Skip to content

Commit

Permalink
added robustness for mixed entry types in ID column of input vcf, cre…
Browse files Browse the repository at this point in the history 
…ated test case
  • Loading branch information
Mück committed May 7, 2024
1 parent 3138ca4 commit 7891417
Show file tree
Hide file tree
Showing 12 changed files with 265 additions and 2 deletions.
4 changes: 2 additions & 2 deletions deeprvat/annotations/annotations.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1737,8 +1737,8 @@ def process_vep(
vcf_file, names=["chrom", "pos", "#Uploaded_variation", "ref", "alt"]
)
if "#Uploaded_variation" in vep_file.columns:
vep_file = vep_file.merge(vcf_df, on="#Uploaded_variation")

vep_file = vep_file.merge(vcf_df, on="#Uploaded_variation", how = 'left')
vep_file.loc[vep_file.chrom.isna(),['chrom','pos','ref','alt']]=vep_file[vep_file['chrom'].isna()]['#Uploaded_variation'].str.replace("_", ":").str.replace("/", ":").str.split(':', expand=True).values
if "pos" in vep_file.columns:
vep_file["pos"] = vep_file["pos"].astype(int)

Expand Down
81 changes: 81 additions & 0 deletions tests/annotations/test_annotations.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -188,6 +188,18 @@ def test_deepsea_pca(
"49",
),
(
"merge_annotations_mixedIDs",
"merged_annotations_expected.parquet",
"test_hg2_deepripe.csv.gz",
"test_k5_deepripe.csv.gz",
"test_parclip.csv.gz",
"variants.parquet",
"test.vcf",
"test_vep.tsv",
"49",
),
]
)
Expand Down Expand Up @@ -325,3 +337,72 @@ def test_aggregate_abscores(
expected_results = pd.read_parquet(expected_path)
assert written_results.shape == expected_results.shape
assert_frame_equal(written_results, expected_results[written_results.columns], check_exact = False)



@pytest.mark.parametrize(
"test_name_dir, absplice_scores, annotations, expected",
[
( "merge_absplice_scores_small",
"abSplice_score_file.parquet",
"vep_deepripe_deepsea.parquet",
"vep_deepripe_deepsea_absplice.parquet",
),
]
)
def test_merge_absplice_scores(
test_name_dir, absplice_scores, annotations, expected, tmp_path
):
current_test_data_dir = tests_data_dir / 'merge_absplice_scores' / test_name_dir
absplice_score_path = current_test_data_dir / 'input' / absplice_scores
annotation_path = current_test_data_dir / 'input' / annotations
expected_path = current_test_data_dir / 'expected' / expected
output_path = tmp_path / 'out.parquet'
cli_runner = CliRunner()
cli_parameters = [
'merge-abscores',
annotation_path.as_posix(),
absplice_score_path.as_posix(),
output_path.as_posix(),
]
result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False)
assert result.exit_code == 0
written_results = pd.read_parquet(output_path)
expected_results = pd.read_parquet(expected_path)
assert written_results.shape == expected_results.shape
assert_frame_equal(written_results, expected_results, check_exact = False)


# @pytest.mark.parametrize(
# "test_name_dir, input_file_1, input_file_2, parameter1, expected",
# [
# ( "test_name_dir",
# "input_file1.parquet",
# "input_file2.parquet",
# "8",
# "expected.parquet",
# ),
# ]
# )
# def template(
# test_data_name_dir, input_file_1, input_file_2, parameter1, expected, tmp_path
# ):
# current_test_data_dir = tests_data_dir / 'test_name' / test_data_name_dir
# input_path1 = current_test_data_dir / 'input' / input_file_1
# input_path2 = current_test_data_dir / 'input' /input_file_2
# expected_path = current_test_data_dir / 'expected' / expected
# output_path = tmp_path / 'out.parquet'
# cli_runner = CliRunner()
# cli_parameters = [
# 'function-name',
# input_path1.as_posix(),
# input_path2.as_posix(),
# output_path.as_posix(),
# parameter1,
# ]
# result = cli_runner.invoke(annotations_cli, cli_parameters, catch_exceptions=False)
# assert result.exit_code == 0
# written_results = pd.read_parquet(output_path)
# expected_results = pd.read_parquet(expected_path)
# assert written_results.shape == expected_results.shape
# assert_frame_equal(written_results, expected_results[written_results.columns], check_exact = False)
Binary file added ...bsplice_scores/merge_absplice_scores_small/expected/vep_deepripe_deepsea_absplice.parquet
View file
Binary file not shown.
