Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/promoter2.py @ 20:a19b3ded8f33 draft

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v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
author peterjc
date Thu, 21 Sep 2017 11:35:20 -0400
parents f3ecd80850e2
children 238eae32483c
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9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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1 #!/usr/bin/env python
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2 """Wrapper for Promoter 2.0 for use in Galaxy.
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3
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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4 This script takes exactly three command line arguments:
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5 * number of threads
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6 * an input DNA FASTA filename
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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7 * output tabular filename.
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8
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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9 It calls the Promoter 2.0 binary (e.g. .../promoter-2.0/bin/promoter_Linux,
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10 bypassing the Perl wrapper script 'promoter' which imposes a significant
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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11 performace overhead for no benefit here (we don't need HTML output for
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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12 example).
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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13
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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14 The main feature is this Python wrapper script parsers the bespoke
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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15 tabular output from Promoter 2.0 and reformats it into a Galaxy friendly
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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16 tab separated table.
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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18 Additionally, in order to take advantage of multiple cores the input FASTA
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19 file is broken into chunks and multiple copies of promoter run at once.
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20 This can be used in combination with the job-splitting available in Galaxy.
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21 Note that rewriting the FASTA input file allows us to avoid a bug in
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22 promoter 2 with long descriptions in the FASTA header line (over 200
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23 characters) which produces stray fragements of the description in the
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24 output file, making parsing non-trivial.
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9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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26 TODO - Automatically extract the sequence containing a promoter prediction?
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27 """
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29 from __future__ import print_function
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30
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31 import commands
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32 import os
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33 import sys
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34 import tempfile
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36 from seq_analysis_utils import run_jobs, split_fasta, thread_count
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9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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37
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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38 FASTA_CHUNK = 500
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39
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eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
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40 if "-v" in sys.argv or "--version" in sys.argv:
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
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41 sys.exit(os.system("promoter -V"))
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42
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43 if len(sys.argv) != 4:
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44 sys.exit("Require three arguments, number of threads (int), input DNA FASTA file & output tabular file. "
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45 "Got %i arguments." % (len(sys.argv) - 1))
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46
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47 num_threads = thread_count(sys.argv[3], default=4)
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48 fasta_file = os.path.abspath(sys.argv[2])
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49 tabular_file = os.path.abspath(sys.argv[3])
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51 tmp_dir = tempfile.mkdtemp()
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52
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53
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54 def get_path_and_binary():
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55 """Determine path and binary names for promoter tool."""
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56 platform = commands.getoutput("uname") # e.g. Linux
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57 shell_script = commands.getoutput("which promoter")
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58 if not os.path.isfile(shell_script):
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59 sys.exit("ERROR: Missing promoter executable shell script")
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60 path = None
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61 for line in open(shell_script):
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62 if line.startswith("setenv"): # could then be tab or space!
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63 parts = line.rstrip().split(None, 2)
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64 if parts[0] == "setenv" and parts[1] == "PROM":
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65 path = parts[2]
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66 if not path:
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67 sys.exit("ERROR: Could not find promoter path (PROM) in %r" % shell_script)
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68 if not os.path.isdir(path):
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69 sys.exit("ERROR: %r is not a directory" % path)
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70 bin = "%s/bin/promoter_%s" % (path, platform)
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71 if not os.path.isfile(bin):
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72 sys.exit("ERROR: Missing promoter binary %r" % bin)
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73 return path, bin
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74
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75
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76 def make_tabular(raw_handle, out_handle):
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77 """Parse text output into tabular, return query count."""
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78 identifier = None
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79 queries = 0
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80 for line in raw_handle:
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81 # print(repr(line))
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82 if not line.strip() or line == "Promoter prediction:\n":
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83 pass
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84 elif line[0] != " ":
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85 identifier = line.strip().replace("\t", " ").split(None, 1)[0]
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86 queries += 1
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87 elif line == " No promoter predicted\n":
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88 # End of a record
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89 identifier = None
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90 elif line == " Position Score Likelihood\n":
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91 assert identifier
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92 else:
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93 try:
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94 position, score, likelihood = line.strip().split(None, 2)
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95 except ValueError:
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96 print("WARNING: Problem with line: %r" % line)
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97 continue
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98 # sys.exit("ERROR: Problem with line: %r" % line)
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99 if likelihood not in ["ignored",
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100 "Marginal prediction",
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101 "Medium likely prediction",
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102 "Highly likely prediction"]:
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103 sys.exit("ERROR: Problem with line: %r" % line)
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104 out_handle.write("%s\t%s\t%s\t%s\n" % (identifier, position, score, likelihood))
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105 return queries
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106
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107
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108 working_dir, bin = get_path_and_binary()
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109
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110 if not os.path.isfile(fasta_file):
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111 sys.exit("ERROR: Missing input FASTA file %r" % fasta_file)
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112
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113 # Note that if the input FASTA file contains no sequences,
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114 # split_fasta returns an empty list (i.e. zero temp files).
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115 # We deliberately omit the FASTA descriptions to avoid a
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116 # bug in promoter2 with descriptions over 200 characters.
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117 fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "promoter"), FASTA_CHUNK, keep_descr=False)
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118 temp_files = [f + ".out" for f in fasta_files]
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119 jobs = ["%s %s > %s" % (bin, fasta, temp)
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120 for fasta, temp in zip(fasta_files, temp_files)]
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121
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122
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123 def clean_up(file_list):
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124 for f in file_list:
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125 if os.path.isfile(f):
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126 os.remove(f)
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127 try:
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128 os.rmdir(tmp_dir)
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129 except Exception:
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130 pass
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131
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132
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133 if len(jobs) > 1 and num_threads > 1:
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134 # A small "info" message for Galaxy to show the user.
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135 print("Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs)))
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136 cur_dir = os.path.abspath(os.curdir)
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137 os.chdir(working_dir)
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138 results = run_jobs(jobs, num_threads)
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139 os.chdir(cur_dir)
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140 for fasta, temp, cmd in zip(fasta_files, temp_files, jobs):
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141 error_level = results[cmd]
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142 if error_level:
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143 try:
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144 output = open(temp).readline()
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145 except IOError:
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146 output = ""
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147 clean_up(fasta_files + temp_files)
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148 sys.exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
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149 error_level)
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150
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151 del results
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152 del jobs
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153
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154 out_handle = open(tabular_file, "w")
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155 out_handle.write("#Identifier\tPosition\tScore\tLikelihood\n")
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156 queries = 0
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157 for temp in temp_files:
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158 data_handle = open(temp)
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159 count = make_tabular(data_handle, out_handle)
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160 data_handle.close()
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161 if not count:
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162 clean_up(fasta_files + temp_files)
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163 sys.exit("No output from promoter2")
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164 queries += count
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165 out_handle.close()
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166
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167 clean_up(fasta_files + temp_files)
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168 print("Results for %i queries" % queries)