BioMCP

Feature: Search for genetic variants via CLI As a researcher I want to search for genetic variants using various criteria So that I can find relevant variants for my research Scenario: Search for variants by gene symbol When I run "biomcp variant search --gene BRCA1" Then each variant should have gene that is equal to BRCA1 Scenario: Filter variants by clinical significance (Pathogenic) When I run "biomcp variant search --gene BRAF --significance Pathogenic" Then each variant should have gene that is equal to BRAF Then each variant should have significance that contains Pathogenic Scenario: Filter variants by clinical significance (Likely Benign) When I run "biomcp variant search --gene TP53 --significance "likely benign" --size 5" Then each variant should have gene that is equal to TP53 Then each variant should have significance that is equal to Likely benign Then the number of variants is less than or equal to 5 Scenario: Filter variants by allele frequency (Range) When I run "biomcp variant search --gene TP53 --min-frequency 0.0002 --max-frequency 0.0003" Then each variant should have gene that is equal to TP53 Then each variant should have frequency that is greater than or equal to 0.0002 Then each variant should have frequency that is less than or equal to 0.0003 Scenario: Filter variants by allele frequency (Minimum only) When I run "biomcp variant search --gene APOE --min-frequency 0.4 --size 3" Then each variant should have gene that is equal to APOE Then each variant should have frequency that is greater than or equal to 0.4 Then the number of variants is less than 3 Scenario: Filter variants by allele frequency (Maximum only) When I run "biomcp variant search --gene TP53 --max-frequency 0.00001 --size 5" Then each variant should have gene that is equal to TP53 Then each variant should have frequency that is less than or equal to 0.00001 Then the number of variants is less than or equal to 5 Scenario: Search for variants by rsID When I run "biomcp variant search --rsid rs1799966" Then each variant should have rsid that is equal to rs1799966 Scenario: Search for variants by protein notation When I run "biomcp variant search --hgvsp p.Val600Glu" Then each variant should have hgvsp that is equal to p.Val600Glu Scenario: Search for variants by cDNA notation When I run "biomcp variant search --hgvsc c.1799T>A" Then each variant should have hgvsc that is equal to c.1799T>A Scenario: Search for variants by genomic region When I run "biomcp variant search --region chr7:140453130-140453140" Then each variant should have chromosome that is equal to 7 And each variant should have position that is greater than or equal to 140453130 And each variant should have position that is less than or equal to 140453140 Scenario: Filter variants by CADD score When I run "biomcp variant search --gene BRCA1 --cadd 20" Then each variant should have gene that is equal to BRCA1 Then each variant should have cadd that is greater than or equal to 20 Scenario: Filter variants by PolyPhen prediction (Possibly Damaging) When I run "biomcp variant search --gene BRCA1 --polyphen P" Then each variant should have gene that is equal to BRCA1 Then each variant should have polyphen that contains P Scenario: Filter variants by PolyPhen prediction (Benign) When I run "biomcp variant search --gene CFTR --polyphen B --size 3" Then each variant should have gene that is equal to CFTR Then each variant should have polyphen that contains B Then the number of variants is less than or equal to 3 Scenario: Filter variants by SIFT prediction (Deleterious) When I run "biomcp variant search --gene BRCA1 --sift D" Then each variant should have gene that is equal to BRCA1 Then each variant should have sift that contains D Scenario: Filter variants by SIFT prediction (Tolerated) When I run "biomcp variant search --gene MTHFR --sift T --size 3" Then each variant should have gene that is equal to MTHFR Then each variant should have sift that contains T Then the number of variants is less than or equal to 3 Scenario: Search with multiple filters combined When I run "biomcp variant search --gene BRCA1 --significance Pathogenic --cadd 20 --max-frequency 0.01" Then each variant should have gene that is equal to BRCA1 Then each variant should have significance that contains Pathogenic Then each variant should have cadd that is greater than or equal to 20 Then each variant should have frequency that is less than or equal to 0.01 Scenario: Limit number of search results (size=5) When I run "biomcp variant search --gene TP53 --size 5" Then each variant should have gene that is equal to TP53 Then the number of variants is less than or equal to 5 Scenario: Limit number of search results (size=1) When I run "biomcp variant search --gene TP53 --size 1" Then each variant should have gene that is equal to TP53 Then the number of variants is equal to 1 # Scenario: Select different sources When I run "biomcp variant search --rsid 'chr17:g.7574024G>A' --sources mutdb" Then each variant should have uniprot_id that contains VAR_018629 Scenario: Search expected to yield no results When I run "biomcp variant search --gene XYZABC123 --rsid rs9999999999" Then the number of variants is equal to 0