diff --git a/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py b/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py index 5a0a7c71..1b4bce6a 100644 --- a/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py +++ b/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py @@ -60,6 +60,7 @@ def save_to_db(self, info, variant_id, conn): self.insert_annotation(variant_id, info, "GnomAD_popmax=", recent_annotation_ids['gnomad_popmax'], conn, value_modifier_function = lambda value : value.upper()) self.insert_annotation(variant_id, info, "GnomAD_AF_popmax=", recent_annotation_ids['gnomad_popmax_AF'], conn) self.insert_annotation(variant_id, info, "GnomADm_AC_hom=", recent_annotation_ids['gnomadm_ac_hom'], conn) + self.insert_annotation(variant_id, info, "GnomAD_AC_popmax=", recent_annotation_ids['gnomad_popmax_AC'], conn) self.insert_annotation(variant_id, info, "BRCA_exchange_clin_sig_short=", recent_annotation_ids['brca_exchange_clinical_significance'], conn, value_modifier_function = lambda value : value.replace('_', ' ').replace(',', ';')) @@ -164,7 +165,7 @@ def write_vcf_annoate_config(self, one_variant): ## add gnomAD annotation if self.job_config['do_gnomad']: - config_file.write(paths.gnomad_path + "\tGnomAD\tAF,AC,hom,hemi,het,popmax,AF_popmax\t\n") + config_file.write(paths.gnomad_path + "\tGnomAD\tAF,AC,hom,hemi,het,popmax,AF_popmax,AC_popmax\t\n") config_file.write(paths.gnomad_m_path + "\tGnomADm\tAC_hom\t\n") ## add BRCA_exchange clinical significance diff --git a/src/common/models.py b/src/common/models.py index 32d649d2..a9d1a592 100644 --- a/src/common/models.py +++ b/src/common/models.py @@ -109,6 +109,7 @@ class AllAnnotations: gnomad_popmax: Annotation = None gnomadm_ac_hom: Annotation = None gnomad_popmax_AF: Annotation = None + gnomad_popmax_AC: Annotation = None brca_exchange_clinical_significance: Annotation = None arup_classification: Annotation = None @@ -881,13 +882,7 @@ def get_preferred_transcripts(self): if len(sortable_dict) == 0: return None - #print("sortable dict:") - #print(sortable_dict) transcripts_sorted, consequences_sorted = functions.sort_transcript_dict(sortable_dict) - #print("transcripts_sorted:") - #print(transcripts_sorted) - #print("consequences_sorted:") - #print(consequences_sorted) result.append(consequences_sorted.pop(0)) # always append the first one for consequence in consequences_sorted: # scan for all mane select transcripts if consequence.transcript.is_mane_select: diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html index c25e2d88..0eba0142 100644 --- a/src/frontend_celery/webapp/templates/index.html +++ b/src/frontend_celery/webapp/templates/index.html @@ -104,6 +104,7 @@

Changelog

  • Added cDNA search
  • Update search help
  • Added COSMIC COSV ids & moved COSMIC links from consequence table to the variant banner.
  • +
  • Added GnomAD popmax allele count (AC) annotation
  • Bugfixes: Known issues: