/tools/metag_tools/shrimp_color_wrapper.py

https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 116 lines · 81 code · 23 blank · 12 comment · 22 complexity · 9f6571f1d00b60b541de5d9590740854 MD5 · raw file

  1. #!/usr/bin/env python
  2. """
  3. SHRiMP wrapper : Color space
  4. """
  5. import os, sys, tempfile, os.path, re
  6. assert sys.version_info[:2] >= (2.4)
  7. def stop_err( msg ):
  8. sys.stderr.write( "%s\n" % msg )
  9. sys.exit()
  10. def __main__():
  11. # SHRiMP path
  12. shrimp = 'rmapper-cs'
  13. # I/O
  14. input_target_file = sys.argv[1] # fasta
  15. input_query_file = sys.argv[2]
  16. shrimp_outfile = sys.argv[3] # shrimp output
  17. # SHRiMP parameters
  18. spaced_seed = '1111001111'
  19. seed_matches_per_window = '2'
  20. seed_hit_taboo_length = '4'
  21. seed_generation_taboo_length = '0'
  22. seed_window_length = '115.0'
  23. max_hits_per_read = '100'
  24. max_read_length = '1000'
  25. kmer = '-1'
  26. sw_match_value = '100'
  27. sw_mismatch_value = '-150'
  28. sw_gap_open_ref = '-400'
  29. sw_gap_open_query = '-400'
  30. sw_gap_ext_ref = '-70'
  31. sw_gap_ext_query = '-70'
  32. sw_crossover_penalty = '-140'
  33. sw_full_hit_threshold = '68.0'
  34. sw_vector_hit_threshold = '60.0'
  35. # TODO: put the threshold on each of these parameters
  36. if len(sys.argv) > 4:
  37. try:
  38. if sys.argv[4].isdigit():
  39. spaced_seed = sys.argv[4]
  40. else:
  41. stop_err('Error in assigning parameter: Spaced seed.')
  42. except:
  43. stop_err('Spaced seed must be a combination of 1s and 0s.')
  44. seed_matches_per_window = sys.argv[5]
  45. seed_hit_taboo_length = sys.argv[6]
  46. seed_generation_taboo_length = sys.argv[7]
  47. seed_window_length = sys.argv[8]
  48. max_hits_per_read = sys.argv[9]
  49. max_read_length = sys.argv[10]
  50. kmer = sys.argv[11]
  51. sw_match_value = sys.argv[12]
  52. sw_mismatch_value = sys.argv[13]
  53. sw_gap_open_ref = sys.argv[14]
  54. sw_gap_open_query = sys.argv[15]
  55. sw_gap_ext_ref = sys.argv[16]
  56. sw_gap_ext_query = sys.argv[17]
  57. sw_crossover_penalty = sys.argv[18]
  58. sw_full_hit_threshold = sys.argv[19]
  59. sw_vector_hit_threshold = sys.argv[20]
  60. # temp file for shrimp log file
  61. shrimp_log = tempfile.NamedTemporaryFile().name
  62. # SHRiMP command
  63. command = ' '.join([shrimp, '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-x', sw_crossover_penalty, '-h', sw_full_hit_threshold, '-v', sw_vector_hit_threshold, input_query_file, input_target_file, '>', shrimp_outfile, '2>', shrimp_log])
  64. try:
  65. os.system(command)
  66. except Exception, e:
  67. if os.path.exists(query_fasta): os.remove(query_fasta)
  68. if os.path.exists(query_qual): os.remove(query_qual)
  69. stop_err(str(e))
  70. # check SHRiMP output: count number of lines
  71. num_hits = 0
  72. if shrimp_outfile:
  73. for i, line in enumerate(file(shrimp_outfile)):
  74. line = line.rstrip('\r\n')
  75. if not line or line.startswith('#'): continue
  76. try:
  77. fields = line.split()
  78. num_hits += 1
  79. except Exception, e:
  80. stop_err(str(e))
  81. if num_hits == 0: # no hits generated
  82. err_msg = ''
  83. if shrimp_log:
  84. for i, line in enumerate(file(shrimp_log)):
  85. if line.startswith('error'): # deal with memory error:
  86. err_msg += line # error: realloc failed: Cannot allocate memory
  87. if re.search('Reads Matched', line): # deal with zero hits
  88. if int(line[8:].split()[2]) == 0:
  89. err_msg = 'Zero hits found.\n'
  90. stop_err('SHRiMP Failed due to:\n' + err_msg)
  91. # remove temp. files
  92. if os.path.exists(shrimp_log): os.remove(shrimp_log)
  93. if __name__ == '__main__': __main__()