From 38bf0dc14712c6437ef16738de294c37cdb52fb5 Mon Sep 17 00:00:00 2001 From: Rapsssito Date: Mon, 11 Dec 2023 13:08:07 +0100 Subject: [PATCH] fix: Fix assessment typo --- CHANGELOG.md | 14 +++---- README.md | 6 +-- example/example.sh | 2 +- .../samples/sample_1/pipelinefn.indel.vcf | 2 +- .../samples/sample_1/pipelinefn.sv.vcf | 2 +- .../samples/sample_1/pipelinefp.indel.vcf | 2 +- .../samples/sample_1/pipelinetp.indel.vcf | 2 +- .../samples/sample_1/pipelinetp.snv.vcf | 2 +- .../samples/sample_2/pipelinefn.indel.vcf | 2 +- .../samples/sample_2/pipelinefn.snv.vcf | 2 +- .../samples/sample_2/pipelinefn.sv.vcf | 2 +- .../samples/sample_2/pipelinefp.indel.vcf | 2 +- .../samples/sample_2/pipelinefp.snv.vcf | 2 +- .../samples/sample_2/pipelinetp.indel.vcf | 2 +- .../samples/sample_2/pipelinetp.snv.vcf | 2 +- .../samples/sample_1/pipelinefn.indel.vcf | 2 +- .../samples/sample_1/pipelinefn.snv.vcf | 2 +- .../samples/sample_1/pipelinefn.sv.vcf | 2 +- .../samples/sample_1/pipelinefp.snv.vcf | 2 +- .../samples/sample_1/pipelinetp.indel.vcf | 2 +- .../samples/sample_1/pipelinetp.snv.vcf | 2 +- .../samples/sample_2/pipelinefn.indel.vcf | 2 +- .../samples/sample_2/pipelinefn.sv.vcf | 2 +- .../samples/sample_2/pipelinefp.indel.vcf | 2 +- .../samples/sample_2/pipelinetp.indel.vcf | 2 +- .../samples/sample_2/pipelinetp.snv.vcf | 2 +- .../samples/sample_1/pipelinefn.indel.vcf | 2 +- .../samples/sample_1/pipelinefn.snv.vcf | 2 +- .../samples/sample_1/pipelinefn.sv.vcf | 2 +- .../samples/sample_1/pipelinefp.sv.vcf | 2 +- .../samples/sample_1/pipelinetp.sv.vcf | 2 +- .../samples/sample_2/pipelinefn.indel.vcf | 2 +- .../samples/sample_2/pipelinefn.snv.vcf | 2 +- .../samples/sample_2/pipelinefn.sv.vcf | 2 +- .../samples/sample_2/pipelinefp.sv.vcf | 2 +- .../samples/sample_2/pipelinetp.sv.vcf | 2 +- .../samples/sample_1/pipelinefn.indel.vcf | 2 +- .../samples/sample_1/pipelinefn.snv.vcf | 2 +- .../samples/sample_1/pipelinefn.sv.vcf | 2 +- .../samples/sample_1/pipelinefp.sv.vcf | 2 +- .../samples/sample_1/pipelinetp.sv.vcf | 2 +- .../samples/sample_2/pipelinefn.indel.vcf | 2 +- .../samples/sample_2/pipelinefn.snv.vcf | 2 +- .../samples/sample_2/pipelinefn.sv.vcf | 2 +- .../samples/sample_2/pipelinefp.sv.vcf | 2 +- .../samples/sample_2/pipelinetp.sv.vcf | 2 +- .../example/example_bulk.sh | 2 - .../example/example_main.sh | 2 - .../.gitignore | 0 .../README.md | 36 ++++++++-------- .../example/.gitignore | 0 .../example/example_bulk.sh | 2 + .../example/example_config.tsv | 0 .../example/example_main.sh | 2 + .../example/fake_ref.fa | 0 .../example/fake_ref.fa.fai | 0 .../example/input/test | 0 .../example/input/truth | 0 .../src/assessment_bulk.py} | 4 +- .../src/assessment_main.py} | 2 +- .../src/indel_sv_converter.py | 0 modules/oncoliner_improvement/README.md | 2 +- modules/oncoliner_ui/README.md | 2 +- .../{assesment_tab.py => assessment_tab.py} | 42 +++++++++---------- .../metrics_panel.html | 0 .../metrics_plot.html | 0 .../pipeline.html | 18 ++++---- .../improvement_tab/pipeline.html | 2 +- ...assesment_tab.html => assessment_tab.html} | 8 ++-- .../src/ui/html_templates/index/base.html | 6 +-- .../html_templates/index/improvement_tab.html | 2 +- .../assessment_dao.py} | 6 +-- .../assessment_pipeline_dao.py} | 2 +- modules/oncoliner_ui/src/ui/ui_manager.py | 18 ++++---- modules/oncoliner_ui/src/ui_main.py | 2 +- oncoliner_launcher.py | 20 ++++----- tools/pipeline_designer/README.md | 2 +- tools/pipeline_designer/src/main.py | 12 +++--- tools/vcf_intersect/README.md | 2 +- tools/vcf_union/README.md | 2 +- 80 files changed, 153 insertions(+), 153 deletions(-) delete mode 100644 modules/oncoliner_assesment/example/example_bulk.sh delete mode 100644 modules/oncoliner_assesment/example/example_main.sh rename modules/{oncoliner_assesment => oncoliner_assessment}/.gitignore (100%) rename modules/{oncoliner_assesment => oncoliner_assessment}/README.md (74%) rename modules/{oncoliner_assesment => oncoliner_assessment}/example/.gitignore (100%) create mode 100644 modules/oncoliner_assessment/example/example_bulk.sh rename modules/{oncoliner_assesment => oncoliner_assessment}/example/example_config.tsv (100%) create mode 100644 modules/oncoliner_assessment/example/example_main.sh rename modules/{oncoliner_assesment => oncoliner_assessment}/example/fake_ref.fa (100%) rename modules/{oncoliner_assesment => oncoliner_assessment}/example/fake_ref.fa.fai (100%) rename modules/{oncoliner_assesment => oncoliner_assessment}/example/input/test (100%) rename modules/{oncoliner_assesment => oncoliner_assessment}/example/input/truth (100%) rename modules/{oncoliner_assesment/src/assesment_bulk.py => oncoliner_assessment/src/assessment_bulk.py} (99%) rename modules/{oncoliner_assesment/src/assesment_main.py => oncoliner_assessment/src/assessment_main.py} (99%) rename modules/{oncoliner_assesment => oncoliner_assessment}/src/indel_sv_converter.py (100%) rename modules/oncoliner_ui/src/ui/{assesment_tab.py => assessment_tab.py} (54%) rename modules/oncoliner_ui/src/ui/html_templates/{assesment_tab => assessment_tab}/metrics_panel.html (100%) rename modules/oncoliner_ui/src/ui/html_templates/{assesment_tab => assessment_tab}/metrics_plot.html (100%) rename modules/oncoliner_ui/src/ui/html_templates/{assesment_tab => assessment_tab}/pipeline.html (68%) rename modules/oncoliner_ui/src/ui/html_templates/index/{assesment_tab.html => assessment_tab.html} (65%) rename modules/oncoliner_ui/src/ui/model/{assesment/assesment_dao.py => assessment/assessment_dao.py} (92%) rename modules/oncoliner_ui/src/ui/model/{assesment/assesment_pipeline_dao.py => assessment/assessment_pipeline_dao.py} (98%) diff --git a/CHANGELOG.md b/CHANGELOG.md index f29dffa..0f1bb14 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,7 +22,7 @@ BREAKING CHANGE: Dummy to trigger 1.0.0 ([`de5cfc0`](https://github.com/EUCANCan * feat(UI): Add default column ordering ([`6f792fc`](https://github.com/EUCANCan/oncoliner/commit/6f792fcf399af30013dc0b45e33dde87e88083cf)) -* feat: Add fixed row with the baseline ([`3907eab`](https://github.com/EUCANCan/oncoliner/commit/3907eabed350d85ce2f30e8d30267f93b61af02e)) +* feat: Add fixeassessmenth the baseline ([`3907eab`](https://github.com/EUCANCan/oncoliner/commit/3907eabed350d85ce2f30e8d30267f93b61af02e)) * feat: Add variant callers combinations ([`4fbc459`](https://github.com/EUCANCan/oncoliner/commit/4fbc4595b2de0390fc9600db6d162a29c74469e2)) @@ -68,12 +68,12 @@ Co-authored-by: Henri de Soyres <henri.de-soyres@curie.fr> ([`23cea50`](ht * fix(UI): Remove lateral panels in improvement and harmonization (#2) -* removed left panel for improvement and harmonization views, changed into tab and new component: dropdown tree - -* replaced variant type and size dropdown menu from list to accordion tree - ---------- - +* removed left panel for improvement and harmonization views, changed into tab and new component: dropdown tree + +* replaced variant type and size dropdown menu from list to accordion tree + +--------- + Co-authored-by: Henri de Soyres <henri.de-soyres@curie.fr> ([`a2bc9f9`](https://github.com/EUCANCan/oncoliner/commit/a2bc9f9afe454ce1074f62f6cdf935d7c158bc74)) * fix(UI): Improve FP visibility in assesment ([`9b5c62b`](https://github.com/EUCANCan/oncoliner/commit/9b5c62ba9a1695330617b5a9e827551a74caf244)) diff --git a/README.md b/README.md index 51be7b1..e207dfb 100644 --- a/README.md +++ b/README.md @@ -208,11 +208,11 @@ A standalone tool that allows users to merge two different groups of VCF files. ## Modules -ONCOLINER is divided into three functional modules (assesment, improvement and harmonization) and a UI module. For more information about each module, check the corresponding README file in the [`modules`](/modules) folder: +ONCOLINER is divided into three functional modules (assessment, improvement and harmonization) and a UI module. For more information about each module, check the corresponding README file in the [`modules`](/modules) folder: -* [Assesment README](/modules/oncoliner_assesment/README.md) +* [Assessment README](/modules/oncoliner_assessment/README.md) * [Improvement README](/modules/oncoliner_improvement/README.md) * [Harmonization README](/modules/oncoliner_harmonization/README.md) * [UI README](/modules/oncoliner_ui/README.md) -Each module can be run independently. However, the results of the assesment module are required to run the improvement module and the results of the improvement module are required to run the harmonization module. The UI module generates a report for the results of each module. +Each module can be run independently. However, the results of the assessment module are required to run the improvement module and the results of the improvement module are required to run the harmonization module. The UI module generates a report for the results of each module. diff --git a/example/example.sh b/example/example.sh index 8c0b6c9..768f2c4 100755 --- a/example/example.sh +++ b/example/example.sh @@ -1,5 +1,5 @@ export UI_COMMAND="python3 ../modules/oncoliner_ui/src/ui_main.py" -export ASSESMENT_COMMAND="python3 ../modules/oncoliner_assesment/src/assesment_bulk.py" +export ASSESSMENT_COMMAND="python3 ../modules/oncoliner_assessment/src/assessment_bulk.py" export IMPROVEMENT_COMMAND="python3 ../modules/oncoliner_improvement/src/improvement_main.py" export HARMONIZATION_COMMAND="python3 ../modules/oncoliner_harmonization/src/harmonization_main.py" diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.indel.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.indel.vcf index 5928ef8..a466dcb 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.indel.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 26 . CTTTA C . PASS INDEL GT 0/0 0/1 1 31 . C CAAAAA . PASS INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.sv.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.sv.vcf index 9db4207..107b125 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.sv.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:12100[ . PASS DEL GT 0/0 0/1 1 11100 . N N[1:13100[ . PASS DEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefp.indel.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefp.indel.vcf index 10059ad..c43ce4c 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefp.indel.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefp.indel.vcf @@ -4,6 +4,6 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 126 . CTTTA C . PASS FP;INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.indel.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.indel.vcf index 1ea8bc7..275b11d 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.indel.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 20 . CTTTA C . PASS TP;INDEL GT 0/0 0/1 1 29 . CTTTA C . PASS TP;INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.snv.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.snv.vcf index 6767250..b105070 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.snv.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.snv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 10 . A C . PASS TP;SNV;CSQ=ENSG00000142611|ZSWIM7|protein_altering_variant,ENSG00000142611|PRDM16|protein_altering_variant GT 0/0 0/1 1 11 . A C . PASS TP;SNV GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.indel.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.indel.vcf index fe3ed0e..4da66e0 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.indel.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 26 . CTTTA C . PASS INDEL GT 0/0 0/1 1 29 . CTTTA C . PASS INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.snv.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.snv.vcf index 9767c74..b5d1b42 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.snv.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.snv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11 . A C . PASS SNV GT 0/0 0/1 1 12 . A C . PASS SNV;ONCOLINER_PROT_GENES=TARBP1 GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.sv.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.sv.vcf index 9db4207..107b125 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.sv.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:12100[ . PASS DEL GT 0/0 0/1 1 11100 . N N[1:13100[ . PASS DEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.indel.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.indel.vcf index df1aad3..353b268 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.indel.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 126 . CTTTA C . PASS FP;INDEL GT 0/0 0/1 1 129 . CTTTA C . PASS FP;INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.snv.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.snv.vcf index 2acd8a0..6ed8ffc 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.snv.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.snv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 111 . A C . PASS FP;SNV GT 0/0 0/1 1 112 . A C . PASS FP;SNV GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.indel.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.indel.vcf index f2460e0..1c3931d 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.indel.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 20 . CTTTA C . PASS TP;INDEL GT 0/0 0/1 1 31 . C CAAAAA . PASS TP;INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.snv.vcf b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.snv.vcf index edf0cfb..7ebc8d8 100644 --- a/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.snv.vcf +++ b/example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.snv.vcf @@ -4,6 +4,6 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 10 . A C . PASS TP;SNV;CSQ=ENSG00000142611|ZSWIM7|protein_altering_variant,ENSG00000142611|PRDM16|protein_altering_variant GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.indel.vcf b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.indel.vcf index 54b995c..489be43 100644 --- a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.indel.vcf +++ b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.indel.vcf @@ -4,6 +4,6 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 26 . CTTTA C . PASS INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.snv.vcf b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.snv.vcf index 72112e0..5ffe2b3 100644 --- a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.snv.vcf +++ b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.snv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11 . A C . PASS SNV GT 0/0 0/1 1 12 . A C . PASS SNV;ONCOLINER_PROT_GENES=TARBP1 GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.sv.vcf b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.sv.vcf index 11587e8..a214d30 100644 --- a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.sv.vcf +++ b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:12100[ . PASS DEL GT 0/0 0/1 1 11100 . N N[1:13100[ . PASS DEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefp.snv.vcf b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefp.snv.vcf index 8e90c6c..cdec654 100644 --- a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefp.snv.vcf +++ b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefp.snv.vcf @@ -4,6 +4,6 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 112 . A C . PASS FP;SNV GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinetp.indel.vcf b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinetp.indel.vcf index 5571d63..ae5e1fc 100644 --- a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinetp.indel.vcf +++ b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinetp.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 20 . CTTTA C . PASS TP;INDEL GT 0/0 0/1 1 29 . CTTTA C . PASS TP;INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinetp.snv.vcf b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinetp.snv.vcf index cc3af2f..c68144c 100644 --- a/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinetp.snv.vcf +++ b/example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinetp.snv.vcf @@ -4,6 +4,6 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 10 . A C . PASS TP;SNV;CSQ=ENSG00000142611|ZSWIM7|protein_altering_variant,ENSG00000142611|PRDM16|protein_altering_variant GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefn.indel.vcf b/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefn.indel.vcf index 89b5c48..91cd994 100644 --- a/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefn.indel.vcf +++ b/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefn.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 20 . CTTTA C . PASS INDEL;ONCOLINER_PROT_GENES GT 0/0 0/1 1 26 . CTTTA C . PASS INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefn.sv.vcf b/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefn.sv.vcf index 11587e8..a214d30 100644 --- a/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefn.sv.vcf +++ b/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefn.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:12100[ . PASS DEL GT 0/0 0/1 1 11100 . N N[1:13100[ . PASS DEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefp.indel.vcf b/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefp.indel.vcf index 9b4e917..eb82b30 100644 --- a/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefp.indel.vcf +++ b/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinefp.indel.vcf @@ -4,6 +4,6 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 120 . CTTTA C . PASS FP;INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinetp.indel.vcf b/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinetp.indel.vcf index 4a246c9..5f67651 100644 --- a/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinetp.indel.vcf +++ b/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinetp.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 31 . C CAAAAA . PASS TP;INDEL GT 0/0 0/1 1 34 . C CAAAAA . PASS TP;INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinetp.snv.vcf b/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinetp.snv.vcf index 5852fa2..d330066 100644 --- a/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinetp.snv.vcf +++ b/example/input/callers_folder/variant_caller_2/samples/sample_2/pipelinetp.snv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 10 . A C . PASS TP;SNV;CSQ=ENSG00000142611|ZSWIM7|protein_altering_variant,ENSG00000142611|PRDM16|protein_altering_variant GT 0/0 0/1 1 11 . A C . PASS TP;SNV GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.indel.vcf b/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.indel.vcf index b4bd86e..5b4e4a6 100644 --- a/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.indel.vcf +++ b/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 20 . CTTTA C . PASS INDEL;ONCOLINER_PROT_GENES GT 0/0 0/1 1 26 . CTTTA C . PASS INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.snv.vcf b/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.snv.vcf index 482679f..bc0cb53 100644 --- a/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.snv.vcf +++ b/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.snv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 10 . A C . PASS SNV;CSQ=ENSG00000142611|ZSWIM7|protein_altering_variant,ENSG00000142611|PRDM16|protein_altering_variant GT 0/0 0/1 1 11 . A C . PASS SNV GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.sv.vcf b/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.sv.vcf index 273c806..452be96 100644 --- a/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.sv.vcf +++ b/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefn.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:13100[ . PASS DEL GT 0/0 0/1 1 11100 . N N[1:14100[ . PASS DEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefp.sv.vcf b/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefp.sv.vcf index 1421dfa..a8ae8b8 100644 --- a/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefp.sv.vcf +++ b/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinefp.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 31100 . N N]1:33100] . PASS TP;INV GT 0/0 0/1 1 33100 . N [1:131100[N . PASS FP;INV GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinetp.sv.vcf b/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinetp.sv.vcf index 8d87d86..080a641 100644 --- a/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinetp.sv.vcf +++ b/example/input/callers_folder/variant_caller_3/samples/sample_1/pipelinetp.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:12100[ . PASS TP;DEL GT 0/0 0/1 1 21100 . N ]1:22100]N . PASS TP;DUP GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.indel.vcf b/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.indel.vcf index b4bd86e..5b4e4a6 100644 --- a/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.indel.vcf +++ b/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 20 . CTTTA C . PASS INDEL;ONCOLINER_PROT_GENES GT 0/0 0/1 1 26 . CTTTA C . PASS INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.snv.vcf b/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.snv.vcf index 482679f..bc0cb53 100644 --- a/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.snv.vcf +++ b/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.snv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 10 . A C . PASS SNV;CSQ=ENSG00000142611|ZSWIM7|protein_altering_variant,ENSG00000142611|PRDM16|protein_altering_variant GT 0/0 0/1 1 11 . A C . PASS SNV GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.sv.vcf b/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.sv.vcf index 0243bf9..16b7ba2 100644 --- a/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.sv.vcf +++ b/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefn.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:14100[ . PASS DEL GT 0/0 0/1 1 11100 . N N[1:15100[ . PASS DEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefp.sv.vcf b/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefp.sv.vcf index f99146a..252c11f 100644 --- a/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefp.sv.vcf +++ b/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinefp.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 22100 . N N[1:121100[ . PASS FP;DUP GT 0/0 0/1 1 23100 . N N[1:121100[ . PASS FP;DUP GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinetp.sv.vcf b/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinetp.sv.vcf index 87a545a..c3a7781 100644 --- a/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinetp.sv.vcf +++ b/example/input/callers_folder/variant_caller_3/samples/sample_2/pipelinetp.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_3/config.tsv -p 1 -o ./output/evaluations/variant_caller_3 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:12100[ . PASS TP;DEL GT 0/0 0/1 1 11100 . N N[1:13100[ . PASS TP;DEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.indel.vcf b/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.indel.vcf index 2ffe005..d96b18c 100644 --- a/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.indel.vcf +++ b/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 20 . CTTTA C . PASS INDEL;ONCOLINER_PROT_GENES GT 0/0 0/1 1 26 . CTTTA C . PASS INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.snv.vcf b/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.snv.vcf index fc8e4f7..2321645 100644 --- a/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.snv.vcf +++ b/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.snv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 10 . A C . PASS SNV;CSQ=ENSG00000142611|ZSWIM7|protein_altering_variant,ENSG00000142611|PRDM16|protein_altering_variant GT 0/0 0/1 1 11 . A C . PASS SNV GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.sv.vcf b/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.sv.vcf index 2f28fae..213a827 100644 --- a/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.sv.vcf +++ b/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefn.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:15100[ . PASS DEL GT 0/0 0/1 1 21100 . N ]1:22100]N . PASS DUP GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefp.sv.vcf b/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefp.sv.vcf index c2f8962..668cd13 100644 --- a/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefp.sv.vcf +++ b/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinefp.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 31100 . N N]1:33100] . PASS TP;INV GT 0/0 0/1 1 33100 . N [1:131100[N . PASS FP;INV GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinetp.sv.vcf b/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinetp.sv.vcf index 6667796..43d633f 100644 --- a/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinetp.sv.vcf +++ b/example/input/callers_folder/variant_caller_4/samples/sample_1/pipelinetp.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:12100[ . PASS TP;DEL GT 0/0 0/1 1 11100 . N N[1:13100[ . PASS TP;DEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.indel.vcf b/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.indel.vcf index 2ffe005..d96b18c 100644 --- a/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.indel.vcf +++ b/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.indel.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 20 . CTTTA C . PASS INDEL;ONCOLINER_PROT_GENES GT 0/0 0/1 1 26 . CTTTA C . PASS INDEL GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.snv.vcf b/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.snv.vcf index fc8e4f7..2321645 100644 --- a/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.snv.vcf +++ b/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.snv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 10 . A C . PASS SNV;CSQ=ENSG00000142611|ZSWIM7|protein_altering_variant,ENSG00000142611|PRDM16|protein_altering_variant GT 0/0 0/1 1 11 . A C . PASS SNV GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.sv.vcf b/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.sv.vcf index 7d3e9c1..608b89f 100644 --- a/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.sv.vcf +++ b/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefn.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:15100[ . PASS DEL GT 0/0 0/1 1 21100 . N ]1:22100]N . PASS DUP GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefp.sv.vcf b/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefp.sv.vcf index 9777f45..495bc9e 100644 --- a/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefp.sv.vcf +++ b/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinefp.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 23100 . N N[1:121100[ . PASS FP;DUP GT 0/0 0/1 1 34100 . N N]1:131100] . PASS FP;INV GT 0/0 0/1 diff --git a/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinetp.sv.vcf b/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinetp.sv.vcf index c96f428..ca8721b 100644 --- a/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinetp.sv.vcf +++ b/example/input/callers_folder/variant_caller_4/samples/sample_2/pipelinetp.sv.vcf @@ -4,7 +4,7 @@ ##FORMAT= ##contig= ##contig= -##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip +##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_4/config.tsv -p 1 -o ./output/evaluations/variant_caller_4 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR 1 11100 . N N[1:12100[ . PASS TP;DEL GT 0/0 0/1 1 11100 . N N[1:13100[ . PASS TP;DEL GT 0/0 0/1 diff --git a/modules/oncoliner_assesment/example/example_bulk.sh b/modules/oncoliner_assesment/example/example_bulk.sh deleted file mode 100644 index 180af88..0000000 --- a/modules/oncoliner_assesment/example/example_bulk.sh +++ /dev/null @@ -1,2 +0,0 @@ - -python3 -O ../src/assesment_bulk.py -c example_config.tsv -o output/ --no-gzip \ No newline at end of file diff --git a/modules/oncoliner_assesment/example/example_main.sh b/modules/oncoliner_assesment/example/example_main.sh deleted file mode 100644 index cc163de..0000000 --- a/modules/oncoliner_assesment/example/example_main.sh +++ /dev/null @@ -1,2 +0,0 @@ -mkdir -p output -python3 -O ../src/assesment_main.py -t ./input/truth/sample_1/*.vcf -v ./input/test/sample_1/*.vcf -f fake_ref.fa -o output/single_sample_example_ --no-gzip \ No newline at end of file diff --git a/modules/oncoliner_assesment/.gitignore b/modules/oncoliner_assessment/.gitignore similarity index 100% rename from modules/oncoliner_assesment/.gitignore rename to modules/oncoliner_assessment/.gitignore diff --git a/modules/oncoliner_assesment/README.md b/modules/oncoliner_assessment/README.md similarity index 74% rename from modules/oncoliner_assesment/README.md rename to modules/oncoliner_assessment/README.md index a12aeac..a02fd48 100644 --- a/modules/oncoliner_assesment/README.md +++ b/modules/oncoliner_assessment/README.md @@ -1,4 +1,4 @@ -# ONCOLINER: Assesment module +# ONCOLINER: Assessment module ![ONCOLINER logo](../../docs/images/ONCOLINER_LOGO_COLOR.png) @@ -12,8 +12,8 @@ It is written in Python 3 (**requires Python version 3.6 or higher**). - [Installation](#installation) - [Functional analysis](#functional-analysis) - [Usage](#usage) - - [`assesment_main.py`](#assesment_mainpy) - - [`assesment_bulk.py`](#assesment_bulkpy) + - [`assessment_main.py`](#assessment_mainpy) + - [`assessment_bulk.py`](#assessment_bulkpy) - [Configuration file](#configuration-file) ## Installation @@ -22,35 +22,35 @@ We recommend using the ONCOLINER container or the provided [Dockerfile](../../Do ## Functional analysis -The module will try to obtain the genes affected by the variants from the `INFO` field in the truth files. **WARNING: ONCOLINER does not compute genes linked to false positives.