enforce exon sorting before annotating introns (#163)

ratschlab · Jul 12, 2022 · a1991c8 · a1991c8
1 parent 26b9f3b
commit a1991c8
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Showing 107 changed files with 59 additions and 50 deletions.
diff --git a/spladder/classes/event.py b/spladder/classes/event.py
@@ -1,5 +1,7 @@
 import numpy as np
 
+from ..utils import sort_rows
+
 class Event:
 
     def __init__(self, event_type, chr=None, strand=None):
@@ -68,6 +70,8 @@ def get_intron_lens(self):
         return _introns[:, 1] - _introns[:, 0]
 
     def set_annotation_flag(self, anno_introns):
+
+        self.sort_exons()
 
         ### check annotation status of isoform 1
         self.annotated = 3
@@ -83,3 +87,8 @@ def set_annotation_flag(self, anno_introns):
             if not (self.exons2[i, 1], self.exons2[i + 1, 0]) in anno_introns:
                 self.annotated -= 2
                 break
+
+    def sort_exons(self):
+
+        self.exons1 = sort_rows(self.exons1)
+        self.exons2 = sort_rows(self.exons2)
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.gff3 b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.gff3
@@ -3,11 +3,11 @@
 1	alt_3prime	mRNA	5201	5500	.	+	.	ID=alt_3prime.1_iso1;Parent=alt_3prime.1;GeneName="gene8";HasNovelJunction="Y"
 1	alt_3prime	exon	5201	5300	.	+	.	Parent=alt_3prime.1_iso1
 1	alt_3prime	exon	5401	5500	.	+	.	Parent=alt_3prime.1_iso1
-1	alt_3prime	mRNA	5201	5500	.	+	.	ID=alt_3prime.1_iso2;Parent=alt_3prime.1;GeneName="gene8";HasNovelJunction="Y"
+1	alt_3prime	mRNA	5201	5500	.	+	.	ID=alt_3prime.1_iso2;Parent=alt_3prime.1;GeneName="gene8";HasNovelJunction="N"
 1	alt_3prime	exon	5201	5300	.	+	.	Parent=alt_3prime.1_iso2
 1	alt_3prime	exon	5351	5500	.	+	.	Parent=alt_3prime.1_iso2
 1	alt_3prime	gene	6051	6750	.	+	.	ID=alt_3prime.2;GeneName="gene10";HasNovelJunction="Y"
-1	alt_3prime	mRNA	6051	6750	.	+	.	ID=alt_3prime.2_iso1;Parent=alt_3prime.2;GeneName="gene10";HasNovelJunction="Y"
+1	alt_3prime	mRNA	6051	6750	.	+	.	ID=alt_3prime.2_iso1;Parent=alt_3prime.2;GeneName="gene10";HasNovelJunction="N"
 1	alt_3prime	exon	6051	6200	.	+	.	Parent=alt_3prime.2_iso1
 1	alt_3prime	exon	6551	6750	.	+	.	Parent=alt_3prime.2_iso1
 1	alt_3prime	mRNA	6051	6750	.	+	.	ID=alt_3prime.2_iso2;Parent=alt_3prime.2;GeneName="gene10";HasNovelJunction="Y"
@@ -17,6 +17,6 @@
 1	alt_3prime	mRNA	5551	5850	.	-	.	ID=alt_3prime.5_iso1;Parent=alt_3prime.5;GeneName="gene9";HasNovelJunction="Y"
 1	alt_3prime	exon	5551	5650	.	-	.	Parent=alt_3prime.5_iso1
 1	alt_3prime	exon	5751	5850	.	-	.	Parent=alt_3prime.5_iso1
-1	alt_3prime	mRNA	5551	5850	.	-	.	ID=alt_3prime.5_iso2;Parent=alt_3prime.5;GeneName="gene9";HasNovelJunction="Y"
+1	alt_3prime	mRNA	5551	5850	.	-	.	ID=alt_3prime.5_iso2;Parent=alt_3prime.5;GeneName="gene9";HasNovelJunction="N"
 1	alt_3prime	exon	5551	5700	.	-	.	Parent=alt_3prime.5_iso2
 1	alt_3prime	exon	5751	5850	.	-	.	Parent=alt_3prime.5_iso2
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.icgc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.icgc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.tcga.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.tcga.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.confirmed.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.gff3 b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.gff3
@@ -3,11 +3,11 @@
 1	alt_3prime	mRNA	5201	5500	.	+	.	ID=alt_3prime.1_iso1;Parent=alt_3prime.1;GeneName="gene8";HasNovelJunction="Y"
 1	alt_3prime	exon	5201	5300	.	+	.	Parent=alt_3prime.1_iso1
