Enhancement/agfusion expansion #138
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| Original file line number | Diff line number | Diff line change |
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| ABL1 | ||
| ACVR2A | ||
| AKT1 | ||
| ALK | ||
| AR | ||
| ARAF | ||
| ARHGAP26 | ||
| ATM | ||
| BARD1 | ||
| BCL10 | ||
| BCL2 | ||
| BCL6 | ||
| BCOR | ||
| BCORL1 | ||
| BRAF | ||
| BRCA1 | ||
| BRCA2 | ||
| BRD3 | ||
| BRD4 | ||
| BRIP1 | ||
| CAMTA1 | ||
| CBFB | ||
| CCNB3 | ||
| CCND1 | ||
| CCND3 | ||
| CDK12 | ||
| CHEK1 | ||
| CHEK2 | ||
| CIC | ||
| CREBBP | ||
| CRLF2 | ||
| CSF1 | ||
| CSF1R | ||
| DEK | ||
| DNAJB1 | ||
| EGFR | ||
| EPC1 | ||
| ERBB2 | ||
| ERBB3 | ||
| ERBB4 | ||
| ERG | ||
| ESR1 | ||
| ETV1 | ||
| ETV4 | ||
| ETV5 | ||
| ETV6 | ||
| EWSR1 | ||
| EZH2 | ||
| FGF1 | ||
| FGFR1 | ||
| FGFR2 | ||
| FGFR3 | ||
| FGFR4 | ||
| FGR | ||
| FLT1 | ||
| FLT3 | ||
| FOS | ||
| FOSB | ||
| FOXO1 | ||
| FOXP1 | ||
| FOXR2 | ||
| FUS | ||
| GATA1 | ||
| GLI1 | ||
| GRB7 | ||
| GRM1 | ||
| HMGA2 | ||
| IDH1 | ||
| IDH2 | ||
| IGF1R | ||
| IRF4 | ||
| JAK2 | ||
| JAK3 | ||
| JAZF1 | ||
| KIT | ||
| KMT2A | ||
| KRAS | ||
| LTK | ||
| MALT1 | ||
| MAML2 | ||
| MAP2K1 | ||
| MAP2K2 | ||
| MAST1 | ||
| MBTD1 | ||
| MEAF6 | ||
| MET | ||
| MGEA5 | ||
| MKL2 | ||
| MN1 | ||
| MUSK | ||
| MYB | ||
| MYBL1 | ||
| MYC | ||
| NCOA1 | ||
| NCOA2 | ||
| NCOA3 | ||
| NF1 | ||
| NFATC2 | ||
| NFE2L2 | ||
| NOTCH1 | ||
| NOTCH2 | ||
| NR4A3 | ||
| NRAS | ||
| NRG1 | ||
| NRG2 | ||
| NSD3 | ||
| NTRK1 | ||
| NTRK2 | ||
| NTRK3 | ||
| NUP214 | ||
| NUTM1 | ||
| NUTM2A | ||
| NUTM2B | ||
| PALB2 | ||
| PAX3 | ||
| PAX5 | ||
| PAX7 | ||
| PDGFB | ||
| PDGFD | ||
| PDGFRA | ||
| PDGFRB | ||
| PGR | ||
| PHF1 | ||
| PIK3CA | ||
| PLAG1 | ||
| PPARG | ||
| PRB3 | ||
| PRKACA | ||
| PRKACB | ||
| PRKCA | ||
| PRKCB | ||
| PRKD1 | ||
| PRKD2 | ||
| PRKD3 | ||
| PTCH1 | ||
| PTPN1 | ||
| RAD51B | ||
| RAD51C | ||
| RAD51D | ||
| RAD54L | ||
| RAF1 | ||
| RARA | ||
| RELA | ||
| RET | ||
| RLF | ||
| ROS1 | ||
| RSPO2 | ||
| RSPO3 | ||
| RUNX1 | ||
| SMARCB1 | ||
| SRF | ||
| SS18 | ||
| SS18L1 | ||
| STAT6 | ||
| TAF15 | ||
| TCF12 | ||
| TCF3 | ||
| TERT | ||
| TFE3 | ||
| TFEB | ||
| TFG | ||
| THADA | ||
| TMPRSS2 | ||
| TP63 | ||
| TSC1 | ||
| TSC2 | ||
| USP6 | ||
| VGLL2 | ||
| VGLL3 | ||
| WWTR1 | ||
| YAP1 | ||
| YWHAE |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,109 @@ | ||
| #!/usr/local/bin/Rscript | ||
| # __author__ = "Alexandria Dymun" | ||
| # __email__ = "[email protected]" | ||
| # __version__ = "0.0.1" | ||
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| suppressPackageStartupMessages({ | ||
| library(dplyr) | ||
| library(data.table) | ||
| }) | ||
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| usage <- function() { | ||
| message("Usage:") | ||
| message("add_flags_agfusion_clinical.R --cff-file <file.cff> --agfusion-file <agfusion.tsv> --transcript_allowlist <transcript_allowlist.txt> --out-prefix <prefix>") | ||
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There was a problem hiding this comment. seems like the parameters should actually be cff and agfusion, not cff-file and agfusion-file? |
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| } | ||
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| args = commandArgs(TRUE) | ||
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| if (is.null(args) | length(args)<1) { | ||
| usage() | ||
| quit() | ||
| } | ||
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| #' Parse out options from a string without recourse to optparse | ||
| #' | ||
| #' @param x Long-form argument list like --opt1 val1 --opt2 val2 | ||
| #' | ||
| #' @return named list of options and values similar to optparse | ||
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| parse_args <- function(x){ | ||
| args_list <- unlist(strsplit(x, ' ?--')[[1]])[-1] | ||
