Commit 88c7bddd authored by Pradat Yoann's avatar Pradat Yoann
Browse files

reorganize repo to have python package 'variant_annotator'

parent 4e64984d
Pipeline #8294 failed with stages
in 4 minutes and 11 seconds
[run]
omit = */__init__.py
# Project specific
/htmlcov/
# Logs
log/
*.log
*.coverage
# Mac anc Vim specific
# Mac specific
.DS_Store
.DS_Store?
# Python
__pycache__/
*.pyc
# Python test
*.pytest_cache
*.coverage
*.egg-info/
*htmlcov/
# Open cached files
*.m~
......
language: python
os:
- linux
- osx
python:
- 3.6
- 3.7
- 3.8
- nightly
after_success:
- julia -e 'using Pkg; cd(Pkg.dir("MyPkg")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
- bash <(curl -s https://codecov.io/bash)
branches:
only:
- master
- /^dev/
jobs:
allow_failures:
- julia: nightly
PYTHON ?= python
PYTEST ?= pytest
CTAGS ?= ctags
init:
pip install -r requirements.txt
test:
$(PYTEST) --cov-config=.coveragerc --cov-report term-missing --cov variant_annotator variant_annotator
ctags:
$(CTAGS) --python-kinds=-i --exclude=*/tests/* variant_annotator
clean:
rm -f tags
name: 3.8_bt_variant
channels:
- anaconda
- defaults
dependencies:
- coverage=5.0
- ipython=7.17.0
- numpy=1.19.1
- pandas=1.1.0
- pytest=6.0.1
- pytest-cov=2.10.0
- python=3.8.5
#version 2.4
Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS AF AFR_AF AMR_AF ASN_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER flanking_bps vcf_id vcf_qual ExAC_AF_Adj ExAC_AC_AN_Adj ExAC_AC_AN ExAC_AC_AN_AFR ExAC_AC_AN_AMR ExAC_AC_AN_EAS ExAC_AC_AN_FIN ExAC_AC_AN_NFE ExAC_AC_AN_OTH ExAC_AC_AN_SAS ExAC_FILTER gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF vcf_pos
FAM131C 348487 . GRCh37 1 16386305 16386306 + Intron INS - - C rs372070031 TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 - - c.451+58dup ENST00000375662 FAM131C,intron_variant,,ENST00000375662,NM_182623.2;CLCNKB,downstream_gene_variant,,ENST00000375667,NM_001165945.2;CLCNKB,downstream_gene_variant,,ENST00000375679,NM_000085.4;CLCNKB,downstream_gene_variant,,ENST00000431772,;FAM131C,intron_variant,,ENST00000494078,; C ENSG00000185519 ENST00000375662 Transcript intron_variant rs372070031 1 -1 FAM131C HGNC 26717 protein_coding YES CCDS41270.1 ENSP00000364814 Q96AQ9 UPI000022B016 NM_182623.2 5/6 0.2731 0.3573 0.3581 0.3757 0.5051 MODIFIER 1 insertion PASS GGC rs143272992 50 16386305
ZIC4 84107 . GRCh37 3 147121630 147121631 + Intron DEL TC TC - rs142316820 TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 TC TC c.135+120_135+121del ENST00000525172 ZIC4,intron_variant,,ENST00000383075,NM_032153.5;ZIC4,intron_variant,,ENST00000425731,NM_001168379.1;ZIC4,intron_variant,,ENST00000462748,;ZIC4,intron_variant,,ENST00000463250,;ZIC4,intron_variant,,ENST00000473123,;ZIC4,intron_variant,,ENST00000484399,;ZIC1,intron_variant,,ENST00000488404,;ZIC4,intron_variant,,ENST00000491672,NM_001243256.1;ZIC4,intron_variant,,ENST00000525172,NM_001168378.1;ZIC4,upstream_gene_variant,,ENST00000484586,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,downstream_gene_variant,,ENST00000464144,; - ENSG00000174963 ENST00000525172 Transcript intron_variant rs142316820 1 -1 ZIC4 HGNC 20393 protein_coding YES CCDS54652.1 ENSP00000435509 Q8N9L1 C9JZU7,C9JD04,C9J6T3,B3KPI4 UPI0001914D88 NM_001168378.1 1/4 MODIFIER 1 deletion 1 PASS GATCT . 50 147121629
EIF4G1 1981 . GRCh37 3 184043926 184043927 + Intron DEL AC AC - rs34901174 TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 AC AC c.3243+217_3243+218del ENST00000424196 