Mercurial > repos > charles_s_test > seqsero2

annotate run_seqsero_batch_galaxy_no_comment.py @ 2:0d65b71ff8df draft

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planemo upload commit 464b391afaa5819bc681452e85bea9d882730eb6
author charles_s_test
date Sun, 12 Nov 2017 02:27:32 -0500
parents 6895de35a263
children
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1 #!/usr/bin/python
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2
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3 import os, re, sys, time, sqlite3, 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 database = '/nfs/sw/apps/galaxy/database/universe.sqlite'
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8 seqsero = '/nfs/sw/apps/galaxy/tools/seqsero/SeqSero.py'
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9 test_out = open("/nfs/sw/apps/galaxy/tools/seqsero/test.txt", 'w')
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10 out_path = '/nfs/sw/apps/galaxy/database/files/000'
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11 test_out2 = open("/nfs/sw/apps/galaxy/tools/seqsero/test2.txt", 'w')
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12
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13 #tab_out = open('/nfs/sw/apps/galaxy/tools/seqsero/Seqsero_result.txt', 'w')
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14 #tab_out.write('super monkey')
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15
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16 tab_out = open('Seqsero_result.txt', 'w');
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17 #tab_out.write('super monkey')
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18 #tab_out.close()
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19
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20 #print 'super monkey'
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21 path2sample = '/nfs/sw/apps/galaxy/tools/seqsero/fastq_tmp'
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22
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23 test_out2.write(" Test test test");
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24
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25 test_out.write(" test test ");
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26 test_out.write("");
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27 test_out.write("\t".join(sys.argv)+'\n')
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28
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29 fq_list1 = []
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30 fq_list2 = []
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31
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32 test_out.write(str(len(sys.argv))+"\n")
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33 if len(sys.argv) >= 2:
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34 test_out.write("\t".join(sys.argv)+'\n')
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35 fq_list1 = sys.argv[1]
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36 # fq_list2 = sys.argv[2]
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37
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38 test_out.write(str(len(sys.argv))+"\n")
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39
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40 fastq_files = re.split(",", fq_list1)#+re.split(",", fq_list2)
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41
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42 def print_time():
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43 test_out.write(time.asctime( time.localtime(time.time())))
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44
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45 tmp_path = "/nfs/sw/apps/galaxy/tools/seqsero/fastq_tmp"
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46 if not os.path.exists(tmp_path):
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47 os.system('mkdir '+tmp_path)
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48
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49 test_out.write(str(len(fastq_files))+"\n")
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50
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51 def list_runs(fastq_files):
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52 '''
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53 Creates dict with runs as keys and list with filenames as values.
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54 '''
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55 # print "monkey"
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56 run2fastqs = {}
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57 for file in fastq_files:
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58 run = ''
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59 try:
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60 fastq = open(file, 'r')
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61 i = 0
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62 for line in fastq:
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63 line = line.rstrip("\n")
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64 if i == 0:
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65 run = re.split("\s", line)[0]
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66 run = re.sub('@', '', run)
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67 run = re.sub("\.1", '', run)
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68 else:
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69 break
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70 i += 1
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71 file1 = re.split('/', file)[-1]
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72 file2 = re.sub('.dat$', '_'+run+'.fastq', file1)
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73 new_path_file = tmp_path+'/'+file2
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74 # print run, new_path_file
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75 if file2 not in os.listdir(tmp_path):
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76 os.system('cp '+file+' '+new_path_file)
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77 if run in run2fastqs.keys():
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78 if file not in run2fastqs[run]:
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79 run2fastqs[run].append(new_path_file)
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80 else:
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81 run2fastqs[run] = [new_path_file]
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82 except IOError:
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83 print "Data not found. It is possible for a deleted file to still be listed "\
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84 "in a Galaxy library. Please confirm that the data still exists on this "\
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85 "server. You may need to upload it again."
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86 return run2fastqs
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87
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88 def run_seqsero(run2fastqs):
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89 '''
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90 Takes files from run2fastqs and runs SeqSero.
