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1 # Kenneth Sabir
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2 # Garvan Institute
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3 import sys
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4 import time
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5 import os
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6 import math
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7 import subprocess
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8 import string
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9 import shutil
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10 import pickle
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11 import io
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12 from multiprocessing import Process
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13 from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
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14
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15
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16
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17 def main():
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18 split_program = "split"
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19 cat_program = "cat"
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20 input_filename = sys.argv[1]
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21 output_filename = sys.argv[3]
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22 number_of_processes = 1;
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23 if (len(sys.argv) > 7):
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24 number_of_processes = int(sys.argv[7])
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25 file_prefix = "temp_groomer_part_"
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26
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27 t1 = time.time()
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28 old_path = os.getcwd()
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29
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30 lines_per_process,number_of_lines = calculate_lines_per_process(input_filename, number_of_processes)
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31 temp_dir_name = move_to_temp_dir()
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32 sequences = number_of_lines/4;
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33 args = [split_program, "-l"+str(lines_per_process), input_filename, file_prefix]
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34 # print "The args are: " , args
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35 subprocess.call(args)
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36 # print "Finished"
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37 file_count = 0;
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38 keep_checking = True
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39 processes = []
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40 output_filenames = []
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41 while keep_checking:
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42
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43 # only need to support 26x26 different processes, so do it brute force (ie not in a loop) for 2 chars.
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44 lastchar = string.letters[file_count % len(string.letters)]
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45 firstchar = string.letters[(file_count / len(string.letters)) % len(string.letters)]
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46 temp_input_filename = "%s%c%c" % (file_prefix, firstchar, lastchar)
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47
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48 # print 'looking for ' + temp_input_filename
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49 if os.path.exists(temp_input_filename):
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50 # print 'found ' + temp_input_filename
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51 temp_output_filename = temp_input_filename + "_output"
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52 output_filenames.append(temp_output_filename)
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53 p = Process(target=partition, args=([temp_input_filename, temp_output_filename, file_count]))
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54 p.start()
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55 processes.append(p)
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56 file_count = file_count + 1
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57 else:
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58 break
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59 for p in processes :
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60 p.join()
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61 cat_params = [cat_program]
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62 cat_params.extend(output_filenames)
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63 with open(output_filename, 'w') as catOutputFile:
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64 subprocess.call(cat_params, stdout=catOutputFile)
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65 summarize_input = sys.argv[6] == 'summarize_input'
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66 input_type = sys.argv[2]
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67 output_type = sys.argv[4]
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68 print "Groomed %i %s reads into %s reads." % ( sequences, input_type, output_type )
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69
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70 aggregators = []
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71 if summarize_input:
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72 for temp_output_filename in output_filenames :
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73 with open(temp_output_filename + "_summary", 'r') as summaryLogFile:
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74 temp_aggregator = pickle.load(summaryLogFile)
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75 aggregators.append(temp_aggregator)
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76
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77 print_aggregators(aggregators)
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78 os.chdir(old_path)
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79 shutil.rmtree(temp_dir_name)
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80 time2 = time.time()
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81 print 'Groomer took: %0.3f ms using %d processes' % (((time2 - t1)*1000.0), number_of_processes)
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82
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83 def calculate_lines_per_process(input_filename, number_of_processes):
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84 wc_program = "wc"
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85 p = subprocess.Popen([wc_program, "-l", input_filename], stdout=subprocess.PIPE)
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86 out, err = p.communicate()
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87 number_of_lines = int(string.split(string.lstrip(out), ' ', 1)[0])
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88 exact_lines_per_process = number_of_lines * 1.0 / number_of_processes
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89 lines_per_process = int(math.ceil((exact_lines_per_process / 4.0))) * 4
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90 return lines_per_process,number_of_lines
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91
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92 def move_to_temp_dir():
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93 dirExists = False;
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94 dir_name = None
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95
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96 while not dirExists:
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97 dir_name = "temp_groomer_part_" + str(time.time())
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98 if not os.path.exists(dir_name):
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99 os.makedirs(dir_name)
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100 break;
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101 os.chdir(dir_name)
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102 return dir_name
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103
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104 def print_aggregators(aggregators):
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105 total_ascii_range = [None, None]
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106 total_decimal_range = [None, None]
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107 total_valid_formats = set()
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108 for aggregator in aggregators:
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109 # print "This aggregators valid formats are: " + str(aggregator.get_valid_formats())
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110 total_valid_formats = total_valid_formats.union(set(aggregator.get_valid_formats()))
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111 ascii_range = aggregator.get_ascii_range()
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112 decimal_range = aggregator.get_decimal_range()
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113
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114 if total_ascii_range[0] is None:
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115 total_ascii_range[0] = ascii_range[0]
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116 else:
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117 total_ascii_range[0] = min (total_ascii_range[0], ascii_range[0])
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118
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119 # max of None and a value is the value
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120 total_ascii_range[1] = max (total_ascii_range[1], ascii_range[1])
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121 if total_decimal_range[0] is None:
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122 total_decimal_range[0] = decimal_range[0]
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123 else:
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124 total_decimal_range[0] = min (total_decimal_range[0], decimal_range[0])
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125 # max of None and a value is the value
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126 total_decimal_range[1] = max (total_decimal_range[1], decimal_range[1])
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127 print "total_valid_formats= " + str(total_valid_formats)
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128 print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( total_valid_formats ) or "None" )
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129 print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( total_ascii_range[0] ), ord( total_ascii_range[0] ), repr( total_ascii_range[1] ), ord( total_ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed
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130 print "Input decimal range: %i - %i" % ( total_decimal_range[0], total_decimal_range[1] )
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131
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132
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133 def partition(input_filename, temp_output_filename, fileCount):
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134 # print 'Starting Thread: ' + str(fileCount)
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135 # input_filename = sys.argv[1]
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136 input_type = sys.argv[2]
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137 output_type = sys.argv[4]
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138 force_quality_encoding = sys.argv[5]
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139 summarize_input = sys.argv[6] == 'summarize_input'
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140 if force_quality_encoding == 'None':
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141 force_quality_encoding = None
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142 aggregator = fastqAggregator()
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143 temp_process_file = fastqWriter( open( temp_output_filename, 'wb'), format = output_type, force_quality_encoding = force_quality_encoding )
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144 read_count = None
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145 if summarize_input:
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146 reader = fastqVerboseErrorReader
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147 else:
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148 reader = fastqReader
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149 for read_count, fastq_read in enumerate( reader( open(input_filename, 'rb'), format = input_type, apply_galaxy_conventions = True ) ):
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150 if summarize_input:
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151 aggregator.consume_read( fastq_read )
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152 temp_process_file.write( fastq_read )
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153 # print "Just wrote (%d): " % read_count + str(fastq_read)
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154 temp_process_file.close()
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155 if read_count is not None:
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156 if input_type != output_type and 'solexa' in [ input_type, output_type ]:
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157 print "Converted between Solexa and PHRED scores."
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158 if summarize_input:
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159 with open(temp_output_filename + "_summary", 'w') as summaryLogFile :
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160 pickle.dump(aggregator, summaryLogFile)
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161 else:
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162 print "No valid FASTQ reads were provided."
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163
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164 if __name__ == "__main__": main()
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