Mercurial > repos > charles_s_test > seqsero2

annotate run_seqsero2.py @ 11:b4484db557ab draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Wed, 29 Nov 2017 12:46:19 -0500
parents acc5cd06a36a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/python
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2
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3 import os, re, sys, time, datetime
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4 import subprocess
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5 from subprocess import Popen, PIPE
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6
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7
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8 # Declare Variables
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9 # paths to files and scripts
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10
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11 fileDir = os.path.dirname(os.path.realpath('__file__'))
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12 print(fileDir)
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13
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14 fq_list1 = []
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15 Tool_directory = sys.argv[2]
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16 database = Tool_directory + '/universe.sqlite'
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17 seqsero = Tool_directory + 'SeqSero.py'
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18 test_out = open(Tool_directory + "/test.txt", 'w')
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19 out_path = Tool_directory + '/files/000'
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20 test_out2 = open(Tool_directory + "/test2.txt", 'w')
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21
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22 path2sample = Tool_directory + 'fastq_tmp'
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24
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25 #test_out2.write(" Test test test");
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26
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27 test_out.write("monkey ");
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28 #test_out.write("");
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29 test_out.write("\t".join(sys.argv)+'\n')
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33
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34 print(Tool_directory + ' path printed ')
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35
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36 test_out.write(str(len(sys.argv))+"\n")
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37 if len(sys.argv) >= 2:
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38 test_out.write("\t".join(sys.argv)+'\n')
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39 fq_list1 = sys.argv[1]
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40
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41 test_out.write(str(len(sys.argv))+"\n")
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42
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43 fastq_files = re.split(",", fq_list1)
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44
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45 def print_time():
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46 test_out.write(time.asctime( time.localtime(time.time())))
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47
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48 tmp_path = "fastq_tmp"
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49 if not os.path.exists(tmp_path):
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50 os.system('mkdir '+tmp_path)
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51
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52 test_out.write(str(len(fastq_files))+"\n")
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53
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54 def list_runs(fastq_files):
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55 '''
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56 Creates dict with runs as keys and list with filenames as values.
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57 '''
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58 # print("monkey")
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59 run2fastqs = {}
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60 for file in fastq_files:
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61 run = ''
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62 try:
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63 fastq = open(file, 'r')
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64 i = 0
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65 for line in fastq:
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66 line = line.rstrip("\n")
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67 if i == 0:
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68 run = re.split("\s", line)[0]
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69 run = re.sub('@', '', run)
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70 run = re.sub("\.1", '', run)
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71 else:
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72 break
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73 i += 1
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74 file1 = re.split('/', file)[-1]
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75 file2 = re.sub('.dat$', '_'+run+'.fastq', file1)
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76 new_path_file = tmp_path+'/'+file2
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77 # print run, new_path_file
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78 if file2 not in os.listdir(tmp_path):
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79 os.system('cp '+file+' '+new_path_file)
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80 if run in run2fastqs.keys():
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81 if file not in run2fastqs[run]:
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82 run2fastqs[run].append(new_path_file)
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83 else:
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84 run2fastqs[run] = [new_path_file]
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85 except IOError:
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86 print("Data not found. It is possible for a deleted file to still be listed "\
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87 "in a Galaxy library. Please confirm that the data still exists on this "\
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88 "server. You may need to upload it again.")
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89 return run2fastqs
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90
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91 def run_seqsero(run2fastqs):
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92 '''
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93 Takes files from run2fastqs and runs SeqSero.
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94 '''
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95 outputs = []
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96 for run in run2fastqs:
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97 seqsero_cmd = []
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98 if len(run2fastqs[run]) == 2:
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99 seqsero_cmd = ['python', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]]
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100 elif len(run2fastqs[run]) == 1:
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101 seqsero_cmd = ['python', seqsero, '-m', '1', '-i', run2fastqs[run][0]]
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102 p = Popen(seqsero_cmd, stdout=PIPE)
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103 output = p.communicate()
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104 outputs.append(output)
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105 return outputs
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106
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107 def get_serotypes(outputs):
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108 '''
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109 '''
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110 fastq2comment = {}
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111 fastq2serotype = {}
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112 for sample in outputs:
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113 fastqs = ''
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114 lines_used = []
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115 for line in sample: # line is actually the entire seqsero output.
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116 line = str(line)
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117 linel = re.split("\n", line)
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118 # print(linel)
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119 #lines_used = []
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120 for element in linel: # element is a line of seqsero output.