 1	alt_3prime	exon	5401	5500	.	+	.	Parent=alt_3prime.1_iso1
-1	alt_3prime	mRNA	5201	5500	.	+	.	ID=alt_3prime.1_iso2;Parent=alt_3prime.1;GeneName="gene8";HasNovelJunction="Y"
+1	alt_3prime	mRNA	5201	5500	.	+	.	ID=alt_3prime.1_iso2;Parent=alt_3prime.1;GeneName="gene8";HasNovelJunction="N"
 1	alt_3prime	exon	5201	5300	.	+	.	Parent=alt_3prime.1_iso2
 1	alt_3prime	exon	5351	5500	.	+	.	Parent=alt_3prime.1_iso2
 1	alt_3prime	gene	6051	6750	.	+	.	ID=alt_3prime.2;GeneName="gene10";HasNovelJunction="Y"
-1	alt_3prime	mRNA	6051	6750	.	+	.	ID=alt_3prime.2_iso1;Parent=alt_3prime.2;GeneName="gene10";HasNovelJunction="Y"
+1	alt_3prime	mRNA	6051	6750	.	+	.	ID=alt_3prime.2_iso1;Parent=alt_3prime.2;GeneName="gene10";HasNovelJunction="N"
 1	alt_3prime	exon	6051	6200	.	+	.	Parent=alt_3prime.2_iso1
 1	alt_3prime	exon	6551	6750	.	+	.	Parent=alt_3prime.2_iso1
 1	alt_3prime	mRNA	6051	6750	.	+	.	ID=alt_3prime.2_iso2;Parent=alt_3prime.2;GeneName="gene10";HasNovelJunction="Y"
@@ -17,7 +17,7 @@
 1	alt_3prime	mRNA	6301	6750	.	+	.	ID=alt_3prime.3_iso1;Parent=alt_3prime.3;GeneName="gene10";HasNovelJunction="Y"
 1	alt_3prime	exon	6301	6450	.	+	.	Parent=alt_3prime.3_iso1
 1	alt_3prime	exon	6601	6750	.	+	.	Parent=alt_3prime.3_iso1
-1	alt_3prime	mRNA	6301	6750	.	+	.	ID=alt_3prime.3_iso2;Parent=alt_3prime.3;GeneName="gene10";HasNovelJunction="Y"
+1	alt_3prime	mRNA	6301	6750	.	+	.	ID=alt_3prime.3_iso2;Parent=alt_3prime.3;GeneName="gene10";HasNovelJunction="N"
 1	alt_3prime	exon	6301	6450	.	+	.	Parent=alt_3prime.3_iso2
 1	alt_3prime	exon	6551	6750	.	+	.	Parent=alt_3prime.3_iso2
 1	alt_3prime	gene	6301	6750	.	+	.	ID=alt_3prime.4;GeneName="gene10";HasNovelJunction="Y"
@@ -31,6 +31,6 @@
 1	alt_3prime	mRNA	5551	5850	.	-	.	ID=alt_3prime.5_iso1;Parent=alt_3prime.5;GeneName="gene9";HasNovelJunction="Y"
 1	alt_3prime	exon	5551	5650	.	-	.	Parent=alt_3prime.5_iso1
 1	alt_3prime	exon	5751	5850	.	-	.	Parent=alt_3prime.5_iso1
-1	alt_3prime	mRNA	5551	5850	.	-	.	ID=alt_3prime.5_iso2;Parent=alt_3prime.5;GeneName="gene9";HasNovelJunction="Y"
+1	alt_3prime	mRNA	5551	5850	.	-	.	ID=alt_3prime.5_iso2;Parent=alt_3prime.5;GeneName="gene9";HasNovelJunction="N"
 1	alt_3prime	exon	5551	5700	.	-	.	Parent=alt_3prime.5_iso2
 1	alt_3prime	exon	5751	5850	.	-	.	Parent=alt_3prime.5_iso2
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.pickle b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.pickle
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_3prime_C3.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.icgc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.icgc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.tcga.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.tcga.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.confirmed.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.txt.gz b/tests/testcase_events/results_merged/merge_graphs_alt_5prime_C3.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.icgc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.icgc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.tcga.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.tcga.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.confirmed.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.txt.gz b/tests/testcase_events/results_merged/merge_graphs_exon_skip_C3.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.icgc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.icgc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.tcga.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.tcga.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.confirmed.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.pickle b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.pickle
