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Merge pull request #255 from monarch-initiative/counts_table
Counts table
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,158 @@ | ||
| import typing | ||
|
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| from jinja2 import Environment, PackageLoader | ||
| from collections import namedtuple, defaultdict | ||
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| from gpsea.model import Cohort, Variant, VariantEffect | ||
| from ._formatter import VariantFormatter | ||
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| ToDisplay = namedtuple('ToDisplay', ['hgvs_cdna', 'hgvsp', 'variant_effects']) | ||
|
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| VariantData = namedtuple('VariantData', ['variant_key', 'hgvs_cdna', 'hgvsp', 'variant_effects']) | ||
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| class CohortVariantViewer: | ||
| """ | ||
| `CohortVariantViewer` creates an HTML report with the cohort variants. | ||
| The report can be either written into an HTML file or displayed in a Jupyter notebook. | ||
| See :ref:show-cohort-variants: for an example usage. | ||
| """ | ||
|
|
||
| def __init__( | ||
| self, | ||
| tx_id: str | ||
| ): | ||
| """ | ||
| Args: | ||
| tx_id (str): The transcript identifier (Usually, the MANE RefSeq transcript, that should start with "NM_") | ||
| """ | ||
| environment = Environment(loader=PackageLoader('gpsea.view', 'templates')) | ||
| self._cohort_template = environment.get_template("all_variants.html") | ||
| self._var_formatter = VariantFormatter(tx_id) | ||
| if not tx_id.startswith("NM"): | ||
| print(f"[WARNING] Non-RefSeq transcript id: {tx_id}") | ||
| self._transcript_id = tx_id | ||
|
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||
| def process( | ||
| self, | ||
| cohort: Cohort, | ||
| only_hgvs: bool = True | ||
| ) -> str: | ||
| """ | ||
| Create an HTML that should be shown with ``display(HTML(..))`` of the ipython package. | ||
| Args: | ||
| cohort (Cohort): The cohort being analyzed in the current notebook. | ||
| only_hgvs (bool): Do not show the transcript ID part of the HGVS annotation, just the annotation. | ||
| Returns: | ||
| str: an HTML string with parameterized template for rendering | ||
| """ | ||
| context = self._prepare_context(cohort, only_hgvs=only_hgvs) | ||
| return self._cohort_template.render(context) | ||
|
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| def _prepare_context( | ||
| self, | ||
| cohort: Cohort, | ||
| only_hgvs: bool, | ||
| ) -> typing.Mapping[str, typing.Any]: | ||
| variant_count_dictionary = defaultdict(int) | ||
| variant_effect_count_dictionary = defaultdict(int) | ||
| variant_key_to_variant = dict() | ||
| for var in cohort.all_variants(): | ||
| var_key = var.variant_info.variant_key | ||
| vdata = self._get_variant_data(var, only_hgvs) | ||
| variant_key_to_variant[var_key] = vdata | ||
| variant_count_dictionary[var_key] += 1 | ||
| for v_eff in vdata.variant_effects: | ||
| variant_effect_count_dictionary[v_eff] += 1 | ||
| variant_counts = list() | ||
| variant_effect_counts = list() | ||
| for var_key, count in variant_count_dictionary.items(): | ||
| var_data = variant_key_to_variant[var_key] | ||
| variant_counts.append( | ||
| { | ||
| "variant_key": var_data.variant_key, | ||
| "variant": var_data.hgvs_cdna, | ||
| "variant_name": var_data.hgvs_cdna, | ||
| "protein_name": var_data.hgvsp, | ||
| "variant_effects": ", ".join(var_data.variant_effects), | ||
| "count": count, | ||
| } | ||
| ) | ||
| for v_effect, count in variant_effect_count_dictionary.items(): | ||
| variant_effect_counts.append( | ||
| { | ||
| "effect": v_effect, | ||
| "count": count | ||
| } | ||
| ) | ||
| variant_counts = sorted(variant_counts, key=lambda row: row.get("count"), reverse=True) | ||
| variant_effect_counts = sorted(variant_effect_counts, key=lambda row: row.get("count"), reverse=True) | ||
|
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| # The following dictionary is used by the Jinja2 HTML template | ||
| return { | ||
| "has_transcript": False, | ||
| "variant_count_list": variant_counts, | ||
| "variant_effect_count_list": variant_effect_counts, | ||
| "total_unique_allele_count": len(variant_counts) | ||
| } | ||
|
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| def _get_variant_data( | ||
| self, | ||
| variant: Variant, | ||
| only_hgvs: bool | ||
| ) -> VariantData: | ||
| """ | ||
| Get user-friendly strings (e.g., HGVS for our target transcript) to match to the chromosomal strings | ||
| Args: | ||
| variant (Variant): The variant to be formatted. | ||
| only_hgvs (bool): do not show the transcript ID part of the HGVS annotation, just the annotation. | ||
| Returns: | ||
| VariantData: a named tuple with variant data formatted for human consumption. | ||
| """ | ||
| variant_key = variant.variant_info.variant_key | ||
| if variant.variant_info.has_sv_info(): | ||
| sv_info = variant.variant_info.sv_info | ||
| gene_symbol = sv_info.gene_symbol | ||
| display = f"SV involving {gene_symbol}" | ||
| effect = VariantEffect.structural_so_id_to_display(so_term=sv_info.structural_type) | ||
| return VariantData( | ||
| variant_key=variant_key, | ||
| hgvs_cdna=display, | ||
| hgvsp="p.?", | ||
| variant_effects=[effect], | ||
| ) | ||
| else: | ||
| variant_key = variant.variant_info.variant_key | ||
| display = self._var_formatter.format_as_string(variant) | ||
| tx_annotation = variant.get_tx_anno_by_tx_id(self._transcript_id) | ||
| if tx_annotation is not None: | ||
| hgvsp = tx_annotation.hgvsp | ||
| var_effects = [var_eff.to_display() for var_eff in tx_annotation.variant_effects] | ||
| else: | ||
| hgvsp = None | ||
| var_effects = [] | ||
| if only_hgvs: | ||
| # do not show the transcript id | ||
| fields_dna = display.split(":") | ||
| if len(fields_dna) > 1: | ||
| display_hgvs_cDNA = fields_dna[1] | ||
| else: | ||
| display_hgvs_cDNA = fields_dna[0] | ||
|
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| fields_ps = hgvsp.split(":") if hgvsp is not None else (None,) | ||
| if len(fields_ps) > 1: | ||
| hgvsp = fields_ps[1] | ||
| else: | ||
| hgvsp = fields_ps[0] | ||
| return VariantData( | ||
| variant_key=variant_key, | ||
| hgvs_cdna=display_hgvs_cDNA, | ||
| hgvsp=hgvsp, | ||
| variant_effects=var_effects, | ||
| ) |
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