Binary file added ..._data/merge_absplice_scores/merge_absplice_scores_small/input/abSplice_score_file.parquet
View file
Binary file not shown.
Binary file added ...data/merge_absplice_scores/merge_absplice_scores_small/input/vep_deepripe_deepsea.parquet
View file
Binary file not shown.
Binary file added ...merge_annotations/merge_annotations_mixedIDs/expected/merged_annotations_expected.parquet
View file
Binary file not shown.
60 changes: 60 additions & 0 deletions tests/annotations/test_data/merge_annotations/merge_annotations_mixedIDs/input/test.vcf
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,60 @@
chr3 3474106 . C T
chr3 6134790 rs881 A G
chr3 6492413 . A G
chr3 7479092 . T A
chr3 10151779 . G T
chr3 10963200 . C A
chr3 13336897 rs178 T A
chr3 25565017 rs37 C G
chr3 28027872 rs721 T C
chr3 30429305 rs135 T C
chr3 39059372 rs23 A C
chr3 47378509 rs727 T A
chr3 47839379 rs268 C T
chr3 55062103 rs873 A G
chr3 56288165 rs664 G C
chr3 64813843 rs815 A G
chr3 70306576 rs107 C G
chr3 72140079 rs492 A T
chr3 72906610 rs930 T G
chr3 74562325 rs523 G T
chr3 78839934 rs583 G A
chr3 81414874 rs170 A T
chr3 97458263 rs548 A T
chr3 97649369 rs546 C G
chr3 97949211 rs543 G A
chr3 99075824 rs838 T C
chr3 101580812 rs311 A C
chr3 103151123 rs382 C A
chr3 103329532 rs179 T C
chr3 103928516 rs19 A T
chr3 105180981 rs341 A G
chr3 111113126 rs470 A G
chr3 111866541 rs467 T A
chr3 117455785 rs718 C A
chr3 120258434 rs506 A C
chr3 120364684 rs367 T G
chr3 122803142 rs488 A C
chr3 125013245 rs146 A G
chr3 127342540 rs318 G T
chr3 133734681 rs104 G A
chr3 139349025 rs665 T C
chr3 140275153 rs791 G C
chr3 145304395 rs102 C G
chr3 147901161 rs274 C T
chr3 150051584 rs123 C A
chr3 150399452 rs648 T A
chr3 158349305 rs748 T A
chr3 158851780 rs408 A T
chr3 160382108 rs963 A C
chr3 168465216 rs751 G C
chr3 171089322 rs197 A T
chr3 177499702 rs376 G C
chr3 185836100 rs581 G T
chr3 191856146 rs596 G C
chr3 192824921 rs701 C G
chr3 193390684 rs434 A C
chr3 194577309 rs70 T G
chr3 194762766 rs598 G A
chr3 197345633 rs356 T A
chr3 197732094 rs693 G T
Binary file added ...ons/test_data/merge_annotations/merge_annotations_mixedIDs/input/test_hg2_deepripe.csv.gz
View file
Binary file not shown.
Binary file added ...ions/test_data/merge_annotations/merge_annotations_mixedIDs/input/test_k5_deepripe.csv.gz
View file
Binary file not shown.
Binary file added ...otations/test_data/merge_annotations/merge_annotations_mixedIDs/input/test_parclip.csv.gz
View file
Binary file not shown.
