Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/psortb.py @ 17:e6cc27d182a8 draft

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Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
author peterjc
date Fri, 21 Nov 2014 08:19:09 -0500
parents 99b82a2b1272
children eb6ac44d4b8e
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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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9
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10 psort $type -c $cutoff -d $divergent -o long $sequence > $outfile
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11
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12 Call this:
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13
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14 psort $threads $type $cutoff $divergent $sequence $outfile
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15
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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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24 import sys
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25 import os
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26 import tempfile
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27 from seq_analysis_utils import stop_err, split_fasta, run_jobs, thread_count
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28
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29 FASTA_CHUNK = 500
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30
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31 if "-v" in sys.argv or "--version" in sys.argv:
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32 """Return underlying PSORTb's version"""
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33 sys.exit(os.system("psort --version"))
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34
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35 if len(sys.argv) != 8:
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36 stop_err("Require 7 arguments, number of threads (int), type (e.g. archaea), "
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37 "output (e.g. terse/normal/long), cutoff, divergent, input protein "
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38 "FASTA file & output tabular file")
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39
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40 num_threads = thread_count(sys.argv[1], default=4)
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41 org_type = sys.argv[2]
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42 out_type = sys.argv[3]
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43 cutoff = sys.argv[4]
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44 if cutoff.strip() and float(cutoff.strip()) != 0.0:
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45 cutoff = "-c %s" % cutoff
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46 else:
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47 cutoff = ""
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48 divergent = sys.argv[5]
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49 if divergent.strip() and float(divergent.strip()) != 0.0:
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50 divergent = "-d %s" % divergent
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51 else:
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52 divergent = ""
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53 fasta_file = sys.argv[6]
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54 tabular_file = sys.argv[7]
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55
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56 if out_type == "terse":
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57 header = ['SeqID', 'Localization', 'Score']
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58 elif out_type == "normal":
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59 stop_err("Normal output not implemented yet, sorry.")
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60 elif out_type == "long":
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61 if org_type == "-n":
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62 #Gram negative bacteria
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63 header = ['SeqID', 'CMSVM-_Localization', 'CMSVM-_Details', 'CytoSVM-_Localization', 'CytoSVM-_Details',
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64 'ECSVM-_Localization', 'ECSVM-_Details', 'ModHMM-_Localization', 'ModHMM-_Details',
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65 'Motif-_Localization', 'Motif-_Details', 'OMPMotif-_Localization', 'OMPMotif-_Details',
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66 'OMSVM-_Localization', 'OMSVM-_Details', 'PPSVM-_Localization', 'PPSVM-_Details',
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67 'Profile-_Localization', 'Profile-_Details',
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68 'SCL-BLAST-_Localization', 'SCL-BLAST-_Details', 'SCL-BLASTe-_Localization', 'SCL-BLASTe-_Details',
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69 'Signal-_Localization', 'Signal-_Details',
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70 'Cytoplasmic_Score', 'CytoplasmicMembrane_Score', 'Periplasmic_Score', 'OuterMembrane_Score',
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71 'Extracellular_Score', 'Final_Localization', 'Final_Localization_Details', 'Final_Score',
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72 'Secondary_Localization', 'PSortb_Version']
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73 elif org_type == "-p":
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74 #Gram positive bacteria
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75 header = ['SeqID', 'CMSVM+_Localization', 'CMSVM+_Details', 'CWSVM+_Localization', 'CWSVM+_Details',
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76 'CytoSVM+_Localization', 'CytoSVM+_Details', 'ECSVM+_Localization', 'ECSVM+_Details',
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77 'ModHMM+_Localization', 'ModHMM+_Details', 'Motif+_Localization', 'Motif+_Details',
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78 'Profile+_Localization', 'Profile+_Details',
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79 'SCL-BLAST+_Localization', 'SCL-BLAST+_Details', 'SCL-BLASTe+_Localization', 'SCL-BLASTe+_Details',
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80 'Signal+_Localization', 'Signal+_Details',
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81 'Cytoplasmic_Score', 'CytoplasmicMembrane_Score', 'Cellwall_Score',
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82 'Extracellular_Score', 'Final_Localization', 'Final_Localization_Details', 'Final_Score',
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83 'Secondary_Localization', 'PSortb_Version']
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84 elif org_type == "-a":
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85 #Archaea
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86 header = ['SeqID', 'CMSVM_a_Localization', 'CMSVM_a_Details', 'CWSVM_a_Localization', 'CWSVM_a_Details',
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87 'CytoSVM_a_Localization', 'CytoSVM_a_Details', 'ECSVM_a_Localization', 'ECSVM_a_Details',
