Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/psortb.py @ 21:238eae32483c draft

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"Check this is up to date with all 2020 changes (black etc)"
author peterjc
date Thu, 17 Jun 2021 08:21:06 +0000
parents a19b3ded8f33
children
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1 #!/usr/bin/env python
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2 """Wrapper for psortb for use in Galaxy.
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3
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4 This script takes exactly six command line arguments - which includes the
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5 number of threads, and the input protein FASTA filename and output
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6 tabular filename. It then splits up the FASTA input and calls multiple
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7 copies of the standalone psortb v3 program, then collates the output.
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8 e.g. Rather than this,
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10 psort $type -c $cutoff -d $divergent -o long $sequence > $outfile
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12 Call this:
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14 psort $threads $type $cutoff $divergent $sequence $outfile
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16 If ommitting -c or -d options, set $cutoff and $divergent to zero or blank.
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17
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18 Note that this is somewhat redundant with job-splitting available in Galaxy
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19 itself (see the SignalP XML file for settings), but both can be applied.
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20
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21 Additionally it ensures the header line (with the column names) starts
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22 with a # character as used elsewhere in Galaxy.
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23 """
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25 from __future__ import print_function
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26
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27 import os
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28 import sys
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29 import tempfile
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31 from seq_analysis_utils import run_jobs, split_fasta, thread_count
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33 FASTA_CHUNK = 500
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34
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35 if "-v" in sys.argv or "--version" in sys.argv:
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36 """Return underlying PSORTb's version"""
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37 sys.exit(os.system("psort --version"))
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38
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39 if len(sys.argv) != 8:
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40 sys.exit(
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41 "Require 7 arguments, number of threads (int), type (e.g. archaea), "
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42 "output (e.g. terse/normal/long), cutoff, divergent, input protein "
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43 "FASTA file & output tabular file"
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44 )
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46 num_threads = thread_count(sys.argv[1], default=4)
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47 org_type = sys.argv[2]
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48 out_type = sys.argv[3]
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49 cutoff = sys.argv[4]
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50 if cutoff.strip() and float(cutoff.strip()) != 0.0:
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51 cutoff = "-c %s" % cutoff
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52 else:
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53 cutoff = ""
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54 divergent = sys.argv[5]
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55 if divergent.strip() and float(divergent.strip()) != 0.0:
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56 divergent = "-d %s" % divergent
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57 else:
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58 divergent = ""
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59 fasta_file = sys.argv[6]
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60 tabular_file = sys.argv[7]
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61
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62 if out_type == "terse":
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63 header = ["SeqID", "Localization", "Score"]
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64 elif out_type == "normal":
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65 sys.exit("Normal output not implemented yet, sorry.")
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66 elif out_type == "long":
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67 if org_type == "-n":
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68 # Gram negative bacteria
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69 header = [
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70 "SeqID",
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71 "CMSVM-_Localization",
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72 "CMSVM-_Details",
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73 "CytoSVM-_Localization",
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74 "CytoSVM-_Details",
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75 "ECSVM-_Localization",
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76 "ECSVM-_Details",
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77 "ModHMM-_Localization",
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78 "ModHMM-_Details",
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79 "Motif-_Localization",
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80 "Motif-_Details",
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81 "OMPMotif-_Localization",
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82 "OMPMotif-_Details",
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83 "OMSVM-_Localization",
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84 "OMSVM-_Details",
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85 "PPSVM-_Localization",
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86 "PPSVM-_Details",
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87 "Profile-_Localization",
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88 "Profile-_Details",
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89 "SCL-BLAST-_Localization",
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90 "SCL-BLAST-_Details",
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91 "SCL-BLASTe-_Localization",
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92 "SCL-BLASTe-_Details",
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93 "Signal-_Localization",
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94 "Signal-_Details",
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95 "Cytoplasmic_Score",
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96 "CytoplasmicMembrane_Score",
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97 "Periplasmic_Score",
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98 "OuterMembrane_Score",
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99 "Extracellular_Score",
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100 "Final_Localization",
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101 "Final_Localization_Details",
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102 "Final_Score",
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103 "Secondary_Localization",
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104 "PSortb_Version",
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105 ]
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106 elif org_type == "-p":
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107 # Gram positive bacteria
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108 header = [
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109 "SeqID",
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110 "CMSVM+_Localization",
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111 "CMSVM+_Details",
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112 "CWSVM+_Localization",
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113 "CWSVM+_Details",
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114 "CytoSVM+_Localization",
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115 "CytoSVM+_Details",
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116 "ECSVM+_Localization",
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117 "ECSVM+_Details",
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118 "ModHMM+_Localization",
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119 "ModHMM+_Details",
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120 "Motif+_Localization",
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121 "Motif+_Details",
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122 "Profile+_Localization",
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123 "Profile+_Details",
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124 "SCL-BLAST+_Localization",
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125 "SCL-BLAST+_Details",
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126 "SCL-BLASTe+_Localization",
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127 "SCL-BLASTe+_Details",
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128 "Signal+_Localization",
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129 "Signal+_Details",
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130 "Cytoplasmic_Score",
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131 "CytoplasmicMembrane_Score",
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132 "Cellwall_Score",