** ONCOLINER's assesment module is compatible with the following functional analysis tools annotations: +The module will try to obtain the genes affected by the variants from the `INFO` field in the truth files. **WARNING: ONCOLINER does not compute genes linked to false positives.** ONCOLINER's assessment module is compatible with the following functional analysis tools annotations: * ONCOLINER. * [**VEP**](https://www.ensembl.org/info/docs/tools/vep/index.html): Variant Effect Predictor from Ensembl. ## Usage -The main executable code is in the [`src/`](./src/) folder. There are two executable files: [`assesment_main.py`](#assesment_mainpy) and [`assesment_bulk.py`](#assesment_bulkpy). The first one is the main executable file and the second one is a wrapper for the first one that allows to execute the assesment in multiple samples at the same time taking advantage of multiple processors. +The main executable code is in the [`src/`](./src/) folder. There are two executable files: [`assessment_main.py`](#assessment_mainpy) and [`assessment_bulk.py`](#assessment_bulkpy). The first one is the main executable file and the second one is a wrapper for the first one that allows to execute the assessment in multiple samples at the same time taking advantage of multiple processors. There is an example of usage in the [`example/`](./example/) folder for each executable file: [`example/example_main.sh`](./example/example_main.sh) and [`example/example_bulk.sh`](./example/example_bulk.sh). -_Note_: It is recommended to normalize indels and SNVs before executing the assesment. For this purpose, we recommend using pre.py from [Illumina's Haplotype Comparison Tools (hap.py)](https://github.com/Illumina/hap.py). We provide an standalone and containerized **[EUCANCan's pre.py wrapper](https://github.com/EUCANCan/prepy-wrapper)** for this purpose. +_Note_: It is recommended to normalize indels and SNVs before executing the assessment. For this purpose, we recommend using pre.py from [Illumina's Haplotype Comparison Tools (hap.py)](https://github.com/Illumina/hap.py). We provide an standalone and containerized **[EUCANCan's pre.py wrapper](https://github.com/EUCANCan/prepy-wrapper)** for this purpose. -### `assesment_main.py` +### `assessment_main.py` Main executable file. It allows to compare a series of (VCF/BCF/VCF.GZ) files generated by any variant callers against a series of (VCF/BCF/VCF.GZ) truth files for **only one sample**. It is provided as a standalone command line tool. Example of usage: ``` -python3 -O src/assesment_main.py -t truth.vcf -v test.vcf -o output_ +python3 -O src/assessment_main.py -t truth.vcf -v test.vcf -o output_ ``` Check the example of usage in [`example/example_main.sh`](./example/example_main.sh) for more information. #### Interface ``` -usage: assesment_main.py [-h] -t TRUTHS [TRUTHS ...] -v TESTS [TESTS ...] -o OUTPUT_PREFIX -f FASTA_REF [-it INDEL_THRESHOLD] [-wr WINDOW_RADIUS] [--sv-size-bins SV_SIZE_BINS [SV_SIZE_BINS ...]] +usage: assessment_main.py [-h] -t TRUTHS [TRUTHS ...] -v TESTS [TESTS ...] -o OUTPUT_PREFIX -f FASTA_REF [-it INDEL_THRESHOLD] [-wr WINDOW_RADIUS] [--sv-size-bins SV_SIZE_BINS [SV_SIZE_BINS ...]] [--contigs CONTIGS [CONTIGS ...]] [--keep-intermediates] [--no-gzip] -ONCOLINER Assesment +ONCOLINER Assessment options: -h, --help show this help message and exit @@ -76,7 +76,7 @@ options: #### Output -`assesment_main.py` outputs a series of files: +`assessment_main.py` outputs a series of files: * `{OUTPUT_PREFIX}tp.[snv|indel|sv].vcf.gz`: VCF files with the true positives (TP) variants. One file per variant type (SNV, indel and SV). * `{OUTPUT_PREFIX}fp.[snv|indel|sv].vcf.gz`: VCF files with the false positives (FP) variants. One file per variant type (SNV, indel and SV). * `{OUTPUT_PREFIX}fn.[snv|indel|sv].vcf.gz`: VCF files with the false negatives (FN) variants. One file per variant type (SNV, indel and SV). @@ -95,12 +95,12 @@ options: * `protein_affected_genes`: List of genes affected by the variants (separated by `;`). * `protein_affected_driver_genes`: List of cancer driver genes affected by the variants (separated by `;`). -### `assesment_bulk.py` +### `assessment_bulk.py` -Wrapper for `assesment_main.py`. It allows to compare a series of (VCF/BCF/VCF.GZ) files generated by any variant callers against a series of (VCF/BCF/VCF.GZ) truth files for **multiple samples**. It takes advantage of multiple processors and is also able to recover from a previous execution (if the execution was interrupted). It is provided as a standalone command line tool. Example of usage: +Wrapper for `assessment_main.py`. It allows to compare a series of (VCF/BCF/VCF.GZ) files generated by any variant callers against a series of (VCF/BCF/VCF.GZ) truth files for **multiple samples**. It takes advantage of multiple processors and is also able to recover from a previous execution (if the execution was interrupted). It is provided as a standalone command line tool. Example of usage: ``` -python3 -O src/assesment_main.py -c config.tsv -o output_ +python3 -O src/assessment_main.py -c config.tsv -o output_ ``` Check the example of usage in [`example/example_bulk.sh`](./example/example_bulk.sh) for more information. @@ -116,10 +116,10 @@ The configuration file is a TSV file with the following columns: #### Interface ``` -usage: assesment_bulk.py [-h] -c CONFIG_FILE -o OUTPUT_FOLDER [-it INDEL_THRESHOLD] [-wr WINDOW_RADIUS] [--sv-size-bins SV_SIZE_BINS [SV_SIZE_BINS ...]] [--contigs CONTIGS [CONTIGS ...]] [--keep-intermediates] +usage: assessment_bulk.py [-h] -c CONFIG_FILE -o OUTPUT_FOLDER [-it INDEL_THRESHOLD] [-wr WINDOW_RADIUS] [--sv-size-bins SV_SIZE_BINS [SV_SIZE_BINS ...]] [--contigs CONTIGS [CONTIGS ...]] [--keep-intermediates] [--no-gzip] [-p MAX_PROCESSES] -ONCOLINER Assesment Bulk +ONCOLINER Assessment Bulk options: -h, --help show this help message and exit @@ -143,6 +143,6 @@ options: #### Output -`assesment_bulk.py` outputs the same files as `assesment_main.py` for each sample. The output files for each sample are stored in the `OUTPUT_FOLDER/samples` folder in a subfolder named after the sample name. +`assessment_bulk.py` outputs the same files as `assessment_main.py` for each sample. The output files for each sample are stored in the `OUTPUT_FOLDER/samples` folder in a subfolder named after the sample name. -`assesment_bulk.py` also outputs a `aggregated_metrics.csv` file, which aggregates the metrics for all the samples. It contains the same columns as `assesment_main.py`'s `metrics.csv` file. Recall related metrics are calculated using the recall samples and precision related metrics are calculated using the precision samples (as described in the configuration file). +`assessment_bulk.py` also outputs a `aggregated_metrics.csv` file, which aggregates the metrics for all the samples. It contains the same columns as `assessment_main.py`'s `metrics.csv` file. Recall related metrics are calculated using the recall samples and precision related metrics are calculated using the precision samples (as described in the configuration file). diff --git a/modules/oncoliner_assesment/example/.gitignore b/modules/oncoliner_assessment/example/.gitignore similarity index 100% rename from modules/oncoliner_assesment/example/.gitignore rename to modules/oncoliner_assessment/example/.gitignore diff --git a/modules/oncoliner_assessment/example/example_bulk.sh b/modules/oncoliner_assessment/example/example_bulk.sh new file mode 100644 index 0000000..3419b5a --- /dev/null +++ b/modules/oncoliner_assessment/example/example_bulk.sh @@ -0,0 +1,2 @@ + +python3 -O ../src/assessment_bulk.py -c example_config.tsv -o output/ --no-gzip \ No newline at end of file diff --git a/modules/oncoliner_assesment/example/example_config.tsv b/modules/oncoliner_assessment/example/example_config.tsv similarity index 100% rename from modules/oncoliner_assesment/example/example_config.tsv rename to modules/oncoliner_assessment/example/example_config.tsv diff --git a/modules/oncoliner_assessment/example/example_main.sh b/modules/oncoliner_assessment/example/example_main.sh new file mode 100644 index 0000000..b27e070 --- /dev/null +++ b/modules/oncoliner_assessment/example/example_main.sh @@ -0,0 +1,2 @@ +mkdir -p output +python3 -O ../src/assessment_main.py -t ./input/truth/sample_1/*.vcf -v ./input/test/sample_1/*.vcf -f fake_ref.fa -o output/single_sample_example_ --no-gzip \ No newline at end of file diff --git a/modules/oncoliner_assesment/example/fake_ref.fa b/modules/oncoliner_assessment/example/fake_ref.fa similarity index 100% rename from modules/oncoliner_assesment/example/fake_ref.fa rename to modules/oncoliner_assessment/example/fake_ref.fa diff --git a/modules/oncoliner_assesment/example/fake_ref.fa.fai b/modules/oncoliner_assessment/example/fake_ref.fa.fai similarity index 100% rename from modules/oncoliner_assesment/example/fake_ref.fa.fai rename to modules/oncoliner_assessment/example/fake_ref.fa.fai diff --git a/modules/oncoliner_assesment/example/input/test b/modules/oncoliner_assessment/example/input/test similarity index 100% rename from modules/oncoliner_assesment/example/input/test rename to modules/oncoliner_assessment/example/input/test diff --git a/modules/oncoliner_assesment/example/input/truth b/modules/oncoliner_assessment/example/input/truth similarity index 100% rename from modules/oncoliner_assesment/example/input/truth rename to modules/oncoliner_assessment/example/input/truth diff --git a/modules/oncoliner_assesment/src/assesment_bulk.py b/modules/oncoliner_assessment/src/assessment_bulk.py similarity index 99% rename from modules/oncoliner_assesment/src/assesment_bulk.py rename to modules/oncoliner_assessment/src/assessment_bulk.py index 4ce0d50..c0bae21 100644 --- a/modules/oncoliner_assesment/src/assesment_bulk.py +++ b/modules/oncoliner_assessment/src/assessment_bulk.py @@ -4,7 +4,7 @@ import glob from concurrent.futures import ProcessPoolExecutor -from assesment_main import main # noqa +from assessment_main import main # noqa from vcf_ops.constants import DEFAULT_CONTIGS, DEFAULT_VARIANT_TYPES, DEFAULT_INDEL_THRESHOLD, DEFAULT_WINDOW_RADIUS, DEFAULT_SV_BINS # noqa from vcf_ops.metrics import aggregate_metrics, combine_precision_recall_metrics # noqa @@ -67,7 +67,7 @@ def aggregate_metrics_from_samples(output_file: str, samples_folder: str, recall if __name__ == '__main__': - parser = argparse.ArgumentParser(description='ONCOLINER Assesment Bulk') + parser = argparse.ArgumentParser(description='ONCOLINER Assessment Bulk') parser.add_argument('-c', '--config-file', required=True, type=str, help='Path to the config TSV file') parser.add_argument('-o', '--output-folder', required=True, type=str, help='Path to the output folder') parser.add_argument('-it', '--indel-threshold', diff --git a/modules/oncoliner_assesment/src/assesment_main.py b/modules/oncoliner_assessment/src/assessment_main.py similarity index 99% rename from modules/oncoliner_assesment/src/assesment_main.py rename to modules/oncoliner_assessment/src/assessment_main.py index d5fcde7..4ca35f7 100644 --- a/modules/oncoliner_assesment/src/assesment_main.py +++ b/modules/oncoliner_assessment/src/assessment_main.py @@ -164,7 +164,7 @@ def main(truth_vcf_paths, test_vcf_paths, output_prefix, fasta_ref, indel_thresh if __name__ == '__main__': - parser = argparse.ArgumentParser(description='ONCOLINER Assesment') + parser = argparse.ArgumentParser(description='ONCOLINER Assessment') parser.add_argument('-t', '--truths', help='Path to the VCF truth files', nargs='+', required=True, type=str) parser.add_argument('-v', '--tests', help='Path to the VCF test files', nargs='+', required=True, type=str) parser.add_argument('-o', '--output_prefix', diff --git a/modules/oncoliner_assesment/src/indel_sv_converter.py b/modules/oncoliner_assessment/src/indel_sv_converter.py similarity index 100% rename from modules/oncoliner_assesment/src/indel_sv_converter.py rename to modules/oncoliner_assessment/src/indel_sv_converter.py diff --git a/modules/oncoliner_improvement/README.md b/modules/oncoliner_improvement/README.md index e04d013..8932a7c 100644 --- a/modules/oncoliner_improvement/README.md +++ b/modules/oncoliner_improvement/README.md @@ -2,7 +2,7 @@ ![ONCOLINER logo](../../docs/images/ONCOLINER_LOGO_COLOR.png) -The improvement module follows the [assessment step](../oncoliner_assesment/) and provides recommendations based on the performance evaluation of the input pipelines and the selected variant callers. Specifically, the recommendations are the best combinations of variant callers to integrate into the pipeline to maximize performance metrics. It is provided as a standalone command line tool. +The improvement module follows the [assessment step](../oncoliner_assessment/) and provides recommendations based on the performance evaluation of the input pipelines and the selected variant callers. Specifically, the recommendations are the best combinations of variant callers to integrate into the pipeline to maximize performance metrics. It is provided as a standalone command line tool. The first step is to perform both the union and the intersection of the pipeline calls with the callers. Then, performance metrics are calculated for these merged results, and combinations are sorted based on them. It provides a list of all possible combinations provided in a CSV file. This allows the user to sort them by any of the metrics between recall, precision, F1-score, or even by the number of affected protein-coding, cancer-driver, or actionable genes. To improve visualization of the most relevant recommendations, they are filtered by selecting the one in the top 5% for each performance metric, prioritizing those with the least number of callers. This follows the