-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
put back standardized curations and convenience files to the pipeline
- Loading branch information
1 parent
7cbf6eb
commit a8e6c6a
Showing
20 changed files
with
2,970 additions
and
3 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| #!/bin/bash -x | ||
| time Rscript main_inf_ctf.R | ||
| time Rscript main_inf_gene.R | ||
| time Rscript main_vac_ctf.R | ||
| time Rscript main_vac_gene.R |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,181 @@ | ||
| # this file is adopted from the original generate_HIPC_submissions.R | ||
|
|
||
| library(R.utils) # for gzip | ||
|
|
||
| save_standardized_curations <- function(df2, base_filename) { | ||
| del_cols <- c( | ||
| "submission_name", "submission_date", | ||
| "template_name", "short_comment", "process_note" | ||
| ) | ||
| df2tmp <- df2[!colnames(df2) %in% del_cols] | ||
| df2tmp <- df2tmp[-1] | ||
|
|
||
| filename <- paste0( | ||
| "../data/standardized_curations/", base_filename, | ||
| "-standardized_denormalized.tsv" | ||
| ) | ||
| write.table(df2tmp, | ||
| file = filename, sep = "\t", | ||
| row.names = FALSE, col.names = TRUE | ||
| ) | ||
| gzip(filename, | ||
| destname = paste0(filename, ".gz"), overwrite = TRUE, | ||
| remove = TRUE | ||
| ) | ||
| } | ||
|
|
||
| save_convenience_files <- function( | ||
| df2, header_rows, base_filename, | ||
| exposure_type, response_type) { | ||
| if (exposure_type != "VACCINE" && exposure_type != "INFECTION") { | ||
| stop("Incorrect exposure type encountered") | ||
| } | ||
| if (response_type != "GENE" && response_type != "CELLTYPE_FREQUENCY") { | ||
| stop("Incorrect response type encountered") | ||
| } | ||
|
|
||
| if (response_type == "GENE") { | ||
| response_behavior_type_var <- "gene expression" | ||
| } else if (response_type == "CELLTYPE_FREQUENCY") { | ||
| response_behavior_type_var <- "cell-type frequency" | ||
| } | ||
|
|
||
| convenience_files <- "../data/convenience_files/" | ||
|
|
||
| uniq_sig_row_ids <- unique(df2$sig_row_id) | ||
| resp_components_annotated <- vector("list", length(uniq_sig_row_ids)) | ||
| recreated_template <- vector("list", length(uniq_sig_row_ids)) | ||
|
|
||
| for (i in seq_along(uniq_sig_row_ids)) { | ||
| df2tmp <- df2[df2$sig_row_id == uniq_sig_row_ids[i], ] | ||
| # Recreate a full signature in one row | ||
| base_row <- df2tmp[1, ] # get first row for this uniqID | ||
|
|
||
| response_rowname <- paste(base_row$publication_reference_id, | ||
| base_row$sig_subm_id, uniq_sig_row_ids[i], | ||
| sep = "_" | ||
| ) | ||
| response_description <- paste("PMID", base_row$publication_reference_id, | ||
| response_behavior_type_var, base_row$sig_subm_id, | ||
| sep = " " | ||
| ) | ||
|
|
||
| # Use the full original set of response components | ||
| # rather than just those for which a valid symbol was found. | ||
| base_row$response_component_original <- paste( | ||
| unique(df2tmp$response_component_original), | ||
| collapse = "; " | ||
| ) | ||
|
|
||
| base_row$exposure_material_id <- paste( | ||
| unique(df2tmp$exposure_material_id), | ||
| collapse = "; " | ||
| ) | ||
| base_row$tissue_type_term_id <- paste( | ||
| unique(df2tmp$tissue_type_term_id), | ||
| collapse = "; " | ||
| ) | ||
|
|
||
| if (response_type == "GENE") { | ||
| base_row$response_component <- paste( | ||
| unique(df2tmp$response_component), | ||
