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“Marcel-Mueck”
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| annotation_column_names: | ||
| 'CADD_RAW' : | ||
| 'CADD_raw': 0 | ||
| 'PrimateAI' : | ||
| 'PrimateAI_score' : 0 | ||
| 'SpliceAI_delta_score' : | ||
| 'SpliceAI_delta_score' : 0 | ||
| 'am_pathogenicity' : | ||
| 'alphamissense' : 0 | ||
| 'af' : | ||
| 'combined_UKB_NFE_AF' : 0 | ||
| 'maf_mb' : | ||
| 'combined_UKB_NFE_AF_MB' : 0 | ||
| 'maf' : | ||
| 'combined_UKB_NFE_MAF' : 1000 | ||
| 'Condel' : | ||
| 'condel_score' : 0 | ||
| 'PolyPhen' : | ||
| 'polyphen_score' : 0 | ||
| 'SIFT' : | ||
| 'sift_score' : 1 | ||
| 'QKI_hg2' : | ||
| 'DeepRipe_plus_QKI_lip_hg2' : 0 | ||
| 'QKI_k5' : | ||
| 'DeepRipe_plus_QKI_clip_k5' : 0 | ||
| 'KHDRBS1_k5' : | ||
| 'DeepRipe_plus_KHDRBS1_clip_k5' : 0 | ||
| 'ELAVL1_parclip' : | ||
| 'DeepRipe_plus_ELAVL1_parclip' : 0 | ||
| 'TARDBP_parclip' : | ||
| 'DeepRipe_plus_TARDBP_parclip' : 0 | ||
| 'HNRNPD_parclip' : | ||
| 'DeepRipe_plus_HNRNPD_parclip' : 0 | ||
| 'MBNL1_parclip' : | ||
| 'DeepRipe_plus_MBNL1_parclip' : 0 | ||
| 'QKI_parclip' : | ||
| 'DeepRipe_plus_QKI_parclip' : 0 | ||
| 'Consequence_splice_acceptor_variant' : | ||
| 'Consequence_splice_acceptor_variant' : 0 | ||
| 'Consequence_splice_donor_variant' : | ||
| 'Consequence_splice_donor_variant' : 0 | ||
| 'Consequence_stop_gained' : | ||
| 'Consequence_stop_gained' : 0 | ||
| 'Consequence_frameshift_variant' : | ||
| 'Consequence_frameshift_variant' : 0 | ||
| 'Consequence_stop_lost' : | ||
| 'Consequence_stop_lost' : 0 | ||
| 'Consequence_start_lost' : | ||
| 'Consequence_start_lost' : 0 | ||
| 'Consequence_inframe_insertion' : | ||
| 'Consequence_inframe_insertion' : 0 | ||
| 'Consequence_inframe_deletion' : | ||
| 'Consequence_inframe_deletion' : 0 | ||
| 'Consequence_missense_variant' : | ||
| 'Consequence_missense_variant' : 0 | ||
| 'Consequence_protein_altering_variant' : | ||
| 'Consequence_protein_altering_variant' : 0 | ||
| 'Consequence_splice_region_variant' : | ||
| 'Consequence_splice_region_variant' : 0 | ||
| 'DeepSEA_PC_1' : | ||
| 'DeepSEA_PC_1' : 0 | ||
| 'DeepSEA_PC_2' : | ||
| 'DeepSEA_PC_2' : 0 | ||
| 'DeepSEA_PC_3' : | ||
| 'DeepSEA_PC_3' : 0 | ||
| 'DeepSEA_PC_4' : | ||
| 'DeepSEA_PC_4' : 0 | ||
| 'DeepSEA_PC_5' : | ||
| 'DeepSEA_PC_5' : 0 | ||
| 'DeepSEA_PC_6' : | ||
| 'DeepSEA_PC_6' : 0 | ||
| 'AF' : | ||
| 'AF' : 0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| name: absplice | ||
| channels: | ||
| - conda-forge | ||
| dependencies: | ||
| - python==3.8 | ||
| - cython | ||
| - tensorflow | ||
| - pytest | ||
| - setuptools | ||
| - scipy | ||
| - pandas | ||
| - tqdm | ||
| - click | ||
| - pip | ||
| - pyarrow | ||
| - pandas | ||
| - numpy==1.23 | ||
| # needed for splicemap | ||
| - seaborn | ||
| - scikit-learn | ||
| - bioconda::pyfaidx | ||
| - bioconda::pyranges>=0.0.71 | ||
| - bioconda::cyvcf2==0.30.16 | ||
| - bioconda::tabix | ||
| - bioconda::snakemake==7.26.0 | ||
| - bioconda::spliceai | ||
| - bioconda::kipoiseq>=0.7 | ||
| - deepdiff | ||
