Mercurial > repos > charles_s_test > seqsero2

annotate run_seqsero_batch_galaxy.py @ 0:6895de35a263 draft

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planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
author charles_s_test
date Thu, 19 Oct 2017 18:16:51 -0400
parents
children 0d65b71ff8df
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0
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1 #!/usr/bin/python
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2
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3 print 'monkey wonders where he is'
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4
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5 import os
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6
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7 # os.system('source /nfs/sw/apps/galaxy-dev/galaxy/.venv/bin/activate')
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8
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9 import re, sys, time, datetime
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10 import subprocess, psycopg2, sqlalchemy
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11 from subprocess import Popen, PIPE
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12 from sqlalchemy import *
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13 from datetime import datetime
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14
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15 print 'monkey found some files', sys.argv
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16 engine = create_engine('postgresql+psycopg2://galaxy:cF$cl0udh9c@galaxyprod.cvkyaz9id4ml.us-east-1.rds.amazonaws.com:5432/galaxy')
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17 print 'monkey says "vroom vroom"'
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18 connection = engine.connect()
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19 print "monkey made a connection!"
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20
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21 # database = '/nfs/sw/apps/galaxy-dev/galaxy/database/universe.sqlite'
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22 seqsero = '/nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/SeqSero.py'
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23 test_out = open("/nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/test.txt", 'w')
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24 out_path = '/nfs/sw/apps/galaxy-dev/galaxy/database/files/000'
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25 test_out2 = open("/nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/test2.txt", 'w')
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26
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27 path2sample = '/nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/fastq_tmp'
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28
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29 test_out.write("monkey ");
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30 test_out.write("\t".join(sys.argv)+'\n')
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31
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32 fq_list1 = []
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33
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34 test_out.write(str(len(sys.argv))+"\n")
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35 if len(sys.argv) >= 2:
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36 test_out.write("\t".join(sys.argv)+'\n')
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37 fq_list1 = sys.argv[1:]
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38
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39 test_out.write(str(len(sys.argv))+"\n")
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40
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41 fastq_files = re.split(",", fq_list1[0]) # fq_list1[0] is a string with commas between the path/filenames.
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42
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43 def print_time():
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44 test_out.write(time.asctime( time.localtime(time.time())))
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45
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46 tmp_path = path2sample
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47 if not os.path.exists(tmp_path):
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48 os.system('mkdir '+tmp_path)
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49
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50 test_out.write(str(len(fastq_files))+"\n")
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51
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52 def list_runs(fastq_files):
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53 '''
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54 Creates dict with runs as keys and list with filenames as values.
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55 '''
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56 run2fastqs = {}
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57 is_fastq = 'yes'
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58 for file in fastq_files:
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59 print 'monkey found', file
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60 run = ''
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61 try:
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62 fastq = open(file, 'r')
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63 i = 0
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64 for line in fastq:
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65 line = line.rstrip("\n")
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66 if i == 0:
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67 run = re.split("\s", line)[0]
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68 run = re.sub('@', '', run)
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69 run = re.split("\.", run)[0]
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70 if not re.search('^@', line):
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71 is_fastq = 'no'
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72 else:
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73 break
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74 i += 1
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75 file1 = re.split('/', file)[-1]
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76 dataset_id = re.split('_', file1)
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77 dataset_id = re.sub('.dat', '', dataset_id[-1])
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78 print dataset_id, type(dataset_id)
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79 result = connection.execute('SELECT name FROM history_dataset_association WHERE dataset_id = '+dataset_id+';')
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80 original_filename = ''
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81 for row in result:
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82 print 'monkey says the original_filename is something like', row[0]
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83 original_filename = row[0]
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84 if re.search('fasta$', original_filename):
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85 if is_fastq == 'yes':
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86 original_filename = re.sub('fasta', 'fastq', original_filename)
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87 else:
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88 print 'The input file is not a fastq file.'
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89 file2 = re.sub('.dat$', '_'+original_filename, file1)
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90 print 'monkey renamed the file', file2
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91 new_path_file = tmp_path+'/'+file2
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92 if file2 not in os.listdir(tmp_path):
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93 print file, new_path_file
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94 os.system('cp '+file+' '+new_path_file)
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95 if run in run2fastqs.keys():
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96 if file not in run2fastqs[run]:
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97 run2fastqs[run].append(new_path_file)
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98 else:
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99 run2fastqs[run] = [new_path_file]
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100 except IOError:
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101 print "Data not found. It is possible for a deleted file to still be listed "\
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102 "in a Galaxy library. Please confirm that the data still exists on this "\
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103 "server. You may need to upload it again."
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104 return run2fastqs
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105
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106 def run_seqsero(run2fastqs):
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107 '''
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108 Takes files from run2fastqs and runs SeqSero.
