{% extends "layout.html" %} {% from "utils.html" import comments_panel, activity_panel %} {% from "variant/utils.html" import overlapping_panel, genes_panel, transcripts_panel, proteins_panel, pin_button, causative_button, modal_causative %} {% from "variant/tx_overview.html" import disease_associated, transcripts_overview %} {% from "variant/variant_details.html" import frequencies, gtcall_panel, observations_panel, old_observations, mappability_list, severity_list %} {% from "variant/buttons.html" import database_buttons, variant_tag_button, variant_tier_button, dismiss_variant_button, mosaic_variant_button, splice_junctions_button %} {% from "variant/components.html" import alignments, compounds_panel, clinsig_table, external_links, external_scripts, external_stylesheets, matching_variants, panel_classify, variant_scripts %} {% from "variant/sanger.html" import modal_cancel_sanger, modal_sanger, sanger_button %} {% from "variant/gene_disease_relations.html" import omim_phenotypes %} {% from "variant/rank_score_results.html" import rankscore_panel %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }} {% endblock %} {% block css %} {{ super() }} {{ external_stylesheets() }} {% endblock %} {% block top_nav %} {{ super() }} {% endblock %} {% block top_nav_right %} {% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {% endif %} {{ super() }} {% endblock %} {% block content_main %}
{% if variant.missing_data %}
Showing only first 30 genes!
{% endif %} {{ matching_variants(managed_variant, causatives, variant.matching_ranked, variant.matching_tiered) }}
{{ panel_classify(variant, institute, case, ACMG_OPTIONS, manual_rank_options, cancer_tier_options, dismiss_variant_options, mosaic_variant_options, evaluations) }}
{{ panel_summary() }}
{{ frequencies(variant) }} {% if config['LOQUSDB_SETTINGS'] %} {{ observations_panel(variant, observations, case) }} {% endif %} {{ old_observations(variant) }}
{{ severity_list(variant) }}
{{ panel_comment() }}
{{ panel_quality() }}
{{ gtcall_panel(variant) }}
{{ omim_phenotypes(variant) }}
{{ transcripts_overview(variant) }}
{{ overlapping_panel(variant, overlapping_vars, case, institute) }}
{% if rank_score_results %}
{{ rankscore_panel(rank_score_results) }}
{% endif %}
{% if variant.compounds %}
{{ compounds_panel(institute, case, variant) }}
{% endif %}
{{ external_links(case, variant, cancer, str) }}
{{ activity_panel(events|reverse) }}
{% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {{ modal_sanger(institute, case, variant, current_user) }} {% endif %} {% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {{ modal_cancel_sanger(institute, case, variant, current_user) }} {% endif %}
{{ modal_causative(case, institute, variant) }} {% endblock %} {% macro panel_quality() %}
Quality
Mappability (fracMatch)
{% if variant.callers and variant.callers|length > 0%}
Variant callers
{% endif %}
{% endmacro %} {% macro panel_comment() %}
{{ comments_panel(institute, case, current_user, variant.comments, variant_id=variant._id) }}
{% endmacro %} {% macro panel_summary() %}
Summary
{% set tmp_gene_info = [] %} {% if variant.first_rep_gene %} {% for transcript in variant.first_rep_gene.transcripts %} {% if transcript.is_primary %} {% do tmp_gene_info.append(variant.first_rep_gene) %} {% do tmp_gene_info.append(transcript) %} {% endif %} {% endfor %} {% if tmp_gene_info | length == 0 %} {% for transcript in variant.first_rep_gene.transcripts %} {% if transcript.refseq_id and transcript.refseq_id.startswith('NM_') %} {% do tmp_gene_info.append(variant.first_rep_gene) %} {% do tmp_gene_info.append(transcript) %} {% endif %} {% endfor %} {% endif %} {% endif %} {% set primary_gene = tmp_gene_info[0] %} {% if tmp_gene_info %} {% set primary_transcript = tmp_gene_info[1] %} {% set nr_genes = variant.genes | length %}
{{ primary_gene.hgnc_symbol }}; {{ primary_gene.description }} {% if nr_genes > 1 %} + {{ nr_genes-1 }} genes{% endif %}
{% endif %}
Alignment
{{ alignments(institute, case, variant, current_user, config, igv_tracks, rna_tracks) }}
{% endmacro %} {% block scripts %} {{ super() }} {{ external_scripts() }} {{ variant_scripts() }} {% endblock %}