update demo config with changes to variant params

quinlan-lab · Nov 30, 2023 · 9934b03 · 9934b03
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Showing 3 changed files with 39 additions and 36 deletions.
diff --git a/test/data/gnomad_v3.1.1_KCNQ2_SNVs.bed b/test/data/gnomad_v3.1.1_KCNQ2_SNVs.bed
@@ -88,7 +88,6 @@ chr20	63400800	63400801	C	T	3	152200	0.000019710906701708278	missense_variant
 chr20	63400801	63400802	G	A	3	152162	0.000019715829182055967	missense_variant
 chr20	63400809	63400810	C	G	1	152204	0.000006570129562954982	missense_variant
 chr20	63400810	63400811	C	T	1	152220	0.000006569438969911969	missense_variant
-chr20	63400820	63400821	G	A	lof_flag"	1	152208	stop_gained
 chr20	63400821	63400822	C	A	1	152206	0.000006570043230884459	missense_variant
 chr20	63400822	63400823	G	A	1	152214	0.0000065696979252893955	missense_variant
 chr20	63400823	63400824	C	T	21	152210	0.00013796728204454371	missense_variant
@@ -1065,7 +1064,6 @@ chr20	63438464	63438465	A	G	7	152110	0.00004601932811780948	missense_variant
 chr20	63438465	63438466	C	T	2	152220	0.000013138877939823939	synonymous_variant
 chr20	63438474	63438475	T	A	1	152112	0.000006574103292310929	synonymous_variant
 chr20	63438475	63438476	C	A	1	152190	0.000006570733950982325	missense_variant
-chr20	63438479	63438480	G	A	lof_flag"	2	152124	stop_gained
 chr20	63438479	63438480	G	C	1	152124	0.000006573584707212537	missense_variant
 chr20	63438493	63438494	T	C	2	152124	0.000013147169414425074	missense_variant
 chr20	63438503	63438504	G	C	2	152168	0.00001314336785657957	missense_variant
@@ -1075,7 +1073,6 @@ chr20	63438511	63438512	G	T	2	152162	0.000013143886121370644	missense_variant
 chr20	63438511	63438512	G	A	870	152162	0.00571759046279623	missense_variant
 chr20	63438514	63438515	G	T	1	152178	0.000006571252086372537	missense_variant
 chr20	63438515	63438516	T	C	1	152170	0.0000065715975553657095	missense_variant
-chr20	63438520	63438521	C	T	lof_flag"	8	152134	stop_gained
 chr20	63438523	63438524	C	T	7	152190	0.00004599513765687627	missense_variant
 chr20	63438530	63438531	C	A	11	152186	0.00007227997319070085	missense_variant
 chr20	63438530	63438531	C	T	1	152186	0.000006570906653700077	missense_variant
@@ -1088,7 +1085,6 @@ chr20	63438570	63438571	A	C	1	152116	0.000006573930421520419	synonymous_variant
 chr20	63438574	63438575	T	A	2	152092	0.00001314993556531573	missense_variant
 chr20	63438574	63438575	T	C	1	152092	0.000006574967782657865	missense_variant
 chr20	63438576	63438577	G	A	7	152186	0.000045996346575900545	synonymous_variant
-chr20	63438579	63438580	C	T	lof_flag"	3	152150	stop_gained
 chr20	63438584	63438585	A	G	1	152180	0.000006571165724799579	missense_variant
 chr20	63438589	63438590	G	C	1	152134	0.0000065731526154574255	missense_variant
 chr20	63438594	63438595	T	C	1	152184	0.000006570993008463439	synonymous_variant

diff --git a/test/test.yaml b/test/test.yaml
@@ -17,54 +17,61 @@ intron_size: 20
 
 plot_UTRs: True
 plot_direction: True
+plot_variants: True
+
+min_lollipop_height: 15
+lollipop_radius: 5
+lollipop_line_width: 2
+
+default_y_axis: 'AC' # can be toggled with HTML output
+default_y_axis_scale: 'log' # can be toggled with HTML output
 
 glyph_colors:
     intron: 'gray 11'
     exon: 'davys gray'
     arrow: '#e8e8e8'
     UTR: '#969696'
-    variant: 'charcoal' #default lollipop color if no severity information
 