EIF4G1,intron_variant,,ENST00000319274,;EIF4G1,intron_variant,,ENST00000342981,NM_182917.4;EIF4G1,intron_variant,,ENST00000346169,NM_198241.2;EIF4G1,intron_variant,,ENST00000350481,NM_198242.2;EIF4G1,intron_variant,,ENST00000352767,NM_001194947.1;EIF4G1,intron_variant,,ENST00000382330,NM_001194946.1;EIF4G1,intron_variant,,ENST00000392537,NM_198244.2;EIF4G1,intron_variant,,ENST00000411531,;EIF4G1,intron_variant,,ENST00000414031,;EIF4G1,intron_variant,,ENST00000424196,;EIF4G1,intron_variant,,ENST00000427845,;EIF4G1,intron_variant,,ENST00000434061,NM_004953.4;EIF4G1,intron_variant,,ENST00000435046,;EIF4G1,intron_variant,,ENST00000441154,;EIF2B5,intron_variant,,ENST00000444495,;EIF4G1,intron_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000421110,;EIF4G1,downstream_gene_variant,,ENST00000426123,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000428387,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000444861,;EIF4G1,downstream_gene_variant,,ENST00000450424,;EIF4G1,downstream_gene_variant,,ENST00000457456,;SNORD66,downstream_gene_variant,,ENST00000390856,NR_003055.1;EIF4G1,intron_variant,,ENST00000442406,;EIF4G1,intron_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000413967,;EIF4G1,upstream_gene_variant,,ENST00000422614,;EIF4G1,upstream_gene_variant,,ENST00000460829,;EIF4G1,upstream_gene_variant,,ENST00000464548,;EIF4G1,upstream_gene_variant,,ENST00000475721,;EIF4G1,upstream_gene_variant,,ENST00000482303,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,downstream_gene_variant,,ENST00000493299,; - ENSG00000114867 ENST00000424196 Transcript intron_variant rs34901174 1 1 EIF4G1 HGNC 3296 protein_coding YES CCDS54687.1 ENSP00000416255 Q04637 Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556 UPI00015E0966 20/31 MODIFIER 1 deletion 1 PASS AAACA rs112208190 50 184043925
STEAP1B 256227 . GRCh37 7 22533452 22533453 + Frame_Shift_Del DEL CA CA - novel TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 CA CA c.87_88del p.His29GlnfsTer24 p.H29Qfs*24 ENST00000404369 3/5 STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000404369,NM_001164460.1;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000424363,;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000439708,;STEAP1B,intron_variant,,ENST00000406890,NM_207342.2;STEAP1B,splice_region_variant,,ENST00000483679,; - ENSG00000105889 ENST00000404369 Transcript frameshift_variant,splice_region_variant 503-504/1515 87-88/1029 29-30/342 HE/QX caTGag/caag 1 -1 STEAP1B HGNC 41907 protein_coding YES CCDS56469.1 ENSP00000384370 C9JL51,C9JE84,B5MCI2 UPI000173A267 NM_001164460.1 3/5 PANTHER:PTHR14239:SF3,PANTHER:PTHR14239 HIGH 1 deletion PASS CTCAT rs116873396 50 22533451
TEX12 56158 . GRCh37 11 112042480 112042480 + Intron DEL T T - rs1225064086 TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 T T c.228-9del ENST00000280358 TEX12,intron_variant,,ENST00000280358,NM_031275.4;TEX12,intron_variant,,ENST00000530752,;AP002884.3,intron_variant,,ENST00000532612,;BCO2,upstream_gene_variant,,ENST00000357685,;BCO2,upstream_gene_variant,,ENST00000361053,NM_001256398.1;BCO2,upstream_gene_variant,,ENST00000393032,NM_031938.5;BCO2,upstream_gene_variant,,ENST00000438022,;BCO2,upstream_gene_variant,,ENST00000526088,NM_001037290.2,NM_001256397.1;BCO2,upstream_gene_variant,,ENST00000531169,;BCO2,upstream_gene_variant,,ENST00000532593,NM_001256400.1;RP11-356J5.4,intron_variant,,ENST00000527589,;SDHD,intron_variant,,ENST00000525468,;SDHD,intron_variant,,ENST00000525987,;SDHD,intron_variant,,ENST00000531744,;SDHD,intron_variant,,ENST00000532699,;BCO2,upstream_gene_variant,,ENST00000460924,;BCO2,upstream_gene_variant,,ENST00000461480,;BCO2,upstream_gene_variant,,ENST00000494860,;BCO2,upstream_gene_variant,,ENST00000527939,;BCO2,upstream_gene_variant,,ENST00000531003,;BCO2,upstream_gene_variant,,ENST00000534122,;BCO2,upstream_gene_variant,,ENST00000534550,; - ENSG00000150783 ENST00000280358 Transcript intron_variant rs1225064086 1 1 TEX12 HGNC 11734 protein_coding YES CCDS31679.1 ENSP00000280358 Q9BXU0 UPI00001377E3 NM_031275.4 4/4 MODIFIER 1 deletion PASS ACTT . 50 1.711e-05 8.319e-05 8.285e-05 1.133e-05 112042479
