oxymetag 1.0.0__py3-none-any.whl

oxymetag/data/pfam_lengths.tsv

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+"Pfam"	"Gene.length"
+"PF00042"	473.91
+"PF00115"	1528.11
+"PF00116"	750.9
+"PF00296"	1098.24
+"PF00510"	773.67
+"PF00916"	2117.37
+"PF01152"	419.37
+"PF01521"	423.06
+"PF01871"	700.41
+"PF02579"	1028.22
+"PF02906"	1566.93
+"PF03063"	1722.42
+"PF05425"	1056.6
+"PF05721"	894
+"PF08530"	2247.99
+"PF10371"	3937.35
+"PF13597"	2691.6
+"PF16870"	2981.01
+"PF17773"	950.7
+"PF17910"	2188.41

oxymetag/scripts/predict_oxygen.R

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+#!/usr/bin/env Rscript
+
+# Load required libraries
+suppressPackageStartupMessages({
+  library(dplyr)
+  library(tidyr)
+  library(rlang)
+  library(mgcv)
+})
+
+# Parse command line arguments
+args <- commandArgs(trailingOnly = TRUE)
+
+if (length(args) < 7) {
+  stop("Usage: Rscript predict_oxygen.R <input_dir> <output_file> <package_data_dir> <mode> <idcut> <ecut> <bitcut>")
+}
+
+input_dir <- args[1]
+output_file <- args[2] 
+package_data_dir <- args[3]
+mode <- args[4]
+idcut <- as.numeric(args[5])
+ecut <- as.numeric(args[6])
+bitcut <- as.numeric(args[7])
+
+predict_oxygen <- function(input_dir, output_file, package_data_dir, mode, idcut, ecut, bitcut) {
+  
+  # Load package data files (these come from oxymetag/data/)
+  map_file <- file.path(package_data_dir, "pfam_headers_table.txt")
+  lengths_file <- file.path(package_data_dir, "pfam_lengths.tsv")
+  model_file <- file.path(package_data_dir, "oxygen_model.rds")
+  pfams_file <- file.path(package_data_dir, "Oxygen_pfams.csv")
+  
+  # Check if package data files exist
+  if (!file.exists(map_file)) stop(paste("Package data file not found:", map_file))
+  if (!file.exists(lengths_file)) stop(paste("Package data file not found:", lengths_file))
+  if (!file.exists(model_file)) stop(paste("Package data file not found:", model_file))
+  if (!file.exists(pfams_file)) stop(paste("Package data file not found:", pfams_file))
+  
+  # Load package data
+  map <- read.table(map_file, sep = "\t", header = TRUE, stringsAsFactors = FALSE, quote = "") %>%
+    separate(Header, into = c("Header", "Junk"), sep = " ") %>%
+    select(-Junk) %>%
+    filter(!duplicated(Header))
+  
+  pfam_gene_length <- read.delim(lengths_file)
+  
+  # Load the trained model and oxygen classifications
+  oxygen_model <- readRDS(model_file)
+  
+  # Get aerobic and anaerobic pfam lists (you'll need to define these)
+  oxygen_pfams <- read.csv(pfams_file, stringsAsFactors = FALSE)
+  aerobic_pfams <- oxygen_pfams %>% filter(Oxygen == "aerobic")
+  anaerobic_pfams <- oxygen_pfams %>% filter(Oxygen == "anaerobic")
+  
+  # Find diamond output files (user's working directory)
+  files <- list.files(input_dir, pattern = "*_diamond.tsv", full.names = TRUE)
+  
+  if (length(files) == 0) {
+    stop(paste("No *_diamond.tsv files found in", input_dir))
+  }
+  
+  # Initialize results dataframe
+  results <- data.frame(
+    SampleID = character(length(files)),
+    ratio = numeric(length(files)),
+    aerobe_pfams = integer(length(files)),
+    anaerobe_pfams = integer(length(files)),
+    Per_aerobe = numeric(length(files)),
+    stringsAsFactors = FALSE
+  )
+  
+  # Process each file
+  for (i in 1:length(files)) {
+    
+    # Extract sample ID from filename
+    sample_id <- basename(files[i])
+    sample_id <- gsub("_diamond.tsv$", "", sample_id)
+    results$SampleID[i] <- sample_id
+    
+    # Read and filter diamond output
+    if (file.size(files[i]) == 0) {
+      message("Warning: Empty file ", files[i])
+      next
+    }
+    
+    d <- read.table(files[i], stringsAsFactors = FALSE) %>%
+      set_names(c("qseqid",	"sseqid",	"pident",	"length",	"qstart",	"qend",	
+                  "sstart",	"send",	"evalue",	"bitscore"))
+    
+    # Apply filtering based on mode
+    if (mode == "modern") {
+      d <- d %>%
+        filter(pident >= 60, evalue < 0.001, bitscore >= 50)
+    } else if (mode == "ancient") {
+      d <- d %>%
+        filter(pident >= 45, evalue < 0.1, bitscore >= 25)
+    } else if (mode == "custom") {
+      d <- d %>%
+        filter(pident >= idcut, evalue < ecut, bitscore >= bitcut)
+    }
+    
+    if (nrow(d) == 0) {
+      message("Warning: No significant hits for ", sample_id)
+      results$ratio[i] <- 0
+      results$aerobe_pfams[i] <- 0
+      results$anaerobe_pfams[i] <- 0
+      next
+    }
+    
+    # Join with pfam mapping
+    d <- d %>% left_join(map, by = c("sseqid" = "Header"))
+    
+    # Count pfams
+    pf_count <- as.data.frame(table(d$Pfam))
+    results$Pfams[i] <- nrow(pf_count)
+    results$aerobe_pfams[i] <- sum(as.character(pf_count$Var1) %in% aerobic_pfams$Pfam)
+    results$anaerobe_pfams[i] <- sum(as.character(pf_count$Var1) %in% anaerobic_pfams$Pfam)
+    
+    # Calculate gene hits and length correction
+    gene.hits <- d %>% 
+      group_by(Pfam) %>% 
+      summarise(total_count = n())
+    
+    gene.hit.length.correction <- gene.hits %>%
+      left_join(., pfam_gene_length, by = "Pfam") %>%
+      mutate(RPK = total_count / (1000*Gene.length)) %>%
+      left_join(., oxygen_pfams, by = "Pfam")
+    
+    # Sum by oxygen type
+    oxygen_rpk <- gene.hit.length.correction %>%
+      group_by(Oxygen) %>%
+      summarize(RPKsum = sum(RPK))
+    
+    # Calculate the ratio and add it to the dataframe
+    results$ratio[i] <- oxygen_rpk$RPKsum[1] / oxygen_rpk$RPKsum[2]
+    
+    # Processing message
+    message("Processed sample ", i, "/", length(files), ": ", sample_id)
+  }
+  
+  # Make predictions using the GAM model
+  new_data <- data.frame(ratio = results$ratio)
+  results$Per_aerobe <- predict(oxygen_model, newdata = new_data)
+  
+  # Constrain predictions to 0-100% and set to 100% if ratio > 35
+  results <- results %>%
+    mutate(Per_aerobe = ifelse(Per_aerobe > 100, 100, Per_aerobe)) %>%
+    mutate(Per_aerobe = ifelse(Per_aerobe < 0, 0, Per_aerobe)) %>%
+    mutate(Per_aerobe = ifelse(ratio > 35, 100, Per_aerobe))
+  
+  # Save results
+  write.table(results, output_file, sep = "\t", row.names = FALSE, quote = FALSE)
+  message("Results saved to: ", output_file)
+  
+  return(results)
+}
+
+# Run the function
+predict_oxygen(input_dir, output_file, package_data_dir, mode, idcut, ecut, bitcut)