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.txt.gz b/tests/testcase_events/results_merged/merge_graphs_intron_retention_C3.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mult_exon_skip_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_mult_exon_skip_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.icgc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.icgc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.tcga.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.tcga.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.confirmed.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.counts.hdf5 b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.counts.hdf5
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.struc.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.struc.txt.gz
diff --git a/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.txt.gz b/tests/testcase_events/results_merged/merge_graphs_mutex_exons_C3.txt.gz
diff --git a/tests/testcase_events/results_merged/testing/plots/count_distribution.exon_skip.log10.pdf b/tests/testcase_events/results_merged/testing/plots/count_distribution.exon_skip.log10.pdf
diff --git a/tests/testcase_events/results_merged/testing/plots/count_distribution.exon_skip.pdf b/tests/testcase_events/results_merged/testing/plots/count_distribution.exon_skip.pdf
diff --git a/tests/testcase_events/results_merged/testing/plots/dispersion_adjusted_exon_skip.pdf b/tests/testcase_events/results_merged/testing/plots/dispersion_adjusted_exon_skip.pdf
diff --git a/tests/testcase_events/results_merged/testing/plots/dispersion_fitted_exon_skip.pdf b/tests/testcase_events/results_merged/testing/plots/dispersion_fitted_exon_skip.pdf
diff --git a/tests/testcase_events/results_merged/testing/plots/dispersion_raw_exon_skip.pdf b/tests/testcase_events/results_merged/testing/plots/dispersion_raw_exon_skip.pdf
diff --git a/tests/testcase_events/results_merged/testing/plots/ma_plot_exon_skip.pdf b/tests/testcase_events/results_merged/testing/plots/ma_plot_exon_skip.pdf
diff --git a/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.adj.log10.pdf b/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.adj.log10.pdf
diff --git a/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.adj.pdf b/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.adj.pdf
diff --git a/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.log10.pdf b/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.log10.pdf
diff --git a/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.pdf b/tests/testcase_events/results_merged/testing/plots/qq_plot_exon_skip.pdf
diff --git a/tests/testcase_events/results_merged/testing/test_results_C3_exon_skip.gene_unique.tsv b/tests/testcase_events/results_merged/testing/test_results_C3_exon_skip.gene_unique.tsv
@@ -1,7 +1,7 @@
 event_id	chrm	exon_pos	alt_usage	gene_id	gene_name	p_val	p_val_adj	dPSI	mean_event_count_A	mean_event_count_B	log2FC_event_count	mean_gene_exp_A	mean_gene_exp_B	log2FC_gene_exp
-exon_skip.1	1	50-200:300-400:600-750	0:1:0	gene1	gene1	4.811778753222029e-10	2.8870672519332174e-09	0.616702306794285	35.08586895323417	9.376311915134902	1.9037976245357355	334.1722765209043	292.7045199476639	0.19114702598382038