122 changes: 122 additions & 0 deletions tests/annotations/test_data/merge_annotations/merge_annotations_mixedIDs/input/test_vep.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,122 @@
## ENSEMBL VARIANT EFFECT PREDICTOR v110.1
## Output produced at 2024-04-24 15:05:38
## Using cache in repo_dir/ensembl-vep/cache/homo_sapiens/110_GRCh38
## Using API version 110, DB version ?
## ensembl-variation version 110.d34d25e
## ensembl-io version 110.b1a0d57
## ensembl version 110.584a8f3
## ensembl-funcgen version 110.24e6da6
## dbSNP version 154
## 1000genomes version phase3
## gencode version GENCODE 44
## polyphen version 2.2.3
## sift version 6.2.1
## gnomADe version r2.1.1
## ClinVar version 202301
## HGMD-PUBLIC version 20204
## assembly version GRCh38.p14
## COSMIC version 97
## regbuild version 1.0
## gnomADg version v3.1.2
## genebuild version 2014-07
## Column descriptions:
## Uploaded_variation : Identifier of uploaded variant
## Location : Location of variant in standard coordinate format (chr:start or chr:start-end)
## Allele : The variant allele used to calculate the consequence
## Gene : Stable ID of affected gene
## Feature : Stable ID of feature
## Feature_type : Type of feature - Transcript, RegulatoryFeature or MotifFeature
## Consequence : Consequence type
## cDNA_position : Relative position of base pair in cDNA sequence
## CDS_position : Relative position of base pair in coding sequence
## Protein_position : Relative position of amino acid in protein
## Amino_acids : Reference and variant amino acids
## Codons : Reference and variant codon sequence
## Existing_variation : Identifier(s) of co-located known variants
## IMPACT : Subjective impact classification of consequence type
## DISTANCE : Shortest distance from variant to transcript
## STRAND : Strand of the feature (1/-1)
## FLAGS : Transcript quality flags
## BIOTYPE : Biotype of transcript or regulatory feature
## CANONICAL : Indicates if transcript is canonical for this gene
## ENSP : Protein identifer
## SIFT : SIFT prediction and/or score
## PolyPhen : PolyPhen prediction and/or score
## AF : Frequency of existing variant in 1000 Genomes combined population
## CLIN_SIG : ClinVar clinical significance of the dbSNP variant
## SOMATIC : Somatic status of existing variant
## PHENO : Indicates if existing variant(s) is associated with a phenotype, disease or trait; multiple values correspond to multiple variants
## VEP command-line: vep --af --assembly GRCh38 --biotype --cache --canonical --database 0 --dir_cache [PATH]/cache --dir_plugins [PATH]/Plugins --fasta [PATH]/GRCh38.primary_assembly.genome.fa --force_overwrite --fork 5 --format vcf --input_file [PATH]/chr3test_stripped.vcf.gz --no_escape --no_stats --offline --output_file [PATH]/chr3test_vep_anno.tsv --per_gene --pick_order biotype,mane_select,mane_plus_clinical,canonical,appris,tsl,ccds,rank,length,ensembl,refseq --polyphen s --protein --sift s --tab --total_length
#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation IMPACT DISTANCE STRAND FLAGS BIOTYPE CANONICAL ENSP SIFT PolyPhen AF CLIN_SIG SOMATIC PHENO
3_3474106_C/T 3:3474106 T ENSG00000223727 ENST00000420000 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - -
rs881 3:6134790 G - - - intergenic_variant - - - - - rs1007430246 MODIFIER - - - - - - - - - - - -
3_6492413_A/G 3:6492413 G ENSG00000189229 ENST00000655754 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - -
3_7479092_T/A 3:7479092 A ENSG00000196277 ENST00000357716 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000350348 - - - - - -
3_10151779_G/T 3:10151779 T ENSG00000287086 ENST00000660063 Transcript intron_variant,non_coding_transcript_variant - - - - - COSV56556349 MODIFIER - -1 - lncRNA YES - - - - - 1 1
3_10151779_G/T 3:10151779 T ENSG00000134086 ENST00000256474 Transcript 3_prime_UTR_variant 2526/4414 - - - - COSV56556349 MODIFIER - 1 - protein_coding YES ENSP00000256474 - - - - 1 1
3_10963200_C/A 3:10963200 A ENSG00000286962 ENST00000656787 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - -
