Mercurial > repos > charles_s_test > seqsero

annotate run_seqsero_batch_galaxy_09-15-17.py @ 2:381e1e7109fc draft default tip

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planemo upload commit 464b391afaa5819bc681452e85bea9d882730eb6-dirty
author charles_s_test
date Sun, 12 Nov 2017 02:26:17 -0500
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2
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1 #!/usr/bin/python
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2
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3 print "monkey has started"
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4
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5 import os, re, sys, time, datetime
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6 import subprocess
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7 from subprocess import Popen, PIPE
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8
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9 database = '/nfs/sw/apps/galaxy-prd/galaxy/database/universe.sqlite'
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10 seqsero = '/nfs/sw/apps/galaxy-prd/galaxy/tools/seqsero/SeqSero.py'
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11 test_out = open("/nfs/sw/apps/galaxy-prd/galaxy/tools/seqsero/test.txt", 'w')
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12 out_path = '/nfs/sw/apps/galaxy-prd/galaxy/database/files/000'
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13 test_out2 = open("/nfs/sw/apps/galaxy-prd/galaxy/tools/seqsero/test2.txt", 'w')
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14
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15 path2sample = '/nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/fastq_tmp'
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16
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17 #test_out2.write(" Test test test");
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18
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19 test_out.write("monkey ");
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20 #test_out.write("");
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21 test_out.write("\t".join(sys.argv)+'\n')
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22
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23 fq_list1 = []
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24 fq_list2 = []
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25
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26 test_out.write(str(len(sys.argv))+"\n")
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27 if len(sys.argv) >= 2:
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28 test_out.write("\t".join(sys.argv)+'\n')
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29 fq_list1 = sys.argv[1]
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30
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31 test_out.write(str(len(sys.argv))+"\n")
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32
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33 fastq_files = re.split(",", fq_list1)
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34
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35 def print_time():
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36 test_out.write(time.asctime( time.localtime(time.time())))
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37
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38 tmp_path = "/nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/fastq_tmp"
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39 if not os.path.exists(tmp_path):
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40 os.system('mkdir '+tmp_path)
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41
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42 test_out.write(str(len(fastq_files))+"\n")
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43
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44 def list_runs(fastq_files):
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45 '''
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46 Creates dict with runs as keys and list with filenames as values.
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47 '''
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48 # print "monkey"
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49 run2fastqs = {}
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50 for file in fastq_files:
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51 run = ''
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52 try:
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53 fastq = open(file, 'r')
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54 i = 0
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55 for line in fastq:
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56 line = line.rstrip("\n")
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57 if i == 0:
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58 run = re.split("\s", line)[0]
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59 run = re.sub('@', '', run)
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60 run = re.split("\.", run)[0]
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61 #run = re.sub("\.1", '', run)]
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62 else:
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63 break
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64 i += 1
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65 file1 = re.split('/', file)[-1]
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66 file2 = re.sub('.dat$', '_'+run+'.fastq', file1)
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67 new_path_file = tmp_path+'/'+file2
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68 # print run, new_path_file
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69 if file2 not in os.listdir(tmp_path):
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70 os.system('cp '+file+' '+new_path_file)
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71 if run in run2fastqs.keys():
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72 if file not in run2fastqs[run]:
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73 run2fastqs[run].append(new_path_file)
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74 else:
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75 run2fastqs[run] = [new_path_file]
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76 except IOError:
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77 print "Data not found. It is possible for a deleted file to still be listed "\
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78 "in a Galaxy library. Please confirm that the data still exists on this "\
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79 "server. You may need to upload it again."
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80 return run2fastqs
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81
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82 def run_seqsero(run2fastqs):
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83 '''
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84 Takes files from run2fastqs and runs SeqSero.
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85 '''
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86 outputs = []
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87 for run in run2fastqs:
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88 seqsero_cmd = []
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89 if len(run2fastqs[run]) == 2:
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90 seqsero_cmd = ['python', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]]
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91 elif len(run2fastqs[run]) == 1:
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92 seqsero_cmd = ['python', seqsero, '-m', '1', '-i', run2fastqs[run][0]]
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93 p = Popen(seqsero_cmd, stdout=PIPE)
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94 output = p.communicate()
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95 outputs.append(output)
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96 return outputs
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97
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98 def get_serotypes(outputs):
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99 '''
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100 '''
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101 fastq2comment = {}
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102 fastq2serotype = {}
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103 for sample in outputs:
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104 fastqs = ''
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105 lines_used = []
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106 for line in sample: # line is actually the entire seqsero output.
