Fixes JRaviLab#27

Add code for fetching and saving FASTA sequences for Staph-DA

R/Staphylococcus_aureus_DAP.R

@@ -0,0 +1,182 @@
+# config.R
+
+# Specify the URL to download the zipped file directly
+data_url <- "https://card.mcmaster.ca/download/0/broadstreet-v3.3.0.tar.bz2"
+
+# Specify the destination directory where the file will be saved
+data_path <- "C:/Users/Administrator/Desktop/Process CARD Data/"
+bzip_file <- file.path(data_path, "broadstreet-v3.3.0.tar.bz2")
+tar_file <- file.path(data_path, "broadstreet-v3.3.0.tar")
+
+# Function to download the file if it doesn't exist
+download_file <- function(url, destfile) {
+  if (!file.exists(destfile)) {
+    download.file(url, destfile, mode = "wb")
+    cat("Downloaded:", destfile, "\n")
+  } else {
+    cat("File already exists:", destfile, "\n")
+  }
+}
+
+# Call the function to download the file
+download_file(data_url, bzip_file)
+
+# Load the R.utils package for decompression
+if (!requireNamespace("R.utils", quietly = TRUE)) {
+  install.packages("R.utils")
+}
+library(R.utils)
+
+# Decompress the file
+if (file.exists(bzip_file)) {
+  if (!file.exists(tar_file)) {
+    bunzip2(bzip_file, destname = tar_file, remove = FALSE)
+    cat("Decompressed:", tar_file, "\n")
+  } else {
+    cat("Tar file already exists:", tar_file, "\n")
+  }
+} else {
+  cat("Error: Zipped file not found:", bzip_file, "\n")
+}
+
+
+# List the contents of the extraction directory
+list.files("CARD_data")
+
+# Parse the ARO_index.tsv file using read.delim
+aro_index <- read.delim("CARD_data/ARO_index.tsv", header = TRUE, sep = "\t")
+
+
+# Map CARD Short Name
+# Load necessary library
+library(dplyr)
+
+#  Read the files
+aro_index <- read.delim("CARD_data/aro_index.tsv", sep = "\t", header = TRUE)
+antibiotics_data <- read.delim("CARD_data/shortname_antibiotics.tsv", sep = "\t", header = TRUE)
+pathogens_data <- read.delim("CARD_data/shortname_pathogens.tsv", sep = "\t", header = TRUE)
+
+
+# Mutate data
+aro_index <- aro_index %>%
+  mutate(
+    pathogen = sapply(strsplit(CARD.Short.Name, "_"), `[`, 1),   # First part: Pathogen
+    gene = sapply(strsplit(CARD.Short.Name, "_"), `[`, 2),       # Second part: Gene
+    drug = ifelse(sapply(strsplit(CARD.Short.Name, "_"), length) == 3,   # Third part (if present): Drug
+                  sapply(strsplit(CARD.Short.Name, "_"), `[`, 3), NA),
+    Protein.Accession = Protein.Accession   # Include existing Protein.Accession column if present
+  )
+
+# View the mutated data
+head(aro_index)
+
+
+# Extract pathogen, gene, drug, and include Protein.Accession from 'CARD.Short.Name'
+aro_index_clean <- aro_index %>%
+  mutate(
+    pathogen = sapply(strsplit(CARD.Short.Name, "_"), `[`, 1),  # Extract pathogen
+    gene = sapply(strsplit(CARD.Short.Name, "_"), `[`, 2),      # Extract gene
+    drug = ifelse(sapply(strsplit(CARD.Short.Name, "_"), length) == 3,   # Extract drug
+                  sapply(strsplit(CARD.Short.Name, "_"), `[`, 3), NA),