KMT2D 8085 . GRCh37 12 49431403 49431404 + Frame_Shift_Ins INS - - T novel TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 - - c.9735dup p.Pro3246ThrfsTer5 p.P3246Tfs*5 ENST00000301067 34/54 KMT2D,frameshift_variant,p.Pro3246ThrfsTer5,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000549799,; T ENSG00000167548 ENST00000301067 Transcript frameshift_variant 9735-9736/19419 9735-9736/16614 3245-3246/5537 -/X -/A 1 -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 34/54 PANTHER:PTHR22884,PANTHER:PTHR22884:SF324 HIGH 1 insertion 1 PASS GGT . 50 49431403
PDS5B 23047 . GRCh37 13 33332314 33332314 + Frame_Shift_Del DEL A A - novel TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 A A c.3148del p.Thr1050GlnfsTer12 p.T1050Qfs*12 ENST00000315596 27/35 PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000315596,NM_015032.3;PDS5B,frameshift_variant,p.Thr4GlnfsTer12,ENST00000447833,;PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000450460,; - ENSG00000083642 ENST00000315596 Transcript frameshift_variant 3332/7497 3146/4344 1049/1447 Q/X cAa/ca 1 1 PDS5B HGNC 20418 protein_coding YES CCDS41878.1 ENSP00000313851 Q9NTI5 UPI000006D4A9 NM_015032.3 27/35 PANTHER:PTHR12663,PANTHER:PTHR12663:SF1 HIGH 1 deletion 2 PASS ACAA . 50 33332313
CCR7 1236 . GRCh37 17 38712161 38712161 + Intron DEL T T - rs372297045 TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 T T c.61-91del ENST00000246657 CCR7,intron_variant,,ENST00000246657,NM_001838.3;CCR7,intron_variant,,ENST00000578085,;CCR7,intron_variant,,ENST00000579344,; - ENSG00000126353 ENST00000246657 Transcript intron_variant rs372297045 1 -1 CCR7 HGNC 1608 protein_coding YES CCDS11369.1 ENSP00000246657 P32248 J3KTN5,J3KSS9,A0N0Q0 UPI0000001C2F NM_001838.3 2/2 0.004 MODIFIER 1 deletion 1 PASS TCTT . 50 38712160
ATP9A 10079 . GRCh37 20 50342307 50342308 + Intron DEL TC TC - novel TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 TC TC c.327+50_327+51del ENST00000338821 ATP9A,intron_variant,,ENST00000311637,;ATP9A,intron_variant,,ENST00000338821,NM_006045.1;ATP9A,intron_variant,,ENST00000402822,;ATP9A,downstream_gene_variant,,ENST00000477492,;,regulatory_region_variant,,ENSR00001644001,; - ENSG00000054793 ENST00000338821 Transcript intron_variant 1 -1 ATP9A HGNC 13540 protein_coding YES CCDS33489.1 ENSP00000342481 O75110 Q2NLD0,B4DR18 UPI000004D334 NM_006045.1 3/27 MODIFIER 1 deletion PASS TTTCT . 50 50342306
FAM131C 348487 . GRCh37 1 16386305 16386306 + Intron INS - - C rs372070031 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 - - c.451+58dup ENST00000375662 FAM131C,intron_variant,,ENST00000375662,NM_182623.2;CLCNKB,downstream_gene_variant,,ENST00000375667,NM_001165945.2;CLCNKB,downstream_gene_variant,,ENST00000375679,NM_000085.4;CLCNKB,downstream_gene_variant,,ENST00000431772,;FAM131C,intron_variant,,ENST00000494078,; C ENSG00000185519 ENST00000375662 Transcript intron_variant rs372070031 1 -1 FAM131C HGNC 26717 protein_coding YES CCDS41270.1 ENSP00000364814 Q96AQ9 UPI000022B016 NM_182623.2 5/6 0.2731 0.3573 0.3581 0.3757 0.5051 MODIFIER 1 insertion PASS GGC rs143272992 50 16386305
ZIC4 84107 . GRCh37 3 147121630 147121631 + Intron DEL TC TC - rs142316820 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 TC TC c.135+120_135+121del ENST00000525172 ZIC4,intron_variant,,ENST00000383075,NM_032153.5;ZIC4,intron_variant,,ENST00000425731,NM_001168379.1;ZIC4,intron_variant,,ENST00000462748,;ZIC4,intron_variant,,ENST00000463250,;ZIC4,intron_variant,,ENST00000473123,;ZIC4,intron_variant,,ENST00000484399,;ZIC1,intron_variant,,ENST00000488404,;ZIC4,intron_variant,,ENST00000491672,NM_001243256.1;ZIC4,intron_variant,,ENST00000525172,NM_001168378.1;ZIC4,upstream_gene_variant,,ENST00000484586,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,downstream_gene_variant,,ENST00000464144,; - ENSG00000174963 ENST00000525172 Transcript intron_variant rs142316820 1 -1 ZIC4 HGNC 20393 protein_coding YES CCDS54652.1 ENSP00000435509 Q8N9L1 C9JZU7,C9JD04,C9J6T3,B3KPI4 UPI0001914D88 NM_001168378.1 1/4 MODIFIER 1 deletion 1 PASS GATCT . 50 147121629