 palettes_filepath: 'default_colors/palettes.yaml' #filepath to palettes config
 named_colors_filepath: 'default_colors/named_colors.yaml' #filepath to named colors config
 track_palette: 'bang_wong_palette' #palette to draw random track colors from; can be any one palette in palettes.yaml
 ...
 ---
 #variants
-plot_variants: True
-
 #VCF example
-variant_format: 'vcf'
-filepath: 'test/data/gnomad.exomes.chr20.subset.vcf.gz'
-chrom: chr20
-info_annotations: #INFO fields to add to hover boxes (VCF only)
-    - pab_max
-    - popmax
-vep: #VCF only; leave empty if not VEP annotated
-    field_name: vep #name of INFO field with VEP string (e.g. vep, ann, csq)
-    vep_fields: #vep fields to add to hover annotations
-    - SYMBOL
-    - Amino_acids
-    - Consequence
-    annotate_severity_by: max_severity #possible arguments are transcript_severity (use VEP annotations from given transcript) and max_severity (use VEP annotation from most severe transcript specified in 'transcripts' argument); these apply to vep_fields also
+gnomAD_vcf:
+    format: 'vcf'
+    filepath: 'test/data/gnomad.exomes.chr20.subset.vcf.gz'
+    chrom: 'chr20'
+    info_annotations: #INFO fields to add to hover boxes (VCF only)
+        - pab_max
+        - popmax
+    vep: #VCF only; leave empty if not VEP annotated
+        field_name: vep #name of INFO field with VEP string (e.g. vep, ann, csq)
+        vep_fields: #vep fields to add to hover annotations
+        - SYMBOL
+        - Amino_acids
+        - Consequence
+        annotate_severity_by: transcript_severity #possible arguments are transcript_severity (use VEP annotations from given transcript) and max_severity (use VEP annotation from most severe transcript specified in 'transcripts' argument); these apply to vep_fields also
+    color: charcoal
+    variant_severity_colors: #will only be used if consequence_idx is set; overrides "color"
+        LOW: 'apple green'
+        MED: '#f6aa1c'
+        HIGH: '#e01e37'
 
 #BED example
-# variant_format: 'bed' #can be VCF or BED
-# filepath: 'test/data/gnomad_v3.1.1_KCNQ2_SNVs.bed'
-# header: ['Chromosome', 'Start', 'End', 'Reference', 'Alternate', 'Allele Count', 'Allele Number', 'Allele Frequency', 'VEP Annotation'] # BED only
-# chrom: chr20
-
-default_y_axis: 'AC' # can be toggled with HTML output
-default_y_axis_scale: 'log' # can be toggled with HTML output
+# gnomAD_bed:
+#     format: 'bed' #can be VCF or BED
+#     filepath: 'test/data/gnomad_v3.1.1_KCNQ2_SNVs.bed'
+#     chrom: 'chr20'
+#     header: ['Chromosome', 'Start', 'End', 'Reference', 'Alternate', 'AC', 'AN', 'AF', 'VEP Annotation'] # BED only; if 'AC' and 'AF' fields are present, they will be used for lollipop heights
+#     color: saffron
+#     variant_severity_colors: #will only be used if consequence_idx is set; overrides "color"
+#         LOW: 'apple green'
+#         MED: '#f6aa1c'
+#         HIGH: '#e01e37'
+#     consequence_idx: 8 #0-based
 
-min_lollipop_height: 15
-lollipop_radius: 5
-lollipop_line_width: 2
-variant_severity_colors:
-    LOW: 'apple green'
-    MED: '#f6aa1c'
-    HIGH: '#e01e37'
-    NONE: '#171717'
 ...
 
 ---

diff --git a/transcriptionary/glyphs.py b/transcriptionary/glyphs.py
@@ -3,7 +3,7 @@
 from .colors import  color_variants,lighten_hex_color
 import math
 
-def flatten(ls): return sum(ls, [])
+def flatten(ls): return [i for s in ls for i in s]
 
 def center_feature(feature):
     center = feature[0] + (feature[1] - feature[0])/2