rationale that a better recommendation minimizes the cost of adding too many tools to a pipeline and the effort of going through redundant combinations. diff --git a/modules/oncoliner_ui/README.md b/modules/oncoliner_ui/README.md index 16fb20f..529212c 100644 --- a/modules/oncoliner_ui/README.md +++ b/modules/oncoliner_ui/README.md @@ -32,7 +32,7 @@ optional arguments: -h, --help show this help message and exit -pe PIPELINES_EVALUATIONS_FOLDERS [PIPELINES_EVALUATIONS_FOLDERS ...], --pipelines-evaluations-folders PIPELINES_EVALUATIONS_FOLDERS [PIPELINES_EVALUATIONS_FOLDERS ...] Pipelines evaluation folders paths generated by - ONCOLINER assesment module + ONCOLINER assessment module -o OUTPUT_FILE, --output-file OUTPUT_FILE Output file path -pi PIPELINES_IMPROVEMENTS_FOLDERS [PIPELINES_IMPROVEMENTS_FOLDERS ...], --pipelines-improvements-folders PIPELINES_IMPROVEMENTS_FOLDERS [PIPELINES_IMPROVEMENTS_FOLDERS ...] diff --git a/modules/oncoliner_ui/src/ui/assesment_tab.py b/modules/oncoliner_ui/src/ui/assessment_tab.py similarity index 54% rename from modules/oncoliner_ui/src/ui/assesment_tab.py rename to modules/oncoliner_ui/src/ui/assessment_tab.py index bb11834..0d9a6bd 100644 --- a/modules/oncoliner_ui/src/ui/assesment_tab.py +++ b/modules/oncoliner_ui/src/ui/assessment_tab.py @@ -1,48 +1,48 @@ import os -from .model.assesment.assesment_dao import AssesmentDAO +from .model.assessment.assessment_dao import AssessmentDAO from .plots.metrics_plot import MetricsPlot -class AssesmentTab(): - def __init__(self, env, dao: AssesmentDAO): +class AssessmentTab(): + def __init__(self, env, dao: AssessmentDAO): self._env = env - self._assesment_dao = dao + self._assessment_dao = dao def render(self): - return self._env.get_template(os.path.join("index", "assesment_tab.html")).render(ctrl=self) + return self._env.get_template(os.path.join("index", "assessment_tab.html")).render(ctrl=self) def get_pipelines_names(self): - return self._assesment_dao.get_pipelines_names() + return self._assessment_dao.get_pipelines_names() def render_pipeline(self, pipeline_name): - template = self._env.get_template(os.path.join("assesment_tab", "pipeline.html")) + template = self._env.get_template(os.path.join("assessment_tab", "pipeline.html")) return template.render(ctrl=self, pipeline_name=pipeline_name) def render_warning_panel(self, pipeline_name, sample=None): - warnings = self._assesment_dao.get_warnings(pipeline_name, sample) + warnings = self._assessment_dao.get_warnings(pipeline_name, sample) # Check if there are warnings (all values are empty) if not warnings or not any(warnings.values()): return '' template = self._env.get_template(os.path.join("shared", "warning_panel.html")) - return template.render(ctrl=self, id=f'assesment_{pipeline_name}_{sample if sample is not None else ""}', warnings=warnings, single_sample=sample is not None) + return template.render(ctrl=self, id=f'assessment_{pipeline_name}_{sample if sample is not None else ""}', warnings=warnings, single_sample=sample is not None) def render_metrics_panel(self, pipeline_name): - template = self._env.get_template(os.path.join("assesment_tab", "metrics_panel.html")) - metrics_table = self._assesment_dao.get_metrics_table_by_pipeline(pipeline_name) - return template.render(ctrl=self, id=f'assesment_{pipeline_name}', metrics_table=metrics_table, sample=None) + template = self._env.get_template(os.path.join("assessment_tab", "metrics_panel.html")) + metrics_table = self._assessment_dao.get_metrics_table_by_pipeline(pipeline_name) + return template.render(ctrl=self, id=f'assessment_{pipeline_name}', metrics_table=metrics_table, sample=None) def render_sample_metrics_panel(self, pipeline_name, sample): - template = self._env.get_template(os.path.join("assesment_tab", "metrics_panel.html")) - metrics_table = self._assesment_dao.get_metrics_table_by_pipeline_and_sample(pipeline_name, sample) - return template.render(ctrl=self, id=f'assesment_{pipeline_name}_{sample}', metrics_table=metrics_table, sample=sample) + template = self._env.get_template(os.path.join("assessment_tab", "metrics_panel.html")) + metrics_table = self._assessment_dao.get_metrics_table_by_pipeline_and_sample(pipeline_name, sample) + return template.render(ctrl=self, id=f'assessment_{pipeline_name}_{sample}', metrics_table=metrics_table, sample=sample) def render_metrics_table(self, metrics_table, id, table_type, sample): template = self._env.get_template(os.path.join("shared", "table.html")) id_ = table_type + '_' + id - data = self._assesment_dao.transform_and_get_by_table_type(table_type, metrics_table) + data = self._assessment_dao.transform_and_get_by_table_type(table_type, metrics_table) return template.render(ctrl=self, data=data, id=id_, hide_legend=sample is not None) def render_metrics_plot(self, metrics_table, id, plot_type): @@ -59,17 +59,17 @@ def render_metrics_plot(self, metrics_table, id, plot_type): else: raise ValueError('Invalid plot type: ' + plot_type) # Integrate ChartJS object into HTML - template = self._env.get_template(os.path.join("assesment_tab", "metrics_plot.html")) + template = self._env.get_template(os.path.join("assessment_tab", "metrics_plot.html")) return template.render(chart_data=chart_data, id=id_, plot_type=plot_type) def get_samples(self, pipeline_name: str): - return self._assesment_dao.get_samples(pipeline_name) + return self._assessment_dao.get_samples(pipeline_name) def get_sample_types(self, pipeline_name: str, sample: str): - return self._assesment_dao.get_sample_types(pipeline_name, sample) + return self._assessment_dao.get_sample_types(pipeline_name, sample) def get_recall_samples(self, pipeline_name: str): - return self._assesment_dao.get_recall_samples(pipeline_name) + return self._assessment_dao.get_recall_samples(pipeline_name) def get_precision_samples(self, pipeline_name: str): - return self._assesment_dao.get_precision_samples(pipeline_name) + return self._assessment_dao.get_precision_samples(pipeline_name) diff --git a/modules/oncoliner_ui/src/ui/html_templates/assesment_tab/metrics_panel.html b/modules/oncoliner_ui/src/ui/html_templates/assessment_tab/metrics_panel.html similarity index 100% rename from modules/oncoliner_ui/src/ui/html_templates/assesment_tab/metrics_panel.html rename to modules/oncoliner_ui/src/ui/html_templates/assessment_tab/metrics_panel.html diff --git a/modules/oncoliner_ui/src/ui/html_templates/assesment_tab/metrics_plot.html b/modules/oncoliner_ui/src/ui/html_templates/assessment_tab/metrics_plot.html similarity index 100% rename from modules/oncoliner_ui/src/ui/html_templates/assesment_tab/metrics_plot.html rename to modules/oncoliner_ui/src/ui/html_templates/assessment_tab/metrics_plot.html diff --git a/modules/oncoliner_ui/src/ui/html_templates/assesment_tab/pipeline.html b/modules/oncoliner_ui/src/ui/html_templates/assessment_tab/pipeline.html similarity index 68% rename from modules/oncoliner_ui/src/ui/html_templates/assesment_tab/pipeline.html rename to modules/oncoliner_ui/src/ui/html_templates/assessment_tab/pipeline.html index f008bd9..7c627c3 100644 --- a/modules/oncoliner_ui/src/ui/html_templates/assesment_tab/pipeline.html +++ b/modules/oncoliner_ui/src/ui/html_templates/assessment_tab/pipeline.html @@ -1,8 +1,8 @@
-
+
-