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109 '''
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110 outputs = []
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111 for run in run2fastqs:
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112 print run, run2fastqs[run]
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113 seqsero_cmd = []
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114 if len(run2fastqs[run]) == 2:
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115 seqsero_cmd = ['python', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]]
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116 elif len(run2fastqs[run]) == 1:
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117 seqsero_cmd = ['python', seqsero, '-m', '1', '-i', run2fastqs[run][0]]
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118 print seqsero_cmd
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119 p = Popen(seqsero_cmd, stdout=PIPE)
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120 output = p.communicate()
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121 outputs.append(output)
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122 return outputs
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123
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124 def get_serotypes(outputs):
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125 '''
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126 '''
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127 fastq2comment = {}
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128 fastq2serotype = {}
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129 for sample in outputs:
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130 fastqs = ''
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131 lines_used = []
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132 for line in sample: # line is actually the entire seqsero output.
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133 line = str(line)
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134 linel = re.split("\n", line)
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135 # print linel
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136 #lines_used = []
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137 for element in linel: # element is a line of seqsero output.
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138 element = element.rstrip("\n")
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139 test_out.write(element+"\n")
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140 elementl = re.split("\t", element)
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141 if elementl[0] == 'Input files:':
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142 fastqs = elementl[1]
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143 lines_used.append(element)
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144 if elementl[1] not in fastq2serotype.keys():
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145 fastq2serotype[fastqs] = ['']*5
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146 fastq2comment[fastqs] = []
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147 elif elementl[0] == 'O antigen prediction:':
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148 lines_used.append(element)
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149 fastq2serotype[fastqs][0] = elementl[1] # add predicted profile
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150 elif elementl[0] == 'H1 antigen prediction(fliC):':
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151 lines_used.append(element)
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152 fastq2serotype[fastqs][1] = elementl[1] # add predicted profile
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153 elif elementl[0] == 'H2 antigen prediction(fljB):':
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154 lines_used.append(element)
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155 fastq2serotype[fastqs][2] = elementl[1] # add predicted profile
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156 elif elementl[0] == 'Predicted antigenic profile:':
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157 lines_used.append(element)
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158 fastq2serotype[fastqs][3] = elementl[1] # add predicted profile
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159 elif elementl[0] == 'Predicted serotype(s):':
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160 lines_used.append(element)
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161 fastq2serotype[fastqs][4] = elementl[1] # add predicted serotype
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162 if element not in lines_used and re.search("\w", fastqs) and len(element) > 7:
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163 fastq2comment[fastqs].append(element)
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164 #print "\n"
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165 return fastq2serotype, fastq2comment
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166
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167 def print_html(fastq2serotype, fastq2comment):
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168 '''
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169 Takes dict and prints to html file.
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170 '''
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171 tab_out = open('Seqsero_result.txt', 'w');
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172 html_out = open('Seqsero_result.html', 'w')
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173 html_out.write('<!DOCTYPE html>\n')
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174 html_out.write('<html>\n')
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175 html_out.write('<head>\n')
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176 html_out.write('<title>SeqSero Results</title>\n')
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177 html_out.write('</head>\n')
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178 html_out.write('<body>\n')
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179 html_out.write('<body style="font-family:Helvetica;">\n')
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180 html_out.write('<p style="font-size:10px">\n')
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181 html_out.write('<table border=1>\n')
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182 header = 'Input Files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted antigenic profile\tPredicted serotype(s)'
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183 header = re.sub(' ', '_', header)
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184 header_l = ['Input Files', 'O antigen prediction', 'H1 antigen prediction(fliC)', 'H2 antigen prediction(fljB)', 'Predicted antigenic profile', 'Predicted serotype(s)']
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185 html_out.write('<tr>\n')
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186 for element in header_l:
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187 html_out.write('<td>'+element+'</td>\n')
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188 html_out.write('</tr>\n')
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189 tab_out.write(header+"\n")
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190 print "\n\n", header
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191 for fastq in fastq2serotype:
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192 # print fastq, fastq2serotype[fastq]
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193 line_to_print = fastq+'\t'+"\t".join(fastq2serotype[fastq])
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194 tab_out.write(line_to_print+"\n")
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195 html_out.write('<tr>\n')
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196 html_out.write('<td>'+fastq+'</td>\n')
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197 for antigen in fastq2serotype[fastq]:
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198 html_out.write('<td>'+antigen+'</td>\n')
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199 html_out.write('</tr>\n')
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200 print line_to_print
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201 html_out.write('</table>\n')
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202 print "\n"
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203 for fastq in fastq2comment:
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204 tab_out.write("\n"+fastq+"\n")
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205 html_out.write('<tr>\n')
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206 html_out.write('<p>\n')
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207 html_out.write('<td>'+fastq+"<br></td>\n")
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208 for line in fastq2comment[fastq]:
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209 #if len(line) > 7:
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210 html_out.write('<td>'+line+'</td>\n')
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211 tab_out.write(line+"\n")
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212 print line
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213 print "\n"
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214 html_out.write('</p>\n')
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215 html_out.write('</tr>\n')
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216 html_out.write('</body>\n')
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217 html_out.write('</html>\n')
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218 html_out.close()
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219
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220 run2fastqs = list_runs(fastq_files)
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221 #print run2fastqs
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222 outputs = run_seqsero(run2fastqs)
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223 fastq2serotype, fastq2comment = get_serotypes(outputs)
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224 print_html(fastq2serotype, fastq2comment)
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225 print_time()
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226
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227