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121 element = element.rstrip("\n")
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122 test_out.write(element+"\n")
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123 elementl = re.split("\t", element)
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124 if elementl[0] == 'Input files:':
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125 fastqs = elementl[1]
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126 lines_used.append(element)
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127 if elementl[1] not in fastq2serotype.keys():
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128 fastq2serotype[fastqs] = ['']*5
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129 fastq2comment[fastqs] = []
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130 elif elementl[0] == 'O antigen prediction:':
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131 lines_used.append(element)
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132 fastq2serotype[fastqs][0] = elementl[1] # add predicted profile
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133 elif elementl[0] == 'H1 antigen prediction(fliC):':
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134 lines_used.append(element)
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135 fastq2serotype[fastqs][1] = elementl[1] # add predicted profile
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136 elif elementl[0] == 'H2 antigen prediction(fljB):':
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137 lines_used.append(element)
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138 fastq2serotype[fastqs][2] = elementl[1] # add predicted profile
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139 elif elementl[0] == 'Predicted antigenic profile:':
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140 lines_used.append(element)
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141 fastq2serotype[fastqs][3] = elementl[1] # add predicted profile
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142 elif elementl[0] == 'Predicted serotype(s):':
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143 lines_used.append(element)
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144 fastq2serotype[fastqs][4] = elementl[1] # add predicted serotype
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145 if element not in lines_used and re.search("\w", fastqs) and len(element) > 7:
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146 fastq2comment[fastqs].append(element)
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147 #print("\n"
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148 return fastq2serotype, fastq2comment
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149
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150 def print_html(fastq2serotype, fastq2comment):
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151 '''
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152 Takes dict and prints to html file.
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153 '''
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154 tab_out = open('Seqsero_result.txt', 'w');
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155 html_out = open('Seqsero_result.html', 'w')
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156 html_out.write('<!DOCTYPE html>\n')
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charles_s_test
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157 html_out.write('<html>\n')
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charles_s_test
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158 html_out.write('<head>\n')
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charles_s_test
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159 html_out.write('<title>SeqSero Results</title>\n')
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160 html_out.write('</head>\n')
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charles_s_test
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161 html_out.write('<body>\n')
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charles_s_test
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162 html_out.write('<body style="font-family:Helvetica;">\n')
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charles_s_test
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163 html_out.write('<p style="font-size:10px">\n')
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charles_s_test
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164 html_out.write('<table border=1>\n')
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165 header = 'Input Files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted antigenic profile\tPredicted serotype(s)'
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166 header = re.sub(' ', '_', header)
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167 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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168 html_out.write('<tr>\n')
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169 for element in header_l:
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170 html_out.write('<td>'+element+'</td>\n')
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171 html_out.write('</tr>\n')
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172 tab_out.write(header+"\n")
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173 print("\n\n", header)
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174 for fastq in fastq2serotype:
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175 # print(fastq, fastq2serotype[fastq])
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176 line_to_print = fastq+'\t'+"\t".join(fastq2serotype[fastq])
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177 tab_out.write(line_to_print+"\n")
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178 html_out.write('<tr>\n')
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charles_s_test
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179 html_out.write('<td>'+fastq+'</td>\n')
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charles_s_test
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180 for antigen in fastq2serotype[fastq]:
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181 html_out.write('<td>'+antigen+'</td>\n')
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182 html_out.write('</tr>\n')
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183 print(line_to_print)
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184 html_out.write('</table>\n')
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185 print("\n")
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186 for fastq in fastq2comment:
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187 tab_out.write("\n"+fastq+"\n")
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188 html_out.write('<tr>\n')
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charles_s_test
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189 html_out.write('<p>\n')
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charles_s_test
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190 html_out.write('<td>'+fastq+"<br></td>\n")
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charles_s_test
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191 for line in fastq2comment[fastq]:
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192 #if len(line) > 7:
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193 html_out.write('<td>'+line+'</td>\n')
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194 tab_out.write(line+"\n")
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195 print(line)
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196 print("\n")
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197 html_out.write('</p>\n')
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charles_s_test
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198 html_out.write('</tr>\n')
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charles_s_test
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199 html_out.write('</body>\n')
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200 html_out.write('</html>\n')
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201 html_out.close()
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202
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203
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204 def readFile(filename):
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205 filehandle = open(filename)
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206 print(filehandle.read())
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207 filehandle.close()
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208
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209
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210 run2fastqs = list_runs(fastq_files)
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211 outputs = run_seqsero(run2fastqs)
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212 fastq2serotype, fastq2comment = get_serotypes(outputs)
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charles_s_test
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213 print_html(fastq2serotype, fastq2comment)
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214
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215 print_time()
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216
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217