "RREfinder")
return html
def generate_html(region_layer: RegionLayer, results: T2PKSResults,
_record_layer: RecordLayer,
_options_layer: OptionsLayer) -> HTMLSections:
""" Generate the sidepanel HTML with results from the type II PKS module """
html = HTMLSections("t2pks")
predictions = []
for cluster in region_layer.get_unique_clusters():
if cluster.product == "t2pks":
predictions.append(
results.cluster_predictions[cluster.get_cluster_number()])
template = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel.html"))
html.add_sidepanel_section("Type II PKS",
template.render(predictions=predictions))
return html
def generate_html(region_layer: RegionLayer, results: SactiResults,
record_layer: RecordLayer,
options_layer: OptionsLayer) -> HTMLSections:
""" Generates HTML for the module """
html = HTMLSections("sactipeptides")
motifs_in_region = defaultdict(list) # type: Dict[str, List[CDSMotif]]
for locus, motifs in results.motifs_by_locus.items():
for motif in motifs:
if motif.is_contained_by(region_layer.region_feature):
motifs_in_region[locus].append(motif)
sacti_layer = SactipeptideLayer(record_layer, region_layer.region_feature)
detail_tooltip = (
"Lists the possible core peptides for each biosynthetic enzyme, including the predicted class. "
"Each core peptide shows the leader and core peptide sequences, separated by a dash."
)
template = FileTemplate(
path.get_full_path(__file__, "templates", "details.html"))
details = template.render(record=record_layer,
region=sacti_layer,
options=options_layer,
results=motifs_in_region,
tooltip=detail_tooltip)
html.add_detail_section("Sactipeptides", details)
side_tooltip = (
"Lists the possible core peptides in the region. "
"Each core peptide lists its RODEO score and predicted core sequence.")
template = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel.html"))
sidepanel = template.render(record=record_layer,
region=sacti_layer,
options=options_layer,
results=motifs_in_region,
tooltip=side_tooltip)
html.add_sidepanel_section("Sactipeptides", sidepanel, '')
rre_tooltip = (
"Lists the RiPP recognition elements (RREs) detected by RREfinder. ")
template_rre = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel_rre.html"))
RREs = results.get_RREs_for_region(region_layer.region_feature)
html.add_sidepanel_section(
"RREfinder", template_rre.render(results=RREs, tooltip=rre_tooltip),
'RREfinder')
return html
def generate_html(region_layer: RegionLayer, _results: ModuleResults,
_record_layer: RecordLayer,
options_layer: OptionsLayer) -> HTMLSections:
""" Generate the details section of NRPS/PKS domains in the main HTML output """
template = FileTemplate(
path.get_full_path(__file__, 'templates', 'details.html'))
html = HTMLSections("nrps_pks")
if not has_domain_details(region_layer):
return html
# hide lids by default if none have predictions (e.g. in a minimal run)
hide_lids = not domains_have_predictions(region_layer)
section = template.render(has_domain_details=has_domain_details,
region=region_layer,
docs_url=options_layer.urls.docs_baseurl,
hide_lids=hide_lids)
html.add_detail_section("NRPS/PKS domains", section)
return html
def generate_html(region_layer: RegionLayer, results: ThioResults,
record_layer: RecordLayer,
options_layer: OptionsLayer) -> HTMLSections:
""" Generates HTML for the module """
html = HTMLSections("thiopeptides")
if not results:
return html
thio_layer = ThiopeptideLayer(record_layer, results,
region_layer.region_feature)
detail_tooltip = (
"Lists the possible core peptides for each biosynthetic enzyme, including the predicted class. "
"Each core peptide shows the leader and core peptide sequences, separated by a dash. "
"Predicted tail sequences are also shown.")
template = FileTemplate(
path.get_full_path(__file__, "templates", "details.html"))
details = template.render(record=record_layer,
cluster=thio_layer,
options=options_layer,
tooltip=detail_tooltip)
html.add_detail_section("Thiopeptides", details)
side_tooltip = (
"Lists the possible core peptides in the region. "
"Each core peptide lists its possible molecular weights "
"and the scores for cleavage site prediction and RODEO. "
"If relevant, other features, such as macrocycle and amidation, will also be listed."
)
template = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel.html"))
sidepanel = template.render(record=record_layer,
cluster=thio_layer,
options=options_layer,
tooltip=side_tooltip)
html.add_sidepanel_section("Thiopeptides", sidepanel, '')
rre_tooltip = (
"Lists the RiPP recognition elements (RREs) detected by RREfinder. ")
template_rre = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel_rre.html"))
RREs = results.get_RREs_for_region(region_layer.region_feature)
html.add_sidepanel_section(
"RREfinder", template_rre.render(results=RREs, tooltip=rre_tooltip),
'RREfinder')
return html
def generate_html(region_layer: RegionLayer, results: LanthiResults,
_record_layer: RecordLayer,
_options_layer: OptionsLayer) -> HTMLSections:
""" Generates HTML output for the module """
html = HTMLSections("lanthipeptides")
detail_tooltip = (
"Lists the possible core peptides for each biosynthetic enzyme, including the predicted class. "
"Each core peptide shows the leader and core peptide sequences, separated by a dash."