EIF4G1 1981 . GRCh37 3 184043926 184043927 + Intron DEL AC AC - rs34901174 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 AC AC c.3243+217_3243+218del ENST00000424196 EIF4G1,intron_variant,,ENST00000319274,;EIF4G1,intron_variant,,ENST00000342981,NM_182917.4;EIF4G1,intron_variant,,ENST00000346169,NM_198241.2;EIF4G1,intron_variant,,ENST00000350481,NM_198242.2;EIF4G1,intron_variant,,ENST00000352767,NM_001194947.1;EIF4G1,intron_variant,,ENST00000382330,NM_001194946.1;EIF4G1,intron_variant,,ENST00000392537,NM_198244.2;EIF4G1,intron_variant,,ENST00000411531,;EIF4G1,intron_variant,,ENST00000414031,;EIF4G1,intron_variant,,ENST00000424196,;EIF4G1,intron_variant,,ENST00000427845,;EIF4G1,intron_variant,,ENST00000434061,NM_004953.4;EIF4G1,intron_variant,,ENST00000435046,;EIF4G1,intron_variant,,ENST00000441154,;EIF2B5,intron_variant,,ENST00000444495,;EIF4G1,intron_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000421110,;EIF4G1,downstream_gene_variant,,ENST00000426123,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000428387,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000444861,;EIF4G1,downstream_gene_variant,,ENST00000450424,;EIF4G1,downstream_gene_variant,,ENST00000457456,;SNORD66,downstream_gene_variant,,ENST00000390856,NR_003055.1;EIF4G1,intron_variant,,ENST00000442406,;EIF4G1,intron_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000413967,;EIF4G1,upstream_gene_variant,,ENST00000422614,;EIF4G1,upstream_gene_variant,,ENST00000460829,;EIF4G1,upstream_gene_variant,,ENST00000464548,;EIF4G1,upstream_gene_variant,,ENST00000475721,;EIF4G1,upstream_gene_variant,,ENST00000482303,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,downstream_gene_variant,,ENST00000493299,; - ENSG00000114867 ENST00000424196 Transcript intron_variant rs34901174 1 1 EIF4G1 HGNC 3296 protein_coding YES CCDS54687.1 ENSP00000416255 Q04637 Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556 UPI00015E0966 20/31 MODIFIER 1 deletion 1 PASS AAACA rs112208190 50 184043925
STEAP1B 256227 . GRCh37 7 22533452 22533453 + Frame_Shift_Del DEL CA CA - novel TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 CA CA c.87_88del p.His29GlnfsTer24 p.H29Qfs*24 ENST00000404369 3/5 STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000404369,NM_001164460.1;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000424363,;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000439708,;STEAP1B,intron_variant,,ENST00000406890,NM_207342.2;STEAP1B,splice_region_variant,,ENST00000483679,; - ENSG00000105889 ENST00000404369 Transcript frameshift_variant,splice_region_variant 503-504/1515 87-88/1029 29-30/342 HE/QX caTGag/caag 1 -1 STEAP1B HGNC 41907 protein_coding YES CCDS56469.1 ENSP00000384370 C9JL51,C9JE84,B5MCI2 UPI000173A267 NM_001164460.1 3/5 PANTHER:PTHR14239:SF3,PANTHER:PTHR14239 HIGH 1 deletion PASS CTCAT rs116873396 50 22533451
TEX12 56158 . GRCh37 11 112042480 112042480 + Intron DEL T T - rs1225064086 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 T T c.228-9del ENST00000280358 TEX12,intron_variant,,ENST00000280358,NM_031275.4;TEX12,intron_variant,,ENST00000530752,;AP002884.3,intron_variant,,ENST00000532612,;BCO2,upstream_gene_variant,,ENST00000357685,;BCO2,upstream_gene_variant,,ENST00000361053,NM_001256398.1;BCO2,upstream_gene_variant,,ENST00000393032,NM_031938.5;BCO2,upstream_gene_variant,,ENST00000438022,;BCO2,upstream_gene_variant,,ENST00000526088,NM_001037290.2,NM_001256397.1;BCO2,upstream_gene_variant,,ENST00000531169,;BCO2,upstream_gene_variant,,ENST00000532593,NM_001256400.1;RP11-356J5.4,intron_variant,,ENST00000527589,;SDHD,intron_variant,,ENST00000525468,;SDHD,intron_variant,,ENST00000525987,;SDHD,intron_variant,,ENST00000531744,;SDHD,intron_variant,,ENST00000532699,;BCO2,upstream_gene_variant,,ENST00000460924,;BCO2,upstream_gene_variant,,ENST00000461480,;BCO2,upstream_gene_variant,,ENST00000494860,;BCO2,upstream_gene_variant,,ENST00000527939,;BCO2,upstream_gene_variant,,ENST00000531003,;BCO2,upstream_gene_variant,,ENST00000534122,;BCO2,upstream_gene_variant,,ENST00000534550,; - ENSG00000150783 ENST00000280358 Transcript intron_variant rs1225064086 1 1 TEX12 HGNC 11734 protein_coding YES CCDS31679.1 ENSP00000280358 Q9BXU0 UPI00001377E3 NM_031275.4 4/4 MODIFIER 1 deletion PASS ACTT . 50 1.711e-05 8.319e-05 8.285e-05 1.133e-05 112042479