rs178 3:13336897 A ENSG00000132182 ENST00000254508 Transcript missense_variant 3670/7206 3574/5664 1192/1887 I/F Atc/Ttc - MODERATE - -1 - protein_coding YES ENSP00000254508 0.01 0.712 - - - -
rs37 3:25565017 G ENSG00000077092 ENST00000330688 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000332296 - - - - - -
rs721 3:28027872 C ENSG00000235493 ENST00000356047 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA - - - - - - - -
rs135 3:30429305 C ENSG00000289450 ENST00000691186 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - -
rs23 3:39059372 C ENSG00000114742 ENST00000302313 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000307491 - - - - - -
rs727 3:47378509 A ENSG00000260236 ENST00000568593 Transcript downstream_gene_variant - - - - - - MODIFIER 580 -1 - lncRNA YES - - - - - - -
rs727 3:47378509 A ENSG00000076201 ENST00000265562 Transcript upstream_gene_variant - - - - - - MODIFIER 2512 1 - protein_coding YES ENSP00000265562 - - - - - -
rs268 3:47839379 T ENSG00000132153 ENST00000445061 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000405620 - - - - - -
rs873 3:55062103 G ENSG00000157445 ENST00000474759 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000419101 - - - - - -
rs664 3:56288165 C ENSG00000187672 ENST00000288221 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000288221 - - - - - -
rs815 3:64813843 G ENSG00000241684 ENST00000650103 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - -
rs107 3:70306576 G ENSG00000240405 ENST00000642114 Transcript intron_variant,non_coding_transcript_variant - - - - - rs536908099 MODIFIER - 1 - lncRNA YES - - - 0.0002 - - -
rs107 3:70306576 G ENSG00000242120 ENST00000567252 Transcript intron_variant - - - - - rs536908099 MODIFIER - -1 - protein_coding YES ENSP00000490638 - - 0.0002 - - -
rs492 3:72140079 T ENSG00000241163 ENST00000626474 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - -
rs930 3:72906610 G ENSG00000172986 ENST00000389617 Transcript intron_variant - - - - - COSV67474846 MODIFIER - 1 - protein_coding YES ENSP00000374268 - - - - 1 1
rs523 3:74562325 T ENSG00000113805 ENST00000263665 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000263665 - - - - - -
rs583 3:78839934 A ENSG00000169855 ENST00000464233 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000420321 - - - - - -
rs170 3:81414874 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs548 3:97458263 T ENSG00000080224 ENST00000389672 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000374323 - - - - - -
rs546 3:97649369 G ENSG00000080224 ENST00000389672 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000374323 - - - - - -
rs543 3:97949211 A ENSG00000080200 ENST00000389622 Transcript downstream_gene_variant - - - - - - MODIFIER 4227 1 - protein_coding YES ENSP00000374273 - - - - - -
rs543 3:97949211 A ENSG00000170854 ENST00000394198 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000377748 - - - - - -
rs838 3:99075824 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs311 3:101580812 C ENSG00000081154 ENST00000265260 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000265260 - - - - - -
rs311 3:101580812 C ENSG00000242299 ENST00000496294 Transcript upstream_gene_variant - - - - - - MODIFIER 3865 -1 - processed_pseudogene YES - - - - - - -
rs382 3:103151123 A - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs179 3:103329532 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs19 3:103928516 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs341 3:105180981 G - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs470 3:111113126 G ENSG00000177707 ENST00000485303 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000418070 - - - - - -
rs467 3:111866541 A ENSG00000144824 ENST00000431670 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000405405 - - - - - -
rs718 3:117455785 A - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs506 3:120258434 C ENSG00000175697 ENST00000464295 Transcript intron_variant - - - - - rs1470110063 MODIFIER - -1 - protein_coding YES ENSP00000417261 - - - - - -
rs367 3:120364684 G ENSG00000240661 ENST00000634410 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - transcribed_unitary_pseudogene YES - - - - - - -
