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Add loftee_labels and no_lof_flags parameters to filter_vep_transcript_csqs_expr for filtering by loftee labels and flags #753

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Add loftee_labels and no_lof_flags parameters to filter_vep_transcript_csqs_expr for filtering by loftee labels and flags #753

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24 changes: 22 additions & 2 deletions gnomad/utils/vep.py
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Original file line number Diff line number Diff line change
Expand Up @@ -867,6 +867,8 @@ def filter_vep_transcript_csqs_expr(
mane_select: bool = False,
ensembl_only: bool = False,
protein_coding: bool = False,
loftee_labels: Optional[List[str]] = None,
no_lof_flags: bool = False,
csqs: Optional[List[str]] = None,
keep_csqs: bool = True,
genes: Optional[List[str]] = None,
Expand Down Expand Up @@ -896,6 +898,10 @@ def filter_vep_transcript_csqs_expr(
Emsembl. Default is False.
:param protein_coding: Whether to filter to only protein-coding transcripts.
Default is False.
:param loftee_labels: List of LOFTEE labels to filter to. Default is None, which
filters to all LOFTEE labels.
:param no_lof_flags: Whether to filter to consequences with no LOFTEE flags.
Default is False.
:param csqs: Optional list of consequence terms to filter to. Transcript
consequences are filtered to those where 'most_severe_consequence' is in the
list of consequence terms `csqs`. Default is None.
Expand All @@ -919,9 +925,9 @@ def filter_vep_transcript_csqs_expr(
logger.info("Filtering to most severe consequence of synonymous_variant...")
csqs = ["synonymous_variant"]

csq_fields = csq_expr if is_struct else csq_expr.dtype.element_type.fields
if csqs is not None:
fields = csq_expr if is_struct else csq_expr.dtype.element_type.fields
if "most_severe_consequence" not in fields:
if "most_severe_consequence" not in csq_fields:
logger.info("Adding most_severe_consequence annotation...")
csq_expr = add_most_severe_consequence_to_consequence(csq_expr)

Expand Down Expand Up @@ -955,6 +961,20 @@ def _filter_vep_csq_expr(
if protein_coding:
logger.info("Filtering to protein coding transcripts...")
criteria &= csq.biotype == "protein_coding"
if loftee_labels:
logger.info(
"Filtering to consequences with LOFTEE labels: %s...", loftee_labels
)
criteria &= hl.set(loftee_labels).contains(csq.lof)
if no_lof_flags:
logger.info("Filtering to consequences with no LOFTEE flags...")
if "lof_flags" in csq_fields:
criteria &= hl.is_missing(csq.lof_flags) | (csq.lof_flags == "")
else:
logger.warning(
"'lof_flags' not present in consequence struct, no consequences "
"are filtered based on LOFTEE flags"
)
if genes is not None:
logger.info("Filtering to genes of interest...")
gene_field = "gene_symbol" if match_by_gene_symbol else "gene_id"
Expand Down
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