| - pip: | ||
| - mmsplice | ||
| - interpret == 0.2.7 | ||
| - interpret-core == 0.2.7 | ||
| - git+https://github.com/gagneurlab/splicemap.git |
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| Original file line number | Diff line number | Diff line change |
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| gene_map: ../../absplice/precomputed/GENE_MAP.tsv.gz | ||
|
|
||
| # mapping of variants to individuals, result of variant filtering on provided vcfs | ||
| variant_sample_map: ../data/resources/analysis_files/variant_sample_map/{vcf_id}_variant_sample_map.csv | ||
|
|
||
| cat_count_table: | ||
| raw: ../data/resources/analysis_files/absplice_rna_related_files/processed/cat_count_table/tissue_cat={tissue_cat}_count_table_raw.csv | ||
| updated: ../data/resources/analysis_files/absplice_rna_related_files/processed/cat_count_table/tissue_cat={tissue_cat}_count_table.csv | ||
| cat_outliers: | ||
| qual_filtered: | ||
| junction_level: ../data/resources/analysis_files/absplice_rna_related_files/processed/cat_outliers/qual_filtered/tissue_cat={tissue_cat}_junction_level_signif.csv | ||
| gene_level: ../data/resources/analysis_files/absplice_rna_related_files/processed/cat_outliers/qual_filtered/tissue_cat={tissue_cat}_gene_level.csv | ||
| combine_gene_junction: | ||
| gene_junction_signif: ../data/resources/analysis_files/absplice_rna_related_files/processed/cat_outliers/combine_gene_junction/gene_junction_signif/tissue_cat={tissue_cat}_signif.csv | ||
| outlier_with_variant: ../data/resources/analysis_files/absplice_rna_related_files/processed/cat_outliers/combine_gene_junction/outlier_with_variant/{vcf_id}_tissue_cat={tissue_cat}_outlier_with_variant.csv | ||
| minus_log10_pval: ../data/resources/analysis_files/absplice_rna_related_files/processed/cat_outliers/combine_gene_junction/minus_log10_pval/{vcf_id}_tissue_cat={tissue_cat}_FRASER_pval.csv |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| fasta: | ||
| hg19: | ||
| url: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/GRCh37_mapping/GRCh37.primary_assembly.genome.fa.gz | ||
| file: 'GRCh37.primary_assembly.genome.fa' | ||
| hg38: | ||
| url: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/GRCh38.primary_assembly.genome.fa.gz | ||
| file: 'GRCh38.primary_assembly.genome.fa' | ||
|
|
||
| gtf: | ||
| hg19: | ||
| url: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/GRCh37_mapping/gencode.v39lift37.annotation.gtf.gz | ||
| file: 'gencode.v39lift37.annotation.gtf' | ||
| coding_genes: 'hg19_coding_genes.csv' | ||
| hg38: | ||
| url: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/gencode.v39.annotation.gtf.gz | ||
| file: 'gencode.v39.annotation.gtf' | ||
| coding_genes: 'hg38_coding_genes.csv' | ||
|
|
||
| splicemap_dir: 'splicemap_{genome}/' | ||
|
|
||
| splicemap: | ||
| psi3: 'splicemap_{genome}/{tissue}_splicemap_psi3_method=kn_event_filter=median_cutoff.csv.gz' | ||
| psi5: 'splicemap_{genome}/{tissue}_splicemap_psi5_method=kn_event_filter=median_cutoff.csv.gz' | ||
|
|
||
| spliceai_rocksdb: | ||