-exon_skip.9	1	9050-9150:9200-9301:9350-9450	0:1:0	gene15	gene15	0.40524286367664686	0.8995275736632284	-0.09291633522045145	69.93112545739696	53.413988503256235	0.3887171073454452	495.4718317969663	443.33183211071554	0.16041608609064717
-exon_skip.8	1	8550-8650:8700-8801:8850-8950	0:1:0	gene14	gene14	0.6202054655784603	0.8995275736632284	0.003091298657809438	31.080863978941757	38.225154632724674	-0.2984957297324611	310.95618225753054	358.7314939698008	-0.2061931084887263
-exon_skip.6	1	7550-7650:7700-7801:7850-7950	0:1:0	gene12	gene12	0.7776604746323357	0.8995275736632284	0.013616147697528502	27.189141476703583	28.747323146349835	-0.08039702582289543	221.73533171471072	207.16763607554458	0.09804002875719764
-exon_skip.10	1	9550-9650:9700-9801:9850-9950	0:1:0	gene16	gene16	0.8741588278150877	0.8995275736632284	-0.01761397105920376	21.14907293278275	21.33922943817654	-0.012913656875475965	213.94508829780563	224.4741532357582	-0.069308779134718
-exon_skip.7	1	8050-8150:8200-8301:8350-8450	0:1:0	gene13	gene13	0.8995275736632284	0.8995275736632284	-0.01612059250508885	35.55269583213776	37.925583849640844	-0.0932124320420975	313.65982094004676	309.29820779519844	0.020202261426950585
+exon_skip.1	1	50-200:300-400:600-750	0:1:0	gene1	gene1	4.811778753222029e-10	2.8870672519332174e-09	0.616702306794285	35.08586895323417	9.376311915134902	1.9037976245357355	334.17227652090423	292.7045199476639	0.1911470259838186
+exon_skip.9	1	9050-9150:9200-9301:9350-9450	0:1:0	gene15	gene15	0.405242863643404	0.8995275736770822	-0.09291633522045145	69.93112545739696	53.413988503256235	0.3887171073454452	495.4718317969663	443.33183211071554	0.16041608609064717
+exon_skip.8	1	8550-8650:8700-8801:8850-8950	0:1:0	gene14	gene14	0.620205465556835	0.8995275736770822	0.003091298657809438	31.080863978941757	38.225154632724674	-0.2984957297324611	310.9561822575305	358.73149396980085	-0.2061931084887263
+exon_skip.6	1	7550-7650:7700-7801:7850-7950	0:1:0	gene12	gene12	0.7776604746242519	0.8995275736770822	0.013616147697528502	27.189141476703583	28.747323146349835	-0.08039702582289543	221.73533171471072	207.16763607554458	0.09804002875719764
+exon_skip.10	1	9550-9650:9700-9801:9850-9950	0:1:0	gene16	gene16	0.8741588278200897	0.8995275736770822	-0.01761397105920376	21.14907293278275	21.33922943817654	-0.012913656875475965	213.94508829780557	224.4741532357582	-0.069308779134718
+exon_skip.7	1	8050-8150:8200-8301:8350-8450	0:1:0	gene13	gene13	0.8995275736770822	0.8995275736770822	-0.01612059250508885	35.55269583213776	37.925583849640844	-0.0932124320420975	313.65982094004676	309.29820779519844	0.020202261426950585
diff --git a/tests/testcase_events/results_merged/testing/test_results_C3_exon_skip.tsv b/tests/testcase_events/results_merged/testing/test_results_C3_exon_skip.tsv
@@ -1,7 +1,7 @@
 event_id	chrm	exon_pos	alt_usage	gene_id	gene_name	p_val	p_val_adj	dPSI	mean_event_count_A	mean_event_count_B	log2FC_event_count	mean_gene_exp_A	mean_gene_exp_B	log2FC_gene_exp
-exon_skip.1	1	50-200:300-400:600-750	0:1:0	gene1	gene1	4.811778753222029e-10	2.8870672519332174e-09	0.616702306794285	35.08586895323417	9.376311915134902	1.9037976245357355	334.1722765209043	292.7045199476639	0.19114702598382038
-exon_skip.9	1	9050-9150:9200-9301:9350-9450	0:1:0	gene15	gene15	0.40524286367664686	0.8995275736632284	-0.09291633522045145	69.93112545739696	53.413988503256235	0.3887171073454452	495.4718317969663	443.33183211071554	0.16041608609064717
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