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91 '''
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92 outputs = []
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93 for run in run2fastqs:
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94 seqsero_cmd = []
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95 if len(run2fastqs[run]) == 2:
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96 seqsero_cmd = ['python', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]]
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97 elif len(run2fastqs[run]) == 1:
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98 seqsero_cmd = ['python', seqsero, '-m', '1', '-i', run2fastqs[run][0]]
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99 p = Popen(seqsero_cmd, stdout=PIPE)
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100 output = p.communicate()
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101 outputs.append(output)
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102 return outputs
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103
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104
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105 def parse_output(runs_info, out_path):
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106 '''
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107 retrieve seqsero output into a list of lists.
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108 '''
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109 for run in runs_info:
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110 running_path = out_path+'/'+run
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111 # print 'monkey go running ', running_path
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112 running_info = open(running_path, 'r')
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113 for line in running_info:
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114 test_out.write(line, "\n")
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115
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116 def get_serotypes(outputs):
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117 '''
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118 '''
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119 fastq2serotype = {}
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120 for sample in outputs:
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121 for line in sample:
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122 line = str(line)
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123 linel = re.split("\n", line)
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124 # print linel
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125 for element in linel:
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126 elementl = re.split("\t", element)
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127 if elementl[0] == 'Input files:':
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128 fastqs = elementl[1]
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129 if elementl[1] not in fastq2serotype.keys():
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130 fastq2serotype[fastqs] = ['']*5
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131 elif elementl[0] == 'O antigen prediction:':
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132 predicted_profile = elementl[1]
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133 fastq2serotype[fastqs][0] = elementl[1] # add predicted profile
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134 # print elementl[1]
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135 elif elementl[0] == 'H1 antigen prediction(fliC):':
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136 predicted_profile = elementl[1]
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137 fastq2serotype[fastqs][1] = elementl[1] # add predicted profile
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138 # print elementl[1]
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139 elif elementl[0] == 'H2 antigen prediction(fljB):':
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140 predicted_profile = elementl[1]
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141 fastq2serotype[fastqs][2] = elementl[1] # add predicted profile
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142 # print elementl[1]
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143 elif elementl[0] == 'Predicted antigenic profile:':
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144 predicted_profile = elementl[1]
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145 fastq2serotype[fastqs][3] = elementl[1] # add predicted profile
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146 # print elementl[1]
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147 elif elementl[0] == 'Predicted serotype(s):':
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148 fastq2serotype[fastqs][4] = elementl[1] # add predicted serotype
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149 # print elementl[1]
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150 print "\n"
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151 return fastq2serotype
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152
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153 def print_html(fastq2serotype):
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154 '''
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155 Takes dict and prints to html file.
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156 '''
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157 html_out = open('Seqsero_result.html', 'w')
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158 html_out.write('<!DOCTYPE html>\n')
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159 html_out.write('<html>\n')
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160 html_out.write('<head>\n')
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161 html_out.write('<title>SeqSero Results</title>\n')
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162 html_out.write('</head>\n')
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163 html_out.write('<body>\n')
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164 html_out.write('<body style="font-family:Helvetica;">\n')
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165 html_out.write('<p style="font-size:10px">\n')
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166 html_out.write('<table border=1>\n')
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167 header = 'Input Files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted antigenic profile\tPredicted serotype(s)'
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168 header = re.sub(' ', '_', header)
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169 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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170 html_out.write('<tr>\n')
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171 for element in header_l:
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172 html_out.write('<td>'+element+'</td>\n')
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173 html_out.write('</tr>\n')
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174 tab_out.write(header+"\n")
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175 print header
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176 for fastq in fastq2serotype:
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177 # print fastq, fastq2serotype[fastq]
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178 line_to_print = fastq+'\t'+"\t".join(fastq2serotype[fastq])
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179 tab_out.write(line_to_print+"\n")
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180 html_out.write('<tr>\n')
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181 html_out.write('<td>'+fastq+'</td>\n')
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182 for antigen in fastq2serotype[fastq]:
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183 html_out.write('<td>'+antigen+'</td>\n')
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184 html_out.write('</tr>\n')
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185 print line_to_print
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186 html_out.write('</table>\n')
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187 html_out.write('</body>\n')
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188 html_out.write('</html>\n')
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189 html_out.close()
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190
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191 run2fastqs = list_runs(fastq_files)
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192 outputs = run_seqsero(run2fastqs)
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193 fastq2serotype = get_serotypes(outputs)
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194 print_html(fastq2serotype)
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195
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196 print_time()
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197
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198