---
title: "17-uniprot_summaries"
output: html_document
date: "2025-04-02"
---

```{r}
Sys.setenv(ENTREZ_KEY = "8f817031916b3cfee7ec443b712c426d9a08")
install.packages("rentrez")
library(rentrez)
```


```{r}


fetch_ncbi_summary <- function(uniprot_ids, email) {
  entrez_db <- "gene"
  summaries <- list()
  
  for (uniprot_id in uniprot_ids) {
    tryCatch({
      print("hello")
      # Search for the UniProt ID in NCBI Protein database
      search_results <- entrez_search(db = entrez_db, term = uniprot_id, retmax = 1, api_key="8f817031916b3cfee7ec443b712c426d9a08")
      print(search_results)
      if (length(search_results$ids) > 0) {
        ncbi_id <- search_results$ids[1]
        print(ncbi_id)
        # Fetch the summary for the retrieved NCBI ID
        summary_results <- entrez_summary(db = entrez_db, id = ncbi_id, api_key="8f817031916b3cfee7ec443b712c426d9a08")
        print(summary_results$summary)
        summaries[[uniprot_id]] <- summary_results$summary
      } else {
        summaries[[uniprot_id]] <- "No match found"
      }
    }, error = function(e) {
      summaries[[uniprot_id]] <- paste("Error:", e$message)
    })
  }
  
  return(summaries)
}


```

### GOW
```{r}

top_genes <- read.csv("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/Top_50_genes/GOW_topgenes.csv")
# Example usage
uniprot_ids <- c(top_genes$uniprot_accession)  # Replace with your list
email <- "sgleuch@uw.edu"  # Replace with your email

# Set email for NCBI API
set_entrez_key(email)

GOW_summaries <- fetch_ncbi_summary(uniprot_ids, email)

GOW_topgene_summs <- data.frame(UniProt_ID = names(GOW_summaries), Summary = unlist(GOW_summaries), stringsAsFactors = FALSE)

# Write to CSV
write.csv(GOW_topgene_summs, "/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/GOW_topgene_summs.csv", row.names = FALSE)
```

### FOW
```{r}

top_genes <- read.csv("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/Top_50_genes/FOW_topgenes.csv")
# Example usage
uniprot_ids <- c(top_genes$uniprot_accession)  # Replace with your list
email <- "sgleuch@uw.edu"  # Replace with your email

# Set email for NCBI API
set_entrez_key(email)

summaries <- fetch_ncbi_summary(uniprot_ids, email)

topgene_summs <- data.frame(UniProt_ID = names(summaries), Summary = unlist(summaries), stringsAsFactors = FALSE)

# Write to CSV
write.csv(topgene_summs, "/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/FOW_topgene_summs.csv", row.names = FALSE)
```
### GOA
```{r}

top_genes <- read.csv("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/Top_50_genes/GOA_topgenes.csv")
# Example usage
uniprot_ids <- c(top_genes$uniprot_accession)  # Replace with your list
email <- "sgleuch@uw.edu"  # Replace with your email

# Set email for NCBI API
set_entrez_key(email)

summaries <- fetch_ncbi_summary(uniprot_ids, email)

topgene_summs <- data.frame(UniProt_ID = names(summaries), Summary = unlist(summaries), stringsAsFactors = FALSE)

# Write to CSV
write.csv(topgene_summs, "/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/GOA_topgene_summs.csv", row.names = FALSE)
```
### FOA
```{r}

top_genes <- read.csv("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/Top_50_genes/FOA_topgenes.csv")
# Example usage
uniprot_ids <- c(top_genes$uniprot_accession)  # Replace with your list
email <- "sgleuch@uw.edu"  # Replace with your email

# Set email for NCBI API
set_entrez_key(email)

summaries <- fetch_ncbi_summary(uniprot_ids, email)

topgene_summs <- data.frame(UniProt_ID = names(summaries), Summary = unlist(summaries), stringsAsFactors = FALSE)

# Write to CSV
write.csv(topgene_summs, "/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/FOA_topgene_summs.csv", row.names = FALSE)
```

### GDO
```{r}

top_genes <- read.csv("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/Top_50_genes/GDO_topgenes.csv")
# Example usage
uniprot_ids <- c(top_genes$uniprot_accession)  # Replace with your list
email <- "sgleuch@uw.edu"  # Replace with your email

# Set email for NCBI API
set_entrez_key(email)

summaries <- fetch_ncbi_summary(uniprot_ids, email)

topgene_summs <- data.frame(UniProt_ID = names(summaries), Summary = unlist(summaries), stringsAsFactors = FALSE)

# Write to CSV
write.csv(topgene_summs, "/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/GDO_topgene_summs.csv", row.names = FALSE)
```
### FDO
```{r}

top_genes <- read.csv("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/Top_50_genes/FDO_topgenes.csv")
# Example usage
uniprot_ids <- c(top_genes$uniprot_accession)  # Replace with your list
email <- "sgleuch@uw.edu"  # Replace with your email

# Set email for NCBI API
set_entrez_key(email)

summaries <- fetch_ncbi_summary(uniprot_ids, email)

topgene_summs <- data.frame(UniProt_ID = names(summaries), Summary = unlist(summaries), stringsAsFactors = FALSE)

# Write to CSV
write.csv(topgene_summs, "/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Top_gene_summaries/FDO_topgene_summs.csv", row.names = FALSE)
```


```{r}
test_result <- entrez_search(db="gene", term="Q9WVR6", retmax=1, api_key="8f817031916b3cfee7ec443b712c426d9a08")
print(test_result$ids) 


```

```{r}
summary_results <- entrez_summary(db = "gene", id = "84551", api_key="8f817031916b3cfee7ec443b712c426d9a08")
```