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1 #!/usr/bin/env python
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2
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3 """
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4 SHRiMP wrapper : Color space
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5 """
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6
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7 import os, sys, tempfile, os.path, re
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8
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9 assert sys.version_info[:2] >= (2.4)
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10
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11 def stop_err( msg ):
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12
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13 sys.stderr.write( "%s\n" % msg )
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14 sys.exit()
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15
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16
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17 def __main__():
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18
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19 # SHRiMP path
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20 shrimp = 'rmapper-cs'
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21
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22 # I/O
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23 input_target_file = sys.argv[1] # fasta
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24 input_query_file = sys.argv[2]
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25 shrimp_outfile = sys.argv[3] # shrimp output
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26
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27 # SHRiMP parameters
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28 spaced_seed = '1111001111'
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29 seed_matches_per_window = '2'
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30 seed_hit_taboo_length = '4'
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31 seed_generation_taboo_length = '0'
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32 seed_window_length = '115.0'
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33 max_hits_per_read = '100'
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34 max_read_length = '1000'
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35 kmer = '-1'
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36 sw_match_value = '100'
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37 sw_mismatch_value = '-150'
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38 sw_gap_open_ref = '-400'
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39 sw_gap_open_query = '-400'
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40 sw_gap_ext_ref = '-70'
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41 sw_gap_ext_query = '-70'
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42 sw_crossover_penalty = '-140'
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43 sw_full_hit_threshold = '68.0'
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44 sw_vector_hit_threshold = '60.0'
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45
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46 # TODO: put the threshold on each of these parameters
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47 if len(sys.argv) > 4:
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48
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49 try:
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50 if sys.argv[4].isdigit():
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51 spaced_seed = sys.argv[4]
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52 else:
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53 stop_err('Error in assigning parameter: Spaced seed.')
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54 except:
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55 stop_err('Spaced seed must be a combination of 1s and 0s.')
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56
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57 seed_matches_per_window = sys.argv[5]
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58 seed_hit_taboo_length = sys.argv[6]
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59 seed_generation_taboo_length = sys.argv[7]
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60 seed_window_length = sys.argv[8]
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61 max_hits_per_read = sys.argv[9]
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62 max_read_length = sys.argv[10]
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63 kmer = sys.argv[11]
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64 sw_match_value = sys.argv[12]
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65 sw_mismatch_value = sys.argv[13]
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66 sw_gap_open_ref = sys.argv[14]
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67 sw_gap_open_query = sys.argv[15]
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68 sw_gap_ext_ref = sys.argv[16]
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69 sw_gap_ext_query = sys.argv[17]
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70 sw_crossover_penalty = sys.argv[18]
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71 sw_full_hit_threshold = sys.argv[19]
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72 sw_vector_hit_threshold = sys.argv[20]
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73
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74 # temp file for shrimp log file
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75 shrimp_log = tempfile.NamedTemporaryFile().name
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76
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77 # SHRiMP command
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78 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])
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79
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80 try:
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81 os.system(command)
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82 except Exception, e:
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83 if os.path.exists(query_fasta): os.remove(query_fasta)
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84 if os.path.exists(query_qual): os.remove(query_qual)
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85 stop_err(str(e))
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86
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87 # check SHRiMP output: count number of lines
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88 num_hits = 0
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89 if shrimp_outfile:
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90 for i, line in enumerate(file(shrimp_outfile)):
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91 line = line.rstrip('\r\n')
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92 if not line or line.startswith('#'): continue
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93 try:
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94 fields = line.split()
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95 num_hits += 1
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96 except Exception, e:
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97 stop_err(str(e))
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98
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99 if num_hits == 0: # no hits generated
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100 err_msg = ''
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101 if shrimp_log:
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102 for i, line in enumerate(file(shrimp_log)):
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103 if line.startswith('error'): # deal with memory error:
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104 err_msg += line # error: realloc failed: Cannot allocate memory
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105 if re.search('Reads Matched', line): # deal with zero hits
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106 if int(line[8:].split()[2]) == 0:
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107 err_msg = 'Zero hits found.\n'
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108 stop_err('SHRiMP Failed due to:\n' + err_msg)
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109
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110
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111 # remove temp. files
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112 if os.path.exists(shrimp_log): os.remove(shrimp_log)
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113
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114
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115 if __name__ == '__main__': __main__()
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116
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