| collapse = "; " | ||
| ) | ||
| resp_components_annotated[[i]] <- c( | ||
| response_rowname, | ||
| response_description, unique(df2tmp$response_component) | ||
| ) | ||
| } else if (response_type == "CELLTYPE_FREQUENCY") { | ||
| full_sig <- unique(df2tmp$fully_qualified_response_component) | ||
| # FIXME - only response_component is getting put back together? | ||
| base_row$response_component <- paste(full_sig, collapse = "; ") | ||
| base_row$response_component_id <- paste( | ||
| unique(df2tmp$response_component_id), | ||
| collapse = "; " | ||
| ) | ||
| base_row$proterm_and_extra <- paste( | ||
| unique(df2tmp$proterm_and_extra), | ||
| collapse = "; " | ||
| ) | ||
| base_row$fully_qualified_response_component <- paste( | ||
| unique(df2tmp$fully_qualified_response_component), | ||
| collapse = "; " | ||
| ) | ||
| # The pro_ontology_id values are already separated by semicolons, | ||
| # so change to commas | ||
| # before potentially joining two lists of pro-terms. | ||
| df2tmp$pro_ontology_id <- sapply( | ||
| df2tmp$pro_ontology_id, | ||
| function(x) { | ||
| gsub(";", ",", x) | ||
| } | ||
| ) | ||
| base_row$pro_ontology_id <- paste( | ||
| unique(df2tmp$pro_ontology_id), | ||
| collapse = "; " | ||
| ) | ||
|
|
||
| resp_components_annotated[[i]] <- c( | ||
| response_rowname, response_description, full_sig | ||
| ) | ||
| } | ||
|
|
||
| # Reconstitute target_pathogen and exposure_material_id | ||
| if (exposure_type == "VACCINE") { | ||
| base_row$target_pathogen_taxonid <- paste( | ||
| unique(df2tmp$target_pathogen_taxonid), | ||
| collapse = "; " | ||
| ) | ||
| } | ||
|
|
||
| recreated_template[[i]] <- base_row | ||
| } | ||
|
|
||
| names(resp_components_annotated) <- uniq_sig_row_ids | ||
|
|
||
| # consolidate to a single data.frame | ||
| recreated_template_df <- as.data.frame(rbindlist(recreated_template)) | ||
| if (any(colnames(header_rows) != colnames(recreated_template_df))) { | ||
| stop("mismatch between header rows and recreated_template_df rows") | ||
| } | ||
|
|
||
| recreated_template_df <- rbind(header_rows, recreated_template_df) | ||
|
|
||
| # First save a complete version for use in debugging/logging | ||
| del_cols <- c("submission_name", "submission_date", "template_name") | ||
| recreated_template_df <- recreated_template_df[ | ||
| !colnames(recreated_template_df) %in% del_cols | ||
| ] | ||
|
|
||
| # Set that first column name back to blank | ||
| colnames(recreated_template_df)[1] <- "" | ||
|
|
||
| del_cols <- c("sig_subm_id", "sig_row_id") | ||
|
|
||
| recreated_template_df <- recreated_template_df[ | ||
| !colnames(recreated_template_df) %in% del_cols | ||
| ] | ||
| write.table(recreated_template_df, | ||
| file = paste0( | ||
| convenience_files, | ||
| base_filename, "-standardized_curation_template.tsv" | ||
| ), | ||
| sep = "\t", row.names = FALSE | ||
| ) | ||
|
|
||
| gmt_file <- paste0( | ||
| convenience_files, | ||
| base_filename, "-response_components.gmt.txt" | ||
| ) | ||
| if (file.exists(gmt_file)) file.remove(gmt_file) | ||
| lapply( | ||
| resp_components_annotated, | ||
| function(x) { | ||
| write.table(paste(x, collapse = "\t"), | ||
| file = gmt_file, row.names = FALSE, col.names = FALSE, | ||
| quote = FALSE, append = TRUE | ||
| ) | ||
| } | ||
| ) | ||
| message("Finished creating convenience files") | ||
| } |
Oops, something went wrong.