+    Protein.Accession = Protein.Accession  # Include the Protein.Accession column
+  )
+
+# Merge aro_index_clean with the antibiotics_data and pathogens_data
+# For merging with antibiotics_data
+merged_data_antibiotics <- left_join(aro_index_clean, antibiotics_data,
+                                     by = c("gene" = "AAC.Abbreviation"))
+
+# For merging with pathogens_data
+merged_data_pathogens <- left_join(merged_data_antibiotics, pathogens_data,
+                                   by = c("pathogen" = "Abbreviation"))
+
+# View the resulting merged data
+head(merged_data_pathogens)
+
+
+#filter out rows where pathogen is empty
+cleaned_data <- merged_data_pathogens %>%
+  distinct() %>%
+  filter(!is.na(pathogen))
+
+# Group by Pathogen, Gene, Drug, and Protein.Accession, then summarize Antibiotic information
+summarized_data <- cleaned_data %>%
+  group_by(Pathogen = Pathogen, Gene = gene, Drug = drug, Protein_Accession = Protein.Accession) %>%
+  summarize(Antibiotic_Info = paste(unique(Molecule), collapse = ", ")) %>%
+  arrange(Pathogen, Gene, Drug, Protein_Accession)
+
+# Filter for Staphylococcus aureus and DAP (Bug-Drug of Interest)
+staph_aureus_dap_combinations <- summarized_data %>%
+  filter(Pathogen == "Staphylococcus aureus", Drug == "DAP")
+
+# View the filtered data
+head(staph_aureus_dap_combinations)
+
+
+#Fetch FASTA sequences from Entrez using protein accession
+#Load required packages
+library(rentrez)
+library(XML)
+library(stringr)
+
+
+# Fetch FASTA sequence from Entrez
+fetch_fasta_sequence <- function(protein_accession) {
+  tryCatch({
+    # Fetch the FASTA sequence using Entrez
+    fasta_seq <- rentrez::entrez_fetch(db = "protein",
+                                       id = protein_accession,
+                                       rettype = "fasta",
+                                       retmode = "text")
+
+    if (!is.null(fasta_seq)) {
+      # Ensure the first line starts with ">"
+      if (!grepl("^>", fasta_seq[1])) {
+        fasta_seq[1] <- paste0(">", fasta_seq[1])
+      }
+
+      # Split the sequence into lines
+      lines <- str_split(fasta_seq, "\n")[[1]]
+
+      # Join the lines back together
+      fasta_seq <- paste(lines, collapse = "\n")
+
+      return(fasta_seq)
+    } else {
+      warning(paste("Failed to retrieve FASTA sequence for protein accession:", protein_accession))
+      return(NULL)
+    }
+  }, error = function(e) {
+    warning(paste("Error fetching FASTA sequence for protein accession:", protein_accession, ":", e$message))
+    return(NULL)
+  })
+}
+
+# Loop through staph_aureus_dap_combinations to fetch and save FASTA sequences
+combined_sequences <- character()
+
+for (i in 1:nrow(staph_aureus_dap_combinations)) {
+  # Fetch FASTA sequence for each protein accession
+  protein_accession <- staph_aureus_dap_combinations$Protein_Accession[i]
+  fasta_sequence <- fetch_fasta_sequence(protein_accession)
+
+  if (!is.null(fasta_sequence)) {
+    combined_sequences <- c(combined_sequences, fasta_sequence)