| hg19: 'spliceAI_grch37_chr{chromosome}.db' | ||
| hg38: 'spliceAI_grch38_chr{chromosome}.db' | ||
| chromosomes: ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y'] | ||
|
|
||
| gnomad_rocksdb: | ||
| hg19: 'gnomad_maf_db_hg19/gnomad_maf_db_2.1.1.db' | ||
| hg38: 'gnomad_maf_db_hg38/gnomad_maf_db_3.1.2.db' | ||
|
|
||
| all_available_splicemap_tissues: | ||
| - Adipose_Subcutaneous | ||
| - Adipose_Visceral_Omentum | ||
| - Adrenal_Gland | ||
| - Artery_Aorta | ||
| - Artery_Coronary | ||
| - Artery_Tibial | ||
| - Brain_Amygdala | ||
| - Brain_Anterior_cingulate_cortex_BA24 | ||
| - Brain_Caudate_basal_ganglia | ||
| - Brain_Cerebellar_Hemisphere | ||
| - Brain_Cerebellum | ||
| - Brain_Cortex | ||
| - Brain_Frontal_Cortex_BA9 | ||
| - Brain_Hippocampus | ||
| - Brain_Hypothalamus | ||
| - Brain_Nucleus_accumbens_basal_ganglia | ||
| - Brain_Putamen_basal_ganglia | ||
| - Brain_Spinal_cord_cervical_c_1 | ||
| - Brain_Substantia_nigra | ||
| - Breast_Mammary_Tissue | ||
| - Cells_Cultured_fibroblasts | ||
| - Cells_EBV_transformed_lymphocytes | ||
| - Colon_Sigmoid | ||
| - Colon_Transverse | ||
| - Esophagus_Gastroesophageal_Junction | ||
| - Esophagus_Mucosa | ||
| - Esophagus_Muscularis | ||
| - Heart_Atrial_Appendage | ||
| - Heart_Left_Ventricle | ||
| - Kidney_Cortex | ||
| - Liver | ||
| - Lung | ||
| - Minor_Salivary_Gland | ||
| - Muscle_Skeletal | ||
| - Nerve_Tibial | ||
| - Ovary | ||
| - Pancreas | ||
| - Pituitary | ||
| - Prostate | ||
| - Skin_Not_Sun_Exposed_Suprapubic | ||
| - Skin_Sun_Exposed_Lower_leg | ||
| - Small_Intestine_Terminal_Ileum | ||
| - Spleen | ||
| - Stomach | ||
| - Testis | ||
| - Thyroid | ||
| - Uterus | ||
| - Vagina | ||
| - Whole_Blood |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| splicing_pred: | ||
| mmsplice_splicemap: '{genome}/model_scores_from_absplice_features/{vcf_id}_MMSplice_SpliceMap.csv' | ||
| spliceai_vcf: '{genome}/model_scores_from_absplice_features/{vcf_id}_SpliceAI.vcf' | ||
| spliceai: '{genome}/model_scores_from_absplice_features/{vcf_id}_SpliceAI.csv' | ||
| absplice_dna: '{genome}/dna/{vcf_id}_AbSplice_DNA.csv' | ||
| delta_psi_inferred_from_cat: '{genome}/model_scores_from_absplice_features/{vcf_id}_tissue_cat={tissue_cat}_delta_psi_inferred_from_cat.csv' | ||
| cat_outliers: '{genome}/model_scores_from_absplice_features/{vcf_id}_tissue_cat={tissue_cat}_FRASER_pval.csv' | ||
| absplice_rna: '{genome}/{vcf_id}_tissue_cat={tissue_cat}_AbSplice_RNA.csv' | ||
| absplice_rna_with_dna_info: '{genome}/{vcf_id}_tissue_cat={tissue_cat}_AbSplice_all_info.csv' |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,8 @@ | ||
| from absplice import SplicingOutlierResult | ||
|
|
||
| splicing_result = SplicingOutlierResult( | ||
| df_mmsplice=snakemake.input['mmsplice_splicemap'], | ||
| df_spliceai=snakemake.input['spliceai'], | ||
| ) | ||
| splicing_result.predict_absplice_dna(extra_info=snakemake.params['extra_info']) | ||
| splicing_result._absplice_dna.to_csv(snakemake.output['absplice_dna']) |
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