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133 "Extracellular_Score",
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134 "Final_Localization",
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135 "Final_Localization_Details",
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136 "Final_Score",
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137 "Secondary_Localization",
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138 "PSortb_Version",
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139 ]
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140 elif org_type == "-a":
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141 # Archaea
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142 header = [
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143 "SeqID",
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144 "CMSVM_a_Localization",
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145 "CMSVM_a_Details",
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146 "CWSVM_a_Localization",
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147 "CWSVM_a_Details",
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148 "CytoSVM_a_Localization",
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149 "CytoSVM_a_Details",
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150 "ECSVM_a_Localization",
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151 "ECSVM_a_Details",
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152 "ModHMM_a_Localization",
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153 "ModHMM_a_Details",
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154 "Motif_a_Localization",
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155 "Motif_a_Details",
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156 "Profile_a_Localization",
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157 "Profile_a_Details",
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158 "SCL-BLAST_a_Localization",
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159 "SCL-BLAST_a_Details",
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160 "SCL-BLASTe_a_Localization",
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161 "SCL-BLASTe_a_Details",
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162 "Signal_a_Localization",
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163 "Signal_a_Details",
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164 "Cytoplasmic_Score",
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165 "CytoplasmicMembrane_Score",
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166 "Cellwall_Score",
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167 "Extracellular_Score",
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168 "Final_Localization",
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169 "Final_Localization_Details",
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170 "Final_Score",
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171 "Secondary_Localization",
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172 "PSortb_Version",
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173 ]
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174 else:
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175 sys.exit("Expected -n, -p or -a for the organism type, not %r" % org_type)
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176 else:
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177 sys.exit("Expected terse, normal or long for the output type, not %r" % out_type)
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178
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179 tmp_dir = tempfile.mkdtemp()
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180
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181
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182 def clean_tabular(raw_handle, out_handle):
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183 """Clean up tabular TMHMM output, returns output line count."""
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184 global header
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185 count = 0
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186 for line in raw_handle:
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187 if not line.strip() or line.startswith("#"):
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188 # Ignore any blank lines or comment lines
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189 continue
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190 parts = [x.strip() for x in line.rstrip("\r\n").split("\t")]
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191 if parts == header:
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192 # Ignore the header line
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193 continue
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194 if not parts[-1] and len(parts) == len(header) + 1:
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195 # Ignore dummy blank extra column, e.g.
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196 # "...2.0\t\tPSORTb version 3.0\t\n"
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197 parts = parts[:-1]
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198 assert len(parts) == len(header), "%i fields, not %i, in line:\n%r" % (
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199 len(line),
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200 len(header),
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201 line,
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202 )
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203 out_handle.write(line)
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204 count += 1
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205 return count
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206
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207
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208 # Note that if the input FASTA file contains no sequences,
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209 # split_fasta returns an empty list (i.e. zero temp files).
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210 fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "tmhmm"), FASTA_CHUNK)
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211 temp_files = [f + ".out" for f in fasta_files]
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212 jobs = [
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213 "psort %s %s %s -o %s %s > %s"
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214 % (org_type, cutoff, divergent, out_type, fasta, temp)
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215 for fasta, temp in zip(fasta_files, temp_files)
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216 ]
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217
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218
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219 def clean_up(file_list):
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220 for f in file_list:
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221 if os.path.isfile(f):
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222 os.remove(f)
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223 try:
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224 os.rmdir(tmp_dir)
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225 except Exception:
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226 pass
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227
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228
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229 if len(jobs) > 1 and num_threads > 1:
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230 # A small "info" message for Galaxy to show the user.
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231 print("Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs)))
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232 results = run_jobs(jobs, num_threads)
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233 for fasta, temp, cmd in zip(fasta_files, temp_files, jobs):
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234 error_level = results[cmd]
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235 if error_level:
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236 try:
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237 output = open(temp).readline()
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238 except IOError:
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239 output = ""
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240 clean_up(fasta_files + temp_files)
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241 sys.exit(
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242 "One or more tasks failed, e.g. %i from %r gave:\n%s"
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243 % (error_level, cmd, output),
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244 error_level,
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245 )
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246 del results
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247 del jobs
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248
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249 out_handle = open(tabular_file, "w")
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250 out_handle.write("#%s\n" % "\t".join(header))
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251 count = 0
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252 for temp in temp_files:
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253 data_handle = open(temp)
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254 count += clean_tabular(data_handle, out_handle)
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255 data_handle.close()
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256 if not count:
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257 clean_up(fasta_files + temp_files)
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258 sys.exit("No output from psortb")
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259 out_handle.close()
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260 print("%i records" % count)
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261
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262 clean_up(fasta_files + temp_files)