From 5a3059d821cb6e01eced3da2c2d2a3f623faa813 Mon Sep 17 00:00:00 2001 From: a113n Date: Sat, 14 Jan 2017 17:04:59 +0800 Subject: [PATCH] Support more dbNSFP fields annotated by VEP With reference to the PR in brentp/geneimpacts#12 --- vcf2db.py | 42 +++++++++++++++++++++++++++++++++++++++--- 1 file changed, 39 insertions(+), 3 deletions(-) diff --git a/vcf2db.py b/vcf2db.py index 5214850..5c79b74 100644 --- a/vcf2db.py +++ b/vcf2db.py @@ -592,10 +592,26 @@ def variants_gene_columns(self): sql.Column("impact", sql.String(20)), sql.Column("impact_so", sql.String(20)), sql.Column("impact_severity", sql.String(4)), + sql.Column("domains", sql.TEXT()), sql.Column("polyphen_pred", sql.String(20)), sql.Column("polyphen_score", sql.Float()), sql.Column("sift_pred", sql.String(20)), sql.Column("sift_score", sql.Float()), + sql.Column("cadd_phred", sql.Float()), + sql.Column("fathmmmkl_score", sql.Float()), + sql.Column("fathmmmkl_pred", sql.String(20)), + sql.Column("mutationassessor_score", sql.Float()), + sql.Column("mutationassessor_pred", sql.String(20)), + sql.Column("mutationtaster_score", sql.Float()), + sql.Column("mutationtaster_pred", sql.String(20)), + sql.Column("metasvm_score", sql.Float()), + sql.Column("metasvm_pred", sql.String(20)), + sql.Column("metalr_score", sql.Float()), + sql.Column("metalr_pred", sql.String(20)), + sql.Column("provean_score", sql.Float()), + sql.Column("provean_pred", sql.String(20)), + sql.Column("phastcons100way_vertebrate", sql.Float()), + sql.Column("phylop100way_vertebrate", sql.Float()), ] @@ -724,8 +740,12 @@ def gene_info(d_and_impacts_headers): keys = ('gene', 'transcript', 'is_exonic', 'is_coding', 'is_splicing', 'is_lof', 'exon', 'codon_change', 'aa_change', 'aa_length', - 'biotype', 'top_consequence', 'so', 'effect_severity', - 'polyphen_pred', 'polyphen_score', 'sift_pred', 'sift_score') + 'biotype', 'top_consequence', 'so', 'effect_severity', 'domains', + 'polyphen_pred', 'polyphen_score', 'sift_pred', 'sift_score','cadd_phred', + 'fathmmmkl_score', 'fathmmmkl_pred', 'mutationassessor_score', 'mutationassessor_pred', + 'mutationtaster_score', 'mutationtaster_pred', 'metasvm_score', 'metasvm_pred', + 'metalr_score', 'metalr_pred', 'provean_score', 'provean_pred', + 'phastcons100way_vertebrate', 'phylop100way_vertebrate') if has_samples: for k in keys: @@ -764,10 +784,26 @@ def gene_info(d_and_impacts_headers): aa_change=impact.aa_change, aa_length=impact.aa_length, biotype=impact.biotype, top_consequence=impact.top_consequence, impact_so=impact.so, impact_severity=impact.effect_severity, + domains=impact.domains, polyphen_pred=impact.polyphen_pred, polyphen_score=impact.polyphen_score, sift_pred=impact.sift_pred, - sift_score=impact.sift_score)) + sift_score=impact.sift_score, + cadd_phred=impact.cadd_phred, + fathmmmkl_score=impact.fathmmmkl_score, + fathmmmkl_pred=impact.fathmmmkl_pred, + mutationassessor_score=impact.mutationassessor_score, + mutationassessor_pred=impact.mutationassessor_pred, + mutationtaster_score=impact.mutationtaster_score, + mutationtaster_pred=impact.mutationtaster_pred, + metasvm_score=impact.metasvm_score, + metasvm_pred=impact.metasvm_pred, + metalr_score=impact.metalr_score, + metalr_pred=impact.metalr_pred, + provean_score=impact.provean_score, + provean_pred=impact.provean_pred, + phastcons100way_vertebrate=impact.phastcons100way_vertebrate, + phylop100way_vertebrate=impact.phylop100way_vertebrate)) for k in impact.unused(): gimpacts[-1][k.lower()] = impact.effects.get(k, '') return d, gimpacts