oxymetag/utils.py

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+#!/usr/bin/env python3
+"""
+Utility functions for OxyMetaG
+"""
+
+import subprocess
+import pkg_resources
+from pathlib import Path
+import logging
+
+logger = logging.getLogger('oxymetag')
+
+class OxyMetaGError(Exception):
+    """Custom exception for OxyMetaG errors"""
+    pass
+
+def check_dependencies():
+    """Check if required external tools are available"""
+    required_tools = ['kraken2', 'diamond', 'Rscript']
+    missing_tools = []
+    
+    for tool in required_tools:
+        if subprocess.run(['which', tool], capture_output=True).returncode != 0:
+            missing_tools.append(tool)
+    
+    if missing_tools:
+        raise OxyMetaGError(f"Missing required tools: {', '.join(missing_tools)}")
+
+def get_package_data_path(filename: str) -> str:
+    """Get path to package data files"""
+    try:
+        return pkg_resources.resource_filename('oxymetag', f'data/{filename}')
+    except:
+        package_dir = Path(__file__).parent
+        return str(package_dir / 'data' / filename)
+
+def run_kraken2_setup():
+    """Download and set up standard Kraken2 database without fungi"""
+    logger.info("Setting up Kraken2 database (bacteria, archaea, viral)...")
+    
+    db_path = Path.cwd() / "kraken2_db"
+    db_path.mkdir(exist_ok=True)
+    
+    try:
+        # Download taxonomy
+        cmd = ['kraken2-build', '--download-taxonomy', '--db', str(db_path)]
+        logger.info("Downloading taxonomy...")
+        subprocess.run(cmd, check=True)
+        logger.info("Taxonomy downloaded successfully")
+        
+        # Download libraries (excluding fungi)
+        libraries = ['bacteria', 'archaea', 'viral']
+        for lib in libraries:
+            cmd = ['kraken2-build', '--download-library', lib, '--db', str(db_path)]
+            logger.info(f"Downloading {lib} library...")
+            subprocess.run(cmd, check=True)
+            logger.info(f"{lib} library downloaded successfully")
+        
+        # Build database
+        cmd = ['kraken2-build', '--build', '--db', str(db_path), '--threads', '48']
+        logger.info("Building Kraken2 database...")
+        subprocess.run(cmd, check=True)
+        
+        # Clean up temporary files to save space
+        cmd = ['kraken2-build', '--clean', '--db', str(db_path)]
+        logger.info("Cleaning up temporary files...")
+        subprocess.run(cmd, check=True)
+        
+        logger.info(f"Kraken2 database setup complete: {db_path}")
+        logger.info("Database includes: bacteria, archaea, viral (fungi excluded)")
+        
+    except subprocess.CalledProcessError as e:
+        raise OxyMetaGError(f"Failed to setup Kraken2 database: {e}")