KMT2D 8085 . GRCh37 12 49431403 49431404 + Frame_Shift_Ins INS - - T novel TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 - - c.9735dup p.Pro3246ThrfsTer5 p.P3246Tfs*5 ENST00000301067 34/54 KMT2D,frameshift_variant,p.Pro3246ThrfsTer5,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000549799,; T ENSG00000167548 ENST00000301067 Transcript frameshift_variant 9735-9736/19419 9735-9736/16614 3245-3246/5537 -/X -/A 1 -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 34/54 PANTHER:PTHR22884,PANTHER:PTHR22884:SF324 HIGH 1 insertion 1 PASS GGT . 50 49431403
PDS5B 23047 . GRCh37 13 33332314 33332314 + Frame_Shift_Del DEL A A - novel TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 A A c.3148del p.Thr1050GlnfsTer12 p.T1050Qfs*12 ENST00000315596 27/35 PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000315596,NM_015032.3;PDS5B,frameshift_variant,p.Thr4GlnfsTer12,ENST00000447833,;PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000450460,; - ENSG00000083642 ENST00000315596 Transcript frameshift_variant 3332/7497 3146/4344 1049/1447 Q/X cAa/ca 1 1 PDS5B HGNC 20418 protein_coding YES CCDS41878.1 ENSP00000313851 Q9NTI5 UPI000006D4A9 NM_015032.3 27/35 PANTHER:PTHR12663,PANTHER:PTHR12663:SF1 HIGH 1 deletion 2 PASS ACAA . 50 33332313
CCR7 1236 . GRCh37 17 38712161 38712161 + Intron DEL T T - rs372297045 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 T T c.61-91del ENST00000246657 CCR7,intron_variant,,ENST00000246657,NM_001838.3;CCR7,intron_variant,,ENST00000578085,;CCR7,intron_variant,,ENST00000579344,; - ENSG00000126353 ENST00000246657 Transcript intron_variant rs372297045 1 -1 CCR7 HGNC 1608 protein_coding YES CCDS11369.1 ENSP00000246657 P32248 J3KTN5,J3KSS9,A0N0Q0 UPI0000001C2F NM_001838.3 2/2 0.004 MODIFIER 1 deletion 1 PASS TCTT . 50 38712160
ATP9A 10079 . GRCh37 20 50342307 50342308 + Intron DEL TC TC - novel TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 TC TC c.327+50_327+51del ENST00000338821 ATP9A,intron_variant,,ENST00000311637,;ATP9A,intron_variant,,ENST00000338821,NM_006045.1;ATP9A,intron_variant,,ENST00000402822,;ATP9A,downstream_gene_variant,,ENST00000477492,;,regulatory_region_variant,,ENSR00001644001,; - ENSG00000054793 ENST00000338821 Transcript intron_variant 1 -1 ATP9A HGNC 13540 protein_coding YES CCDS33489.1 ENSP00000342481 O75110 Q2NLD0,B4DR18 UPI000004D334 NM_006045.1 3/27 MODIFIER 1 deletion PASS TTTCT . 50 50342306
## ENSEMBL VARIANT EFFECT PREDICTOR v101.0
## Output produced at 2020-09-02 10:28:24
## Output produced at 2020-10-30 16:15:42
## Using cache in /Users/ypradat/.vep/homo_sapiens/101_GRCh37
## Using API version 101, DB version ?
## ensembl-funcgen version 101.b918a49
## ensembl-io version 101.943b6c2
## ensembl version 101.856c8e8
## ensembl-variation version 101.851c7e0
## polyphen version 2.2.2
## ClinVar version 201912
## regbuild version 1.0
## COSMIC version 90
## ensembl version 101.856c8e8
## gnomAD version r2.1
## dbSNP version 153
## gencode version GENCODE 19
## genebuild version 2011-04
## ESP version 20141103
## assembly version GRCh37.p13
## sift version sift5.2.2
## 1000genomes version phase3
## ESP version 20141103
## ClinVar version 201912
## HGMD-PUBLIC version 20194
## gnomAD version r2.1
## genebuild version 2011-04
## dbSNP version 153
## sift version sift5.2.2
## polyphen version 2.2.2
## regbuild version 1.0
## COSMIC version 90
## Column descriptions:
## Uploaded_variation : Identifier of uploaded variant
## Location : Location of variant in standard coordinate format (chr:start or chr:start-end)
......