| args_vals <- lapply(args_list, function(x) scan(text=x, what='character', quiet = TRUE)) | ||
| # Ensure the option vectors are length 2 (key/ value) to catch empty ones | ||
| args_vals <- lapply(args_vals, function(z){ length(z) <- 2; z}) | ||
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| parsed_args <- structure(lapply(args_vals, function(x) x[2]), names = lapply(args_vals, function(x) gsub('-','_',x[1]))) | ||
| parsed_args[! is.na(parsed_args)] | ||
| } | ||
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| args_opt <- parse_args(paste(args,collapse=" ")) | ||
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| possible_args = c("cff", "agfusion","transcript_allowlist", "out_prefix") | ||
| if (length(setdiff(names(args_opt),possible_args)) > 0){ | ||
| message("Invalid options") | ||
| usage() | ||
| quit() | ||
| } | ||
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| required_args <- c("cff","agfusion","transcript_allowlist", "out_prefix") | ||
| if (length(setdiff(required_args,names(args_opt))) > 0) { | ||
| message("Missing required arguments") | ||
| usage() | ||
| quit() | ||
| } | ||
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| agfusion_file = args_opt$agfusion | ||
| cff_file = args_opt$cff | ||
| out_prefix = args_opt$out_prefix | ||
| transcript_allowlist_file <- args_opt$transcript_allowlist | ||
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| cff = fread(cff_file) %>% | ||
| select(gene5_transcript_id,gene3_transcript_id,gene5_breakpoint,gene3_breakpoint,gene5_renamed_symbol,gene3_renamed_symbol,cluster) %>% | ||
| mutate(ID = paste(gene5_transcript_id,gene3_transcript_id,gene5_breakpoint,gene3_breakpoint)) | ||
| agfusion_tab = fread(agfusion_file) %>% | ||
| mutate(ID = paste(`5'_transcript`,`3'_transcript`,`5'_breakpoint`,`3'_breakpoint`)) | ||
| transcript_allowlist <- fread(transcript_allowlist_file) %>% select(ensembl_transcript,refseq_transcript) | ||
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| agfusion_tab <- agfusion_tab %>% mutate(Metafusion_Transcript_Pair = ID %in% cff$ID) | ||
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| agfusion_tab[,ID:=NULL] | ||
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| cff <- cff %>% | ||
| select(gene5_breakpoint,gene3_breakpoint,gene5_renamed_symbol,gene3_renamed_symbol,cluster) %>% | ||
| distinct() | ||
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| agfusion_tab <- merge(agfusion_tab, | ||
| cff, | ||
| by.x = c("5'_gene","3'_gene","5'_breakpoint","3'_breakpoint"), | ||
| by.y = c("gene5_renamed_symbol","gene3_renamed_symbol","gene5_breakpoint","gene3_breakpoint"), | ||
| all.x = T, | ||
| all.y = F) | ||
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| agfusion_tab <- merge(agfusion_tab, | ||
| transcript_allowlist, | ||
| by.x = "5'_transcript", | ||
| by.y = "ensembl_transcript", | ||
| all.x = T, | ||
| all.y = F) | ||
| setnames(agfusion_tab,"refseq_transcript","refseq_transcript_id_5") | ||
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| agfusion_tab <- merge(agfusion_tab, | ||
| transcript_allowlist, | ||
| by.x = "3'_transcript", | ||
| by.y = "ensembl_transcript", | ||
| all.x = T, | ||
| all.y = F) | ||
|
There was a problem hiding this comment. we're not going to filter out agfusion results where one or both transcripts are not on the transcript allowlist? not saying this is wrong, just checking |
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| setnames(agfusion_tab,"refseq_transcript","refseq_transcript_id_3") | ||
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| write.table( | ||
| agfusion_tab, | ||
| paste0(out_prefix, ".expanded_agfusion_transcripts.tsv"), | ||
| row.names = F, | ||
| append = F, | ||
| quote = F, | ||
| sep = "\t" | ||
| ) | ||
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Add a new line for this PR 138