Assesment overview: {{pipeline_name}}

-

Results of the assesment of {{pipeline_name}}. These performance results are the result of aggregating the performance of {{pipeline_name}} over a total of {{ctrl.get_samples(pipeline_name)|length}} samples.

+

Assessment overview: {{pipeline_name}}

+

Results of the assessment of {{pipeline_name}}. These performance results are the result of aggregating the performance of {{pipeline_name}} over a total of {{ctrl.get_samples(pipeline_name)|length}} samples.

Samples used for computing recall related metrics ({{ctrl.get_recall_samples(pipeline_name)|length}}):

    {% for sample in ctrl.get_recall_samples(pipeline_name) %} @@ -20,14 +20,14 @@

    Assesment overview: {{pipeline_name}}

    {{ ctrl.render_metrics_panel(pipeline_name) }}
-

Assesment by sample: {{pipeline_name}}

+

Assessment by sample: {{pipeline_name}}

@@ -36,11 +36,11 @@

Assesment by sample: {% for sample in ctrl.get_samples(pipeline_name) %}

{{sample}} ({{ctrl.get_sample_types(pipeline_name, sample)|join(', ')}})

-

Results of the assesment of {{pipeline_name}} for the sample {{sample}}. {{sample}} is a sample of type {{ctrl.get_sample_types(pipeline_name, sample)|join(', ')}}. +

Results of the assessment of {{pipeline_name}} for the sample {{sample}}. {{sample}} is a sample of type {{ctrl.get_sample_types(pipeline_name, sample)|join(', ')}}. {% if 'precision' not in ctrl.get_sample_types(pipeline_name, sample) %} Since this sample is not part of the precision samples, metrics related to precision were not computed in the aggregated metrics and are not displayed here. {% endif %} diff --git a/modules/oncoliner_ui/src/ui/html_templates/improvement_tab/pipeline.html b/modules/oncoliner_ui/src/ui/html_templates/improvement_tab/pipeline.html index 6026082..e458695 100644 --- a/modules/oncoliner_ui/src/ui/html_templates/improvement_tab/pipeline.html +++ b/modules/oncoliner_ui/src/ui/html_templates/improvement_tab/pipeline.html @@ -2,7 +2,7 @@

Improvement: {{pipeline_name}}

-

Improvement possibilities of {{pipeline_name}} based on its assesment results. These improvements are the result of combining the output of {{pipeline_name}} with the outputs of different variant callers and their combinations.

+

Improvement possibilities of {{pipeline_name}} based on its assessment results. These improvements are the result of combining the output of {{pipeline_name}} with the outputs of different variant callers and their combinations.

+ {% endfor %}
{% for pp in ctrl.get_pipelines_names() %} -
+
{{ ctrl.render_pipeline(pp) }}
{% endfor %} diff --git a/modules/oncoliner_ui/src/ui/html_templates/index/base.html b/modules/oncoliner_ui/src/ui/html_templates/index/base.html index 39c1c65..8c0d0f3 100644 --- a/modules/oncoliner_ui/src/ui/html_templates/index/base.html +++ b/modules/oncoliner_ui/src/ui/html_templates/index/base.html @@ -55,7 +55,7 @@
-