......@@ -30,7 +30,7 @@
##INFO=<ID=VLSC,Number=1,Type=Integer,Description="Final somatic score between 0 and 255 when multiple lines of evidence are available">
##FILTER=<ID=mf1,Description="Filtered out by MuTect v.1">
##FILTER=<ID=oxoG3,Description="Filtered out by OxoG Artifact Filter v3">
##VEP="v101" time="2020-09-02 10:32:28" cache="/Users/ypradat/.vep/homo_sapiens/101_GRCh37" ensembl-variation=101.851c7e0 ensembl=101.856c8e8 ensembl-io=101.943b6c2 ensembl-funcgen=101.b918a49 1000genomes="phase3" COSMIC="90" ClinVar="201912" ESP="20141103" HGMD-PUBLIC="20194" assembly="GRCh37.p13" dbSNP="153" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##VEP="v101" time="2020-10-30 16:15:38" cache="/Users/ypradat/.vep/homo_sapiens/101_GRCh37" ensembl-variation=101.851c7e0 ensembl-io=101.943b6c2 ensembl-funcgen=101.b918a49 ensembl=101.856c8e8 1000genomes="phase3" COSMIC="90" ClinVar="201912" ESP="20141103" HGMD-PUBLIC="20194" assembly="GRCh37.p13" dbSNP="153" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|RefSeq|GENE_PHENO|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL PRIMARY
1 16386305 rs143272992 G GC 50 PASS DB;DP=17;Gene=FAM131C;MQ0=0;SOMATIC;SS=Somatic;VC=Intron;VT=INS;TID=ENST00000375662.4;VLSC=255;CSQ=C|intron_variant|MODIFIER|FAM131C|ENSG00000185519|Transcript|ENST00000375662|protein_coding||5/6|ENST00000375662.4:c.451+58dup|||||||rs372070031|1||-1||1|insertion|HGNC|26717|YES||CCDS41270.1|ENSP00000364814|Q96AQ9||UPI000022B016|NM_182623.2|||||||0.2731|0.3573|0.3581|0.3757|0.5051||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|CLCNKB|ENSG00000184908|Transcript|ENST00000375667|protein_coding||||||||||rs372070031|1|2502|1|||insertion|HGNC|2027|||CCDS57974.1|ENSP00000364819|P51801||UPI000046FF10|NM_001165945.2|1||||||0.2731|0.3573|0.3581|0.3757|0.5051||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|CLCNKB|ENSG00000184908|Transcript|ENST00000375679|protein_coding||||||||||rs372070031|1|2502|1|||insertion|HGNC|2027|YES||CCDS168.1|ENSP00000364831|P51801||UPI000040E261|NM_000085.4|1||||||0.2731|0.3573|0.3581|0.3757|0.5051||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|CLCNKB|ENSG00000184908|Transcript|ENST00000431772|protein_coding||||||||||rs372070031|1|2502|1|cds_start_NF||insertion|HGNC|2027||||ENSP00000389344||Q5T5Q6|UPI000046FF11||1||||||0.2731|0.3573|0.3581|0.3757|0.5051||||||||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|FAM131C|ENSG00000185519|Transcript|ENST00000494078|processed_transcript||4/5|ENST00000494078.1:n.525+58dup|||||||rs372070031|1||-1|||insertion|HGNC|26717|||||||||||||||0.2731|0.3573|0.3581|0.3757|0.5051|||||||||||||||||||| GT:AD:DP:FA:MQ0:BQ:SS:SSC 0/0:11,0:11:0.000:0:.:2:. 0/1:4,2:6:0.333:0:.:2:.
......
......@@ -30,7 +30,7 @@
##INFO=<ID=VLSC,Number=1,Type=Integer,Description="Final somatic score between 0 and 255 when multiple lines of evidence are available">
##FILTER=<ID=mf1,Description="Filtered out by MuTect v.1">
##FILTER=<ID=oxoG3,Description="Filtered out by OxoG Artifact Filter v3">
##VEP="v101" time="2020-09-02 10:32:33" cache="/Users/ypradat/.vep/homo_sapiens/101_GRCh37" ensembl-funcgen=101.b918a49 ensembl=101.856c8e8 ensembl-variation=101.851c7e0 ensembl-io=101.943b6c2 1000genomes="phase3" COSMIC="90" ClinVar="201912" ESP="20141103" HGMD-PUBLIC="20194" assembly="GRCh37.p13" dbSNP="153" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##VEP="v101" time="2020-10-30 14:50:25" cache="/Users/ypradat/.vep/homo_sapiens/101_GRCh37" ensembl-variation=101.851c7e0 ensembl-io=101.943b6c2 ensembl=101.856c8e8 ensembl-funcgen=101.b918a49 1000genomes="phase3" COSMIC="90" ClinVar="201912" ESP="20141103" HGMD-PUBLIC="20194" assembly="GRCh37.p13" dbSNP="153" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|RefSeq|GENE_PHENO|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL PRIMARY
1 44476442 . C T 43 PASS DP=127;Gene=SLC6A9;MQ0=0;SOMATIC;SS=Somatic;VC=5'UTR;VT=SNP;TID=ENST00000372307.3;VLSC=255;CSQ=T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000357730|protein_coding|2/13||ENST00000357730.2:c.200G>A|ENSP00000350362.2:p.Gly67Asp|392/2168|200/1959|67/652|G/D|gGc/gAc|COSV62211565|1||-1|||SNV|HGNC|11056|||CCDS41316.1|ENSP00000350362|P48067|E9PJ65&B7Z589&B7Z3W8|UPI000053030A|NM_006934.3&NM_001261380.1|1|deleterious(0)|probably_damaging(0.999)|Transmembrane_helices:TMhelix&PROSITE_profiles:PS50267&PANTHER:PTHR11616&PANTHER:PTHR11616:SF110&Pfam:PF00209&Superfamily:0053687&Prints:PR00176||||||||||||||||||||1|1||||||,T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000360584|protein_coding|3/14||ENST00000360584.2:c.362G>A|ENSP00000353791.2:p.Gly121Asp|554/2330|362/2121