+  }
+}
+
+# Save the combined FASTA sequences
+filename <- "Staphylococcus_aureus_DAP_sequences4.fasta"
+
+writeLines(combined_sequences, filename)
+print(paste("Combined FASTA sequences saved as", filename))
+
+# Print the first few lines of the combined file
+cat(readLines(filename)[1:10], sep = "\n")
+
+
+#Run FASTA Sequences Through MolEvolvR Web App
+
+library("devtools")
+
+devtools::check()

Staphylococcus_aureus_DAP_sequences4.fasta

@@ -0,0 +1,92 @@
+>CAG41107.1 autoinducer sensor protein response regulator protein [Staphylococcus aureus subsp. aureus MRSA252]
+MKIFICEDDPKQRENMVTIIKNYIMIEEKPMEIALATDNPYEVLEQAKNMNDIGCYFLDIQLSTDINGIK
+LGSEIRKHDPVGNIIFVTSHSELTYLTFVYKVAAMDFIFKDDPAELRTRIIDCLETAHTRLQLLSKDNSV
+ETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNI
+ESIDSKERIVYFKNKEHCYASVRNVKKI
+
+
+>ABD31357.1 cardiolipin synthetase, putative [Staphylococcus aureus subsp. aureus NCTC 8325]
+MIELLSIALKHSNIILNSIFIGAFILNLLFAFTIIFMERRSANSIWAWLLVLVFLPLFGFILYLLLGRQI
+QRDQIFKIDKEDKKGLELIVDEQLAALKNENFSNSNYQIVKFKEMIQMLLYNNAAFLTTDNDLKIYTDGQ
+EKFDDLIQDIRNATDYIHFQYYIIQNDELGRTILNELGKKAEQGVEVKILYDDMGSRGLRKKGLRPFRNK
+GGHAEAFFPSKLPLINLRMNNRNHRKIVVIDGQIGYVGGFNVGDEYLGKSKKFGYWRDTHLRIVGDAVNA
+LQLRFILDWNSQATRDHISYDDRYFPDVNSGGTIGVQIASSGPDEEWEQIKYGYLKMISSAKKSIYIQSP
+YFIPDQAFLDSIKIAALGGVDVNIMIPNKPDHPFVFWATLKNAASLLDAGVKVFHYDNGFLHSKTLVIDD
+EIASVGTANMDHRSFTLNFEVNAFIYDQQIAKKLKQAFIDDLAVSSELTKARYAKRSLWIKFKEGISQLL
+SPIL
+
+
+>ADJ67256.1 MprF [Staphylococcus aureus]
+MNQEVKNKIFSILKITFATALFIFVAITLYRELSGINFKDTLVEFSKINRMSLVLLFIGGGASLVILSMY
+DVILSRALKMDISLGKVLRVSYIINALNAIVGFGGFIGAGVRAMVYKNYTHDKKKLVHFISLILISMLTG
+LSLLSLLIVFHVFDASLILDKITWVRWVLYVVSFFLPLFIIYSMVRPPDKNNRFVGLYCTLVSCVEWLAA
+AVVLYFCGVIVDAHVSFMSFIAIFIIAALSGLVSFIPGGFGAFDLVVLLGFKTLGVPEEKVLLMLLLYRF
+AYYFVPVIIALILSSFEFGTSAKKYIEGSKYFIPAKDVTSFLMSYQKDIIAKIPSLSLAILVFFTSMINL
+TIVYDALYDGNHLTYYILLAIHTSACLLLLLNVVGIYKQSRRAIIFAMISILLITVATFFTYASYILITW
+LAIIFVLLIVAFRRARRLKRPVRMRNIVAMLLFSLFILYVNHIFIAGTLYALDIYTIEMHTSVLRYYFWL
+TILIIAIIIGMIAWLFDYQFSKVRISSKIEDCEEIINQYGGNYLSHLIYSGDKQFFTNENKTAFLMYRYK
+ASSLVVLGDPLGDENAFDELLEAFYNYAEYLGYDVIFYQVTDQHMPLYHNFGNQFFKLGEEAIIDLTQFS
+TSGKKRRGFRATLNKFDELNISFEIIEPPFSTEFINELQHVSDLWLDNRQEMHFSVGEFNEEYLSKAPIG
+VMRNEENEVIAFCSLMPTYFNDAISVDLIRWLPELDLPLMDGLYLHMLLWSKEQGYTKFNMGMATLSNVG
+QLHYSYLRERLAGRVFEHFNGLYRFQGLRRYKSKYNPNWEPRFLVYRKDNSLWESLSKVMRVIRHK
+
+
+>BAB95031.1 phosphatidylglycerophosphate synthase [Staphylococcus aureus subsp. aureus MW2]
+MNIPNQITVFRVVLIPVFILFALVDFGFGNVSFLGGYEIRIELLISGFIFILASLSDFVDGYLARKWNLV
+TNMGKFLDPLADKLLVASALIVLVQLGLTNSVVAIIIIAREFAVTGLRLLQIEQGFVSAAGQLGKIKTAV
+TMVAITWLLLGDPLATLIGLSLGQILLYIGVIFTILSGIEYFYKGRDVFKQK
+
+
+>CAG39568.1 DNA-directed RNA polymerase beta chain protein [Staphylococcus aureus subsp. aureus MRSA252]
+MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLREGLIEMFRDISPIEDFTGNLSLEFVDYR
+LGEPKYDLEESKNRDATYAAPLRVKVRLIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVR
+SPSVYFNEKIDKNGRENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDL
+LGDNEYLRNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNKKLH
+LKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSVIDEPVEIQSIKVY
+VPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFR
+IGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGP
+GGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQI
+DYLTADEEDSYVVAQANSKLDENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLEN
+DDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGV
+EHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVEFNEILADGPSMELGEMALGRNVVVGFMTWDGYNY
+EDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAEVKDGDI
+LVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTLSPGVNQLVR
+VYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAA
+KNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHA
+RSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENIS
+RPSVPESFRVLMKELQSLGLDVKVMDEQDNEIEMTDVDDDDVVERKVDLQQNDAPETQKEVTD
+
+
+>CAG39569.1 DNA-directed RNA polymerase beta' chain protein [Staphylococcus aureus subsp. aureus MRSA252]
+MIDVNNFHYMKIGLASPEKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRY
+KGMVCDRCGVEVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVVVDPG
+PTGLEKKTLLSEAEFRDYYDKYPGQFVAKMGAEGIKDLLEEIDLDEELKLLRDELESATGQRLTRAIKRL
+EVVESFRNSGNKPSWMILDVLPIIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGII
+VQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSL
+KMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAKSKIERMDDEVWDVLEEVIREHPVLLNRAPTLHR
+LGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVT
+PSQDMVLGNYYLTLERKDAVNTGAIFNNTNEVLKAYANGFVHLHTRIGVHASSFNNPTFTEEQNKKILAT
+SVGKIIFNEIIPDSFAYINEPTQENLERKTPNRYFIDPTTLGEGGLKEYFENEELIEPFNKKFLGNIIAE
+VFNRFSITDTSMMLDRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEEE
+RYNAVVEIWTDAKDQIQGELMQSLDKTNPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSS
+FREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMI
+EPFIERIEGRYSKETIRHPETDEVIIRPDELITPEIAKKITDAGIEQMYIRSAFTCNARHGVCEKCYGKN
+LATGEKVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEIFEARNPKGQAVITEIEG
+VVEDIKLAKDRQQEIVVKGANETRSYLASGTSRIIVEIGQPVQRGEVLTEGSIEPKNYLSVAGLNATESY
+LLKEVQKVYRMQGVEIDDKHVEVMVRQMLRKVRIIEAGDTKLLPGSLVDIHNFTDANREAFKHRKRPATA
+KPVLLGITKASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTGMRRYSDVKYE
+KTAKPVAEVESQTEVTE
+
+
+>CAG39047.1 sensor kinase protein [Staphylococcus aureus subsp. aureus MRSA252]
+MKWLKQLQSLHTKLVIVYVLLIIIGMQIIGLYFTNNLEKELLDNFKKNITQYAKQLEISIEKVYDEKGSV
+NAQKDIQNLLSEYANRQEIGEIRFIDKDQIIIATTKQSNRSLINQKANDSSVQKALSLGQSNDHLILKDY
+GGGKDRVWVYNIPVKVDKKVIGNIYIESKINDVYNQLNNINQIFIVGTAISLLITVILGFFIARTITKPI
+TDMRNQTVEMSRGNYTQRVKIYGNDEIGELALAFNNLSKRVQEAQANTESEKRRLDSVITHMSDGIIATD
+RRGRIRIVNDMALKMLGMAKEDIIGYYMLSVLSLEDEFKLEEIQENNDSFLLDLNEEEGLIARVNFSTIV
+QETGFVTGYIAVLHDVTEQQQVERERREFVANVSHELRTPLTSMNSYIEALEEGAWKDEELAPQFLSVTR
+EETERMIRLVNDLLQLSKMDNESDQINKEIIDFNMFINKIINRHEMSTKDTTFIRDIPKKTIFTEFDPDK
+MTQVFDNVITNAMKYSRGDKRVEFHVKQNPLYNRMTIRIKDNGIGIPINKVDKIFDRFYRVDKARTRKMG
+GTGLGLAISKEIVEAHNGRIWANSVEGQGTSIFITLPCEVIEDGDWDE
+
+