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88 'ModHMM_a_Localization', 'ModHMM_a_Details', 'Motif_a_Localization', 'Motif_a_Details',
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89 'Profile_a_Localization', 'Profile_a_Details',
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90 'SCL-BLAST_a_Localization', 'SCL-BLAST_a_Details', 'SCL-BLASTe_a_Localization', 'SCL-BLASTe_a_Details',
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91 'Signal_a_Localization', 'Signal_a_Details',
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92 'Cytoplasmic_Score', 'CytoplasmicMembrane_Score', 'Cellwall_Score',
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93 'Extracellular_Score', 'Final_Localization', 'Final_Localization_Details', 'Final_Score',
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94 'Secondary_Localization', 'PSortb_Version']
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95 else:
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96 stop_err("Expected -n, -p or -a for the organism type, not %r" % org_type)
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97 else:
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98 stop_err("Expected terse, normal or long for the output type, not %r" % out_type)
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99
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100 tmp_dir = tempfile.mkdtemp()
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101
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102 def clean_tabular(raw_handle, out_handle):
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103 """Clean up tabular TMHMM output, returns output line count."""
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104 global header
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105 count = 0
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106 for line in raw_handle:
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107 if not line.strip() or line.startswith("#"):
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108 #Ignore any blank lines or comment lines
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109 continue
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110 parts = [x.strip() for x in line.rstrip("\r\n").split("\t")]
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111 if parts == header:
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112 #Ignore the header line
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113 continue
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114 if not parts[-1] and len(parts) == len(header) + 1:
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115 #Ignore dummy blank extra column, e.g.
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116 #"...2.0\t\tPSORTb version 3.0\t\n"
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117 parts = parts[:-1]
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118 assert len(parts) == len(header), \
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119 "%i fields, not %i, in line:\n%r" % (len(line), len(header), line)
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120 out_handle.write(line)
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121 count += 1
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122 return count
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123
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124 #Note that if the input FASTA file contains no sequences,
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125 #split_fasta returns an empty list (i.e. zero temp files).
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126 fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "tmhmm"), FASTA_CHUNK)
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127 temp_files = [f+".out" for f in fasta_files]
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128 jobs = ["psort %s %s %s -o %s %s > %s" % (org_type, cutoff, divergent, out_type, fasta, temp)
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129 for fasta, temp in zip(fasta_files, temp_files)]
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130
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131 def clean_up(file_list):
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132 for f in file_list:
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133 if os.path.isfile(f):
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134 os.remove(f)
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135 try:
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136 os.rmdir(tmp_dir)
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137 except:
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138 pass
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139
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140 if len(jobs) > 1 and num_threads > 1:
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141 #A small "info" message for Galaxy to show the user.
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142 print "Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs))
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143 results = run_jobs(jobs, num_threads)
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144 for fasta, temp, cmd in zip(fasta_files, temp_files, jobs):
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145 error_level = results[cmd]
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146 if error_level:
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147 try:
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148 output = open(temp).readline()
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149 except IOError:
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150 output = ""
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151 clean_up(fasta_files + temp_files)
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152 stop_err("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
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153 error_level)
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154 del results
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155 del jobs
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156
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157 out_handle = open(tabular_file, "w")
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158 out_handle.write("#%s\n" % "\t".join(header))
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159 count = 0
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160 for temp in temp_files:
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161 data_handle = open(temp)
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162 count += clean_tabular(data_handle, out_handle)
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163 data_handle.close()
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164 if not count:
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165 clean_up(fasta_files + temp_files)
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166 stop_err("No output from psortb")
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167 out_handle.close()
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168 print "%i records" % count
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169
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170 clean_up(fasta_files + temp_files)