|121/706|G/D|gGc/gAc|COSV62211565|1||-1||1|SNV|HGNC|11056|YES||CCDS41317.1|ENSP00000353791|P48067|B7Z589|UPI000053030B|NM_201649.3|1|deleterious(0)|probably_damaging(1)|Transmembrane_helices:TMhelix&PROSITE_profiles:PS50267&PANTHER:PTHR11616:SF110&PANTHER:PTHR11616&Pfam:PF00209&Superfamily:0053687&Prints:PR00176||||||||||||||||||||1|1||||||,T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000372306|protein_coding|3/12||ENST00000372306.3:c.143G>A|ENSP00000361380.3:p.Gly48Asp|283/1926|143/1740|48/579|G/D|gGc/gAc|COSV62211565|1||-1|||SNV|HGNC|11056||||ENSP00000361380||J3KPA5|UPI0001F7803E||1|deleterious(0)|probably_damaging(0.993)|Transmembrane_helices:TMhelix&PROSITE_profiles:PS50267&PANTHER:PTHR11616&PANTHER:PTHR11616:SF110&Pfam:PF00209&Superfamily:0053687&Prints:PR00176||||||||||||||||||||1|1||||||,T|5_prime_UTR_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000372307|protein_coding|2/12||ENST00000372307.3:c.-53G>A||276/2162|||||COSV62211565|1||-1|||SNV|HGNC|11056||||ENSP00000361381||B7Z3A9|UPI0001914B58||1|||||||||||||||||||||||1|1||||||,T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000372310|protein_coding|3/14||ENST00000372310.3:c.143G>A|ENSP00000361384.3:p.Gly48Asp|309/3130|143/1902|48/633|G/D|gGc/gAc|COSV62211565|1||-1|||SNV|HGNC|11056|||CCDS30695.1|ENSP00000361384|P48067|B7Z589|UPI0000204F05|NM_001024845.2|1|deleterious(0)|probably_damaging(0.999)|Transmembrane_helices:TMhelix&PROSITE_profiles:PS50267&PANTHER:PTHR11616:SF110&PANTHER:PTHR11616&Pfam:PF00209&Superfamily:0053687&Prints:PR00176||||||||||||||||||||1|1||||||,T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000466926|protein_coding|4/4||ENST00000466926.1:c.305G>A|ENSP00000433241.1:p.Gly102Asp|547/591|305/349|102/116|G/D|gGc/gAc|COSV62211565|1||-1|cds_end_NF||SNV|HGNC|11056||||ENSP00000433241||E9PLM5|UPI0001F78040||1|deleterious(0)|probably_damaging(1)|Superfamily:0053687&Pfam:PF00209&PANTHER:PTHR11616&PANTHER:PTHR11616:SF110&PROSITE_profiles:PS50267||||||||||||||||||||1|1||||||,T|intron_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000475075|protein_coding||2/11|ENST00000475075.2:c.-14-2147G>A|||||||COSV62211565|1||-1|||SNV|HGNC|11056||||ENSP00000434460||B7Z589|UPI0001914EDD||1|||||||||||||||||||||||1|1||||||,T|non_coding_transcript_exon_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000489764|retained_intron|3/3||ENST00000489764.1:n.352G>A||352/930|||||COSV62211565|1||-1|||SNV|HGNC|11056|||||||||1|||||||||||||||||||||||1|1||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000492434|processed_transcript||3/4|ENST00000492434.2:n.351+39G>A|||||||COSV62211565|1||-1|||SNV|HGNC|11056|||||||||1|||||||||||||||||||||||1|1||||||,T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000528803|protein_coding|3/5||ENST00000528803.1:c.200G>A|ENSP00000435652.1:p.Gly67Asp|321/524|200/403|67/134|G/D|gGc/gAc|COSV62211565|1||-1|cds_end_NF||SNV|HGNC|11056||||ENSP00000435652||E9PJ65|UPI0001F7803F||1|deleterious(0)|probably_damaging(0.999)|PROSITE_profiles:PS50267&PANTHER:PTHR11616:SF110&PANTHER:PTHR11616&Pfam:PF00209&Superfamily:0053687&Prints:PR00176||||||||||||||||||||1|1||||||,T|downstream_gene_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000533007|processed_transcript||||||||||COSV62211565|1|3860|-1|||SNV|HGNC|11056|||||||||1|||||||||||||||||||||||1|1||||||,T|intron_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000537678|protein_coding||2/10|ENST00000537678.1:c.-8-674G>A|||||||COSV62211565|1||-1|||SNV|HGNC|11056||||ENSP00000442523||B7Z9G8|UPI000191543C||1|||||||||||||||||||||||1|1|||||| GT:AD:DP:FA:MQ0:BQ:SS:SSC 0/0:69,0:69:0.000:0:.:2:. 0/1:42,16:58:0.276:0:31:2:.
......
{% set name = "bt_variant_annotator" %}
{% set version = "0.99" %}
package:
name: "{{ name|lower }}"
version: "{{ version }}"
source:
git_rev: v0.99
git_url: https://github.com/durzot/bt_variant_annotator.git
requirements:
run:
- python>=3.5
- numpy>=1.11.0
- pandas>=1.0.0
build:
number: 0
script: python setup.py install --single-version-externally-managed --record=record.txt
about:
home: https://github.com/durzot/bt_variant_annotator
license: MIT
license_family: MIT
license_file: 'LICENSE'
summary: VCF annotator
description: VCF annotator
dev_url: https://github.com/durzot/bt_variant_annotator
from setuptools import setup
setup(
name = "variant_annotator",
version = "1.0.0",
author = "Yoann Pradat",
author_email = "yoann.pradat@centralesupelec.fr",
install_requires = [
"numpy",
"pandas",
],
)
[run]
omit = */__init__.py, *tests*
"""
The :mod:`variant_annotator` module defines functions for annotating variants using a combination of manual, vep and
vcf2maf annotations.