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107 line = str(line)
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108 linel = re.split("\n", line)
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109 # print linel
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110 #lines_used = []
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111 for element in linel: # element is a line of seqsero output.
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112 element = element.rstrip("\n")
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113 test_out.write(element+"\n")
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114 elementl = re.split("\t", element)
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115 if elementl[0] == 'Input files:':
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116 fastqs = elementl[1]
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117 lines_used.append(element)
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118 if elementl[1] not in fastq2serotype.keys():
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119 fastq2serotype[fastqs] = ['']*5
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120 fastq2comment[fastqs] = []
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121 elif elementl[0] == 'O antigen prediction:':
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122 lines_used.append(element)
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123 fastq2serotype[fastqs][0] = elementl[1] # add predicted profile
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124 elif elementl[0] == 'H1 antigen prediction(fliC):':
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125 lines_used.append(element)
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126 fastq2serotype[fastqs][1] = elementl[1] # add predicted profile
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127 elif elementl[0] == 'H2 antigen prediction(fljB):':
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128 lines_used.append(element)
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129 fastq2serotype[fastqs][2] = elementl[1] # add predicted profile
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130 elif elementl[0] == 'Predicted antigenic profile:':
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131 lines_used.append(element)
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132 fastq2serotype[fastqs][3] = elementl[1] # add predicted profile
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133 elif elementl[0] == 'Predicted serotype(s):':
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134 lines_used.append(element)
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135 fastq2serotype[fastqs][4] = elementl[1] # add predicted serotype
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136 if element not in lines_used and re.search("\w", fastqs) and len(element) > 7:
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137 fastq2comment[fastqs].append(element)
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138 #print "\n"
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139 return fastq2serotype, fastq2comment
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140
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141 def print_html(fastq2serotype, fastq2comment):
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142 '''
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143 Takes dict and prints to html file.
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144 '''
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145 tab_out = open('Seqsero_result.txt', 'w');
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146 html_out = open('Seqsero_result.html', 'w')
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147 html_out.write('<!DOCTYPE html>\n')
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148 html_out.write('<html>\n')
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149 html_out.write('<head>\n')
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150 html_out.write('<title>SeqSero Results</title>\n')
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151 html_out.write('</head>\n')
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152 html_out.write('<body>\n')
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153 html_out.write('<body style="font-family:Helvetica;">\n')
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154 html_out.write('<p style="font-size:10px">\n')
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155 html_out.write('<table border=1>\n')
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156 header = 'Input Files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted antigenic profile\tPredicted serotype(s)'
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157 header = re.sub(' ', '_', header)
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158 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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159 html_out.write('<tr>\n')
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160 for element in header_l:
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161 html_out.write('<td>'+element+'</td>\n')
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162 html_out.write('</tr>\n')
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163 tab_out.write(header+"\n")
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164 print "\n\n", header
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165 for fastq in fastq2serotype:
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166 # print fastq, fastq2serotype[fastq]
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167 line_to_print = fastq+'\t'+"\t".join(fastq2serotype[fastq])
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168 tab_out.write(line_to_print+"\n")
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169 html_out.write('<tr>\n')
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170 html_out.write('<td>'+fastq+'</td>\n')
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171 for antigen in fastq2serotype[fastq]:
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172 html_out.write('<td>'+antigen+'</td>\n')
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173 html_out.write('</tr>\n')
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174 print line_to_print
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175 html_out.write('</table>\n')
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176 print "\n"
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177 for fastq in fastq2comment:
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178 tab_out.write("\n"+fastq+"\n")
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179 html_out.write('<tr>\n')
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180 html_out.write('<p>\n')
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181 html_out.write('<td>'+fastq+"<br></td>\n")
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182 for line in fastq2comment[fastq]:
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183 #if len(line) > 7:
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184 html_out.write('<td>'+line+'</td>\n')
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185 tab_out.write(line+"\n")
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186 print line
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187 print "\n"
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188 html_out.write('</p>\n')
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189 html_out.write('</tr>\n')
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190 html_out.write('</body>\n')
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191 html_out.write('</html>\n')
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192 html_out.close()
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193
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194 run2fastqs = list_runs(fastq_files)
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195 outputs = run_seqsero(run2fastqs)
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196 fastq2serotype, fastq2comment = get_serotypes(outputs)
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197 print_html(fastq2serotype, fastq2comment)
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198
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199 print_time()
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200
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201