)
template = FileTemplate(
path.get_full_path(__file__, "templates", "details.html"))
motifs = results.get_motifs_for_region(region_layer.region_feature)
html.add_detail_section(
"Lanthipeptides",
template.render(results=motifs, tooltip=detail_tooltip))
side_tooltip = (
"Lists the possible core peptides in the region. "
"Each core peptide lists the number of lanthionine bridges, possible molecular weights, "
"and the scores for cleavage site prediction and RODEO.")
template = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel.html"))
motifs = results.get_motifs_for_region(region_layer.region_feature)
html.add_sidepanel_section(
"Lanthipeptides", template.render(results=motifs,
tooltip=side_tooltip))
return html
def generate_html(region_layer: RegionLayer, results: SactiResults,
record_layer: RecordLayer,
options_layer: OptionsLayer) -> HTMLSections:
""" Generates HTML for the module """
html = HTMLSections("sactipeptides")
motifs_in_region = defaultdict(list) # type: Dict[str, List[CDSMotif]]
for locus, motifs in results.motifs_by_locus.items():
for motif in motifs:
if motif.is_contained_by(region_layer.region_feature):
motifs_in_region[locus].append(motif)
sacti_layer = SactipeptideLayer(record_layer, region_layer.region_feature)
template = FileTemplate(
path.get_full_path(__file__, "templates", "details.html"))
details = template.render(record=record_layer,
region=sacti_layer,
options=options_layer,
results=motifs_in_region)
html.add_detail_section("Sactipeptides", details)
template = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel.html"))
sidepanel = template.render(record=record_layer,
region=sacti_layer,
options=options_layer,
results=motifs_in_region)
html.add_sidepanel_section("Sactipeptides", sidepanel)
return html
def generate_html(region_layer: RegionLayer, results: ThioResults,
record_layer: RecordLayer,
options_layer: OptionsLayer) -> HTMLSections:
""" Generates HTML for the module """
html = HTMLSections("thiopeptides")
if not results:
return html
thio_layer = ThiopeptideLayer(record_layer, results,
region_layer.region_feature)
template = FileTemplate(
path.get_full_path(__file__, "templates", "details.html"))
details = template.render(record=record_layer,
cluster=thio_layer,
options=options_layer)
html.add_detail_section("Thiopeptides", details)
template = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel.html"))
sidepanel = template.render(record=record_layer,
cluster=thio_layer,
options=options_layer)
html.add_sidepanel_section("Thiopeptides", sidepanel)
return html
def generate_html(region_layer: RegionLayer, results: NRPS_PKS_Results,
record_layer: RecordLayer,
options_layer: OptionsLayer) -> HTMLSections:
""" Generate the sidepanel HTML with results from the NRPS/PKS module """
html = HTMLSections("nrps_pks")
nrps_layer = NrpspksLayer(results, region_layer.region_feature,
record_layer)
features_with_domain_predictions = {} # type: Dict[str, List[str]]
for domain_name, consensus in results.consensus.items():
if not consensus:
continue
domain = record_layer.get_domain_by_name(domain_name)
features_with_domain_predictions[domain.locus_tag] = []
for feature_name, monomers in features_with_domain_predictions.items():
for domain in record_layer.get_cds_by_name(
feature_name).nrps_pks.domains:
monomer = results.consensus.get(domain.feature_name)
if monomer:
monomers.append(monomer)
for filename, name, class_name in [
("products.html", "NRPS/PKS products", "nrps_pks_products"),
("monomers.html", "NRPS/PKS monomers", "")
]:
template = FileTemplate(
path.get_full_path(__file__, "templates", filename))
section = template.render(
record=record_layer,
region=nrps_layer,
results=results,
relevant_features=features_with_domain_predictions,
options=options_layer)
html.add_sidepanel_section(name, section, class_name)
return html
def generate_html(region_layer: RegionLayer, results: RREFinderResults,
_record_layer: RecordLayer,
_options_layer: OptionsLayer) -> HTMLSections:
""" Generates HTML output for the module """
html = HTMLSections("rrefinder")
side_tooltip = ("RREfinder results sidepanel.")
template = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel.html"))
protoclusters = []
for proto in region_layer.get_unique_protoclusters():
if proto.get_protocluster_number() in results.hits_by_protocluster:
protoclusters.append(proto)
if protoclusters:
section = template.render(results=results,
protoclusters=protoclusters,
tooltip=side_tooltip)
html.add_sidepanel_section("RREFinder",
section,
class_name="RREfinder")
return html
def generate_html(region_layer: RegionLayer, results: LanthiResults,
_record_layer: RecordLayer, _options_layer: OptionsLayer
) -> HTMLSections:
""" Generates HTML output for the module """
html = HTMLSections("lanthipeptides")
template = FileTemplate(path.get_full_path(__file__, "templates", "details.html"))
motifs = results.get_motifs_for_region(region_layer.region_feature)
html.add_detail_section("Lanthipeptides", template.render(results=motifs))
template = FileTemplate(path.get_full_path(__file__, "templates", "sidepanel.html"))
motifs = results.get_motifs_for_region(region_layer.region_feature)
html.add_sidepanel_section("Lanthipeptides", template.render(results=motifs))
return html
def generate_html(region_layer: RegionLayer, results: LassoResults,
record_layer: RecordLayer, _options_layer: OptionsLayer) -> HTMLSections:
""" Generates HTML for the module """
html = HTMLSections("lassopeptides")
motifs_in_region = {}
for locus in results.motifs_by_locus:
if record_layer.get_cds_by_name(locus).is_contained_by(region_layer.region_feature):
motifs_in_region[locus] = results.motifs_by_locus[locus]
detail_tooltip = ("Lists the possible core peptides for each biosynthetic enzyme, including the predicted class. "
"Each core peptide shows the leader and core peptide sequences, separated by a dash.")
template = FileTemplate(path.get_full_path(__file__, "templates", "details.html"))
html.add_detail_section("Lasso peptides", template.render(results=motifs_in_region, tooltip=detail_tooltip))
side_tooltip = ("Lists the possible core peptides in the region. "
"Each core peptide lists the number of disulfide bridges, possible molecular weights, "
"and the scores for cleavage site prediction and RODEO.")
template = FileTemplate(path.get_full_path(__file__, "templates", "sidepanel.html"))
html.add_sidepanel_section("Lasso peptides", template.render(results=motifs_in_region, tooltip=side_tooltip))
return html
def generate_html(region_layer: RegionLayer, results: LassoResults,
record_layer: RecordLayer,
_options_layer: OptionsLayer) -> HTMLSections:
""" Generates HTML for the module """
html = HTMLSections("lassopeptides")
motifs_in_region = {}
for locus in results.motifs_by_locus:
if record_layer.get_cds_by_name(locus).is_contained_by(
region_layer.region_feature):
motifs_in_region[locus] = results.motifs_by_locus[locus]
template = FileTemplate(
path.get_full_path(__file__, "templates", "details.html"))
html.add_detail_section("Lasso peptides",
template.render(results=motifs_in_region))
template = FileTemplate(
path.get_full_path(__file__, "templates", "sidepanel.html"))
html.add_sidepanel_section("Lasso peptides",
template.render(results=motifs_in_region))
return html
def generate_webpage(records: List[Record],
results: List[Dict[str, module_results.ModuleResults]],
options: ConfigType) -> None:
""" Generates and writes the HTML itself """
generate_searchgtr_htmls(records, options)
json_records, js_domains = build_json_data(records, results, options)
write_regions_js(json_records, options.output_dir, js_domains)
with open(os.path.join(options.output_dir, 'index.html'),
'w') as result_file:
template = FileTemplate(
path.get_full_path(__file__, "templates", "overview.html"))
options_layer = OptionsLayer(options)
record_layers_with_regions = []
record_layers_without_regions = []
results_by_record_id = {
} # type: Dict[str, Dict[str, module_results.ModuleResults]]
for record, record_results in zip(records, results):
if record.get_regions():
record_layers_with_regions.append(
RecordLayer(record, None, options_layer))
else:
record_layers_without_regions.append(
RecordLayer(record, None, options_layer))
results_by_record_id[record.id] = record_results
regions_written = sum(len(record.get_regions()) for record in records)
job_id = os.path.basename(options.output_dir)
page_title = ""
if options.html_title:
page_title = options.html_title
elif options.sequences:
page_title, _ = os.path.splitext(
os.path.basename(options.sequences[0]))
elif options.reuse_results:
page_title, _ = os.path.splitext(
os.path.basename(options.reuse_results))
html_sections = generate_html_sections(record_layers_with_regions,
results_by_record_id, options)
doc_url = options.urls.docs_baseurl + "understanding_output/#the-antismash-5-region-concept"
svg_tooltip = (
"Shows the layout of the region, marking coding sequences and areas of interest. "
"Clicking a gene will select it and show any relevant details. "
"Clicking an area feature (e.g. a candidate cluster) will select all coding "
"sequences within that area. Double clicking an area feature will zoom to that area. "
"Multiple genes and area features can be selected by clicking them while holding the Ctrl key."
)
svg_tooltip += "<br>More detailed help is available <a href='%s' target='_blank'>here</a>." % doc_url
aux = template.render(
records=record_layers_with_regions,
options=options_layer,
version=options.version,
extra_data=js_domains,
regions_written=regions_written,
sections=html_sections,
results_by_record_id=results_by_record_id,
config=options,
job_id=job_id,
page_title=page_title,
records_without_regions=record_layers_without_regions,
svg_tooltip=svg_tooltip)
result_file.write(aux)