rs367 3:120364684 G ENSG00000282950 ENST00000634744 Transcript downstream_gene_variant - - - - - - MODIFIER 1309 -1 - lncRNA YES - - - - - - -
rs488 3:122803142 C ENSG00000138463 ENST00000261038 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000261038 - - - - - -
rs146 3:125013245 G ENSG00000173706 ENST00000311127 Transcript synonymous_variant 2441/9195 2334/4146 778/1381 L ctT/ctC - LOW - -1 - protein_coding YES ENSP00000311502 - - - - - -
rs318 3:127342540 T ENSG00000244215 ENST00000488425 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - lncRNA YES - - - - - - -
rs104 3:133734681 A ENSG00000291042 ENST00000460564 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - -
rs665 3:139349025 C ENSG00000272656 ENST00000608472 Transcript non_coding_transcript_exon_variant 347/348 - - - - - MODIFIER - -1 - lncRNA YES - - - - - - -
rs665 3:139349025 C ENSG00000184432 ENST00000503326 Transcript downstream_gene_variant - - - - - - MODIFIER 4921 -1 - protein_coding - ENSP00000426682 - - - - - -
rs665 3:139349025 C ENSG00000175110 ENST00000680020 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000505414 - - - - - -
rs791 3:140275153 C ENSG00000158258 ENST00000458420 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000402460 - - - - - -
rs102 3:145304395 G - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs274 3:147901161 T - - - intergenic_variant - - - - - rs1305018800 MODIFIER - - - - - - - - - - - -
rs123 3:150051584 A ENSG00000243944 ENST00000487840 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - -
rs123 3:150051584 A ENSG00000070087 ENST00000497148 Transcript upstream_gene_variant - - - - - - MODIFIER 796 -1 - protein_coding - ENSP00000417817 - - - - - -
rs123 3:150051584 A ENSG00000240477 ENST00000466044 Transcript downstream_gene_variant - - - - - - MODIFIER 128 1 - processed_pseudogene YES - - - - - - -
rs648 3:150399452 A - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs748 3:158349305 A ENSG00000174891 ENST00000611884 Transcript intron_variant - - - - - - MODIFIER - 1 - protein_coding YES ENSP00000481697 - - - - - -
rs408 3:158851780 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs963 3:160382108 C ENSG00000068885 ENST00000326448 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000312778 - - - - - -
rs751 3:168465216 C ENSG00000206120 ENST00000431685 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - transcribed_unitary_pseudogene YES - - - - - - -
rs197 3:171089322 T ENSG00000154310 ENST00000436636 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000399511 - - - - - -
rs376 3:177499702 C ENSG00000252028 ENST00000516219 Transcript downstream_gene_variant - - - - - - MODIFIER 3601 -1 - misc_RNA YES - - - - - - -
rs376 3:177499702 C ENSG00000228221 ENST00000656037 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - -
rs581 3:185836100 T - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs596 3:191856146 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs701 3:192824921 G ENSG00000180611 ENST00000392452 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000376246 - - - - - -
rs434 3:193390684 C - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs70 3:194577309 G - - - intergenic_variant - - - - - - MODIFIER - - - - - - - - - - - -
rs598 3:194762766 A ENSG00000237222 ENST00000667646 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - lncRNA YES - - - - - - -
rs598 3:194762766 A ENSG00000230401 ENST00000422271 Transcript downstream_gene_variant - - - - - - MODIFIER 2472 -1 - lncRNA YES - - - - - - -
rs356 3:197345633 A ENSG00000286870 ENST00000669801 Transcript downstream_gene_variant - - - - - - MODIFIER 4927 1 - lncRNA YES - - - - - - -
rs693 3:197732094 T ENSG00000145016 ENST00000296343 Transcript intron_variant - - - - - - MODIFIER - -1 - protein_coding YES ENSP00000296343 - - - - - -
Binary file added ...annotations/test_data/merge_annotations/merge_annotations_mixedIDs/input/variants.parquet
View file
Binary file not shown.

0 comments on commit 7891417

Please sign in to comment.