"""
from ._main import run_annotator
from ._manual import run_manual_annotator
from ._vcf2maf import run_vcf2maf_annotator
from ._vep import run_vep_annotator
__all__ = [
'run_annotator',
'run_manual_annotator',
'run_vcf2maf_annotator',
'run_vep_annotator'
]
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 13 2020
@created: Aug 13 2020
@modified: Oct 30 2020
@author: Yoann Pradat
CentraleSupelec
......@@ -15,9 +15,9 @@ import numpy as np
import pandas as pd
from typing import Union
from .manual import run_manual_annotator
from .vcf2maf import run_vcf2maf_annotator
from .vep import run_vep_annotator
from ._manual import run_manual_annotator
from ._vcf2maf import run_vcf2maf_annotator
from ._vep import run_vep_annotator
DataFrame = pd.core.frame.DataFrame
......@@ -71,8 +71,8 @@ class Vcf2mafConfig:
overwrite: bool=False
def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: str, tumor_id: str, normal_id: str,
infos_n_reads: list, infos_other: list, dt_folders: dict, vcf2maf_config: Vcf2mafConfig,
vep_config: VepConfig, dt_identifiers: dict=None) -> None:
infos_n_reads: list, infos_other: list, dt_folders: dict, vcf2maf_config: Vcf2mafConfig,
vep_config: VepConfig, dt_identifiers: dict=None) -> None:
"""
Run the manual, vcf2maf and/or vep annotations on one VCF file and assemble.
......
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 13 2020
@created: Aug 13 2020
@modified: Oct 30 220
@author: Yoann Pradat
CentraleSupelec
MICS laboratory
9 rue Juliot Curie, Gif-Sur-Yvette, 91190 France
......@@ -16,7 +15,7 @@ import numpy as np
import pandas as pd
import re
from .util import load_vcf
from ._util import load_vcf
DataFrame = pd.core.frame.DataFrame
......@@ -294,7 +293,6 @@ def process_assemble(df_vcf: DataFrame, df_vcf_info: DataFrame, df_vcf_reads: Da
def run_manual_annotator(vcf_path: str, out_path:str, col_normal: str, col_tumor: str, infos_n_reads: list, infos_other: list):
"""
Manually parse VCF file and save at the path specified.
Paramters
---------
vcf_path: str
......
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 13 2020
@author: Yoann Pradat
CentraleSupelec
MICS laboratory
9 rue Juliot Curie, Gif-Sur-Yvette, 91190 France
Useful functions
"""
......@@ -46,14 +43,12 @@ def get_path_to_repo() -> str:
def load_vcf(filepath: str, no_header: bool=False) -> DataFrame:
"""
Load VCF file from the specified filepath into a pandas DataFrame.
Parameters
----------
filepath: str
Path to the file.
no_header: bool
If True, set column names to default names.
Returns
-------
df: DataFrame
......@@ -61,7 +56,7 @@ def load_vcf(filepath: str, no_header: bool=False) -> DataFrame:
"""
if not os.path.exists(filepath):
raise ValueError("The file %s does not exist.")
raise ValueError("The file %s does not exist." % filepath)
else:
if no_header:
df_vcf = pd.read_csv(
......
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 13 2020
@created: Aug 13 2020
@modified: Oct 30 2020
@author: Yoann Pradat
CentraleSupelec
MICS laboratory
9 rue Juliot Curie, Gif-Sur-Yvette, 91190 France
......@@ -12,12 +11,11 @@ Python wrapper around vcf2maf perl script.
"""
import os
from .util import get_path_to_repo
from ._util import get_path_to_repo
def run_vcf2maf_annotator(vep_data: str, vep_n_fork: int, vcf_path: str, out_path: str, tmp_folder: str, tumor_id: str, normal_id: str, fasta: str, overwrite: bool=False):
"""
Run vcf2maf reannotator. Details may found at https://github.com/mskcc/vcf2maf.
Parameters
----------
vep_data: str
......
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 13 2020
@created: Aug 13 2020
@modified: Oct 30 2020
@author: Yoann Pradat
CentraleSupelec
MICS laboratory
9 rue Juliot Curie, Gif-Sur-Yvette, 91190 France
Python wrapper around VEP command.
"""
import os
from typing import Union
from .util import get_path_to_repo
from typing import Union
from ._util import get_path_to_repo
def run_vep_annotator(vep_data: str, vcf_path: str, out_path: str, fasta: str, vep_custom: Union[str,list]=None, overwrite: bool=False, vep_n_fork: int=4):
"""
Run variant ensembl predictor alone with custom options. See options details at
https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_af
Parameters
---------
vep_data: str
......
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