elprep_sfm.py

#!/usr/bin/env python

# Example script for using elPrep split/merge tools.  

import subprocess
import os
import time
import elprep_io_wrapper

# actual script

def elprep_sfm (argv):
  # set up directories for intermediate results
  file_in = argv[1]
  file_out = argv[2]
  input = os.path.basename(file_in)
  output_prefix, output_extension = os.path.splitext(input)
  stamp = str(time.time())
  split_dir = os.path.join(os.getcwd(), "temp-" + stamp + os.sep)
  result_dir = os.path.join(os.getcwd(), "temp-processed-" + stamp + os.sep)
  os.mkdir(split_dir)
  os.mkdir(result_dir)
  # split command
  nr_of_threads_opt = elprep_io_wrapper.cmd_option("--nr-of-threads", argv)
  intermediate_files_opt = elprep_io_wrapper.cmd_option("--intermediate-files-output-type", argv)
  if intermediate_files_opt:
    intermediate_files_output_type = intermediate_files_opt[1]
  else:
    intermediate_files_output_type = "sam" 
  given_cmd_opts = elprep_io_wrapper.remove_cmd_option(argv[3:], "--intermediate-files-output-type")
  cmd_opts = given_cmd_opts
  elprep_io_wrapper.cmd_wrap_input(["elprep", "split"], file_in, split_dir, ["--output-prefix", output_prefix, "--output-type", intermediate_files_output_type] + nr_of_threads_opt)
  spread_file = os.path.join(split_dir, output_prefix + "-spread." + intermediate_files_output_type)
  splits_path = os.path.join(split_dir, "splits" + os.sep)
  # run filter command for split files
  for root, dirs, files in os.walk(splits_path):
    for file in files:
      ext = os.path.splitext(file)[1]
      if (ext == ".sam" or ext == ".bam" or ext == ".cram"):
        ffile = os.path.join(root, file)
        processed_file = os.path.join(result_dir, os.path.basename(file))
        elprep_io_wrapper.cmd_wrap_io(["elprep"], ffile, processed_file, cmd_opts + ["--split-file"])
        os.remove(ffile)
    os.rmdir(splits_path)
  # command for spread file
  spread_out_file = os.path.join(result_dir, output_prefix + "-spread." + intermediate_files_output_type)
  elprep_io_wrapper.cmd_wrap_io(["elprep"], spread_file, spread_out_file , cmd_opts)
  os.remove(spread_file)
  os.rmdir(split_dir)
  # merge command
  elprep_io_wrapper.cmd_wrap_output(["elprep", "merge"], result_dir, file_out, nr_of_threads_opt)
  # remove directories for intermediate results
  for root, dirs, files in os.walk(result_dir):
    for file in files:
      ffile = os.path.join(root, file)
      os.remove(ffile)
  os.rmdir(result_dir)