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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