Mercurial > repos > yating-l > jbrowsearchivecreator

annotate util/subtools.py @ 6:237707a6b74d draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
author yating-l
date Thu, 15 Feb 2018 17:05:05 -0500
parents
children 5d5fdcb798da
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6
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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1 #!/usr/bin/env python
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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2
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3 """
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4 This file include common used functions for converting file format to gff3
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5 """
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6 from collections import OrderedDict
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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7 import json
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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8 import subprocess
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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9 import os
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10 import sys
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11 import tempfile
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12 import string
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13 import logging
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14
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15 class PopenError(Exception):
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16 def __init__(self, cmd, error, return_code):
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17 self.cmd = cmd
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18 self.error = error
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19 self.return_code = return_code
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21 def __str__(self):
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22 message = "The subprocess {0} has returned the error: {1}.".format(
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23 self.cmd, self.return_code)
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24 message = ','.join(
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25 (message, "Its error message is: {0}".format(self.error)))
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26 return repr(message)
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27
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29 def _handleExceptionAndCheckCall(array_call, **kwargs):
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30 """
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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31 This class handle exceptions and call the tool.
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32 It maps the signature of subprocess.check_call:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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33 See https://docs.python.org/2/library/subprocess.html#subprocess.check_call
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34 """
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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35 stdout = kwargs.get('stdout', subprocess.PIPE)
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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36 stderr = kwargs.get('stderr', subprocess.PIPE)
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37 shell = kwargs.get('shell', False)
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38 stdin = kwargs.get('stdin', None)
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39
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40 cmd = array_call[0]
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41
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42 output = None
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43 error = None
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44
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45 # TODO: Check the value of array_call and <=[0]
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46 logging.debug("Calling {0}:".format(cmd))
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47 logging.debug("%s", array_call)
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48 logging.debug("---------")
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49
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50 # TODO: Use universal_newlines option from Popen?
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51 try:
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52 p = subprocess.Popen(array_call, stdout=stdout,
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53 stderr=stderr, shell=shell, stdin=stdin)
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54
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55 # TODO: Change this because of possible memory issues => https://docs.python.org/2/library/subprocess.html#subprocess.Popen.communicate
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56
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57 output, error = p.communicate()
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58
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59 if stdout == subprocess.PIPE:
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60 logging.debug("\t{0}".format(output))
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61 else:
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62 logging.debug("\tOutput in file {0}".format(stdout.name))
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63 # If we detect an error from the subprocess, then we raise an exception
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64 # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process
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65 # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.
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66 if p.returncode:
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67 if stderr == subprocess.PIPE:
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68 raise PopenError(cmd, error, p.returncode)
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69 else:
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70 # TODO: To Handle properly with a design behind, if we received a option as a file for the error
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71 raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}"
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72 .format(cmd, stderr.name, p.returncode))
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73
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74 except OSError as e:
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75 message = "The subprocess {0} has encountered an OSError: {1}".format(
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76 cmd, e.strerror)
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77 if e.filename:
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78 message = '\n'.join(
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79 (message, ", against this file: {0}".format(e.filename)))
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80 logging.error(message)
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81 sys.exit(-1)
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82 except PopenError as p:
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83 message = "The subprocess {0} has returned the error: {1}.".format(
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84 p.cmd, p.return_code)
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85 message = '\n'.join(
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86 (message, "Its error message is: {0}".format(p.error)))
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87
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88 logging.exception(message)
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89
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90 sys.exit(p.return_code)
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91 except Exception as e:
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92 message = "The subprocess {0} has encountered an unknown error: {1}".format(
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93 cmd, e)
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94 logging.exception(message)
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95
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96 sys.exit(-1)
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97 return p
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98
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99
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100 def write_features(field, attribute, gff3):
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101 """
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102 The function write the features to gff3 format (defined in https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)
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103 field, attribute are ordered dictionary
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104 gff3 is the file handler
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105 """
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106 attr = []
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107 for v in field.values():
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108 gff3.write(str(v) + '\t')
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109 for k, v in attribute.items():
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110 s = str(k) + '=' + str(v)
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111 attr.append(s)
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112 gff3.write(';'.join(attr))
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113 gff3.write('\n')
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114
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115 def twoBitInfo(two_bit_file_name, two_bit_info_file):
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116 """
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117 Call twoBitInfo and write the result into twoBit_info_file
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118 :param two_bit_file_name:
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119 :param two_bit_info_file:
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120 :return the subprocess.check_call return object:
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121 """
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122 array_call = ['twoBitInfo', two_bit_file_name, two_bit_info_file]
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123 p = _handleExceptionAndCheckCall(array_call)
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124 return p
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125
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126
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127 def faToTwoBit(fasta_file_name, twoBitFile):
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128 """
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129 This function call faToTwoBit UCSC tool, and return the twoBitFile
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130 :param fasta_file_name:
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131 :param mySpecieFolder:
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132 :return:
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133 """
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134
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135 array_call = ['faToTwoBit', fasta_file_name, twoBitFile]
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136 _handleExceptionAndCheckCall(array_call)
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137
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138 return twoBitFile
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139
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140 def sortChromSizes(two_bit_info_file_name, chrom_sizes_file_name):
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141 """
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142 Call sort with -k2rn on two_bit_info_file_name and write the result into chrom_sizes_file_name
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143 :param two_bit_info_file_name:
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144 :param chrom_sizes_file_name:
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145 :return:
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146 """
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147 array_call = ['sort', '-k2rn', two_bit_info_file_name,
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148 '-o', chrom_sizes_file_name]
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149 p = _handleExceptionAndCheckCall(array_call)
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150 return p
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151
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152 def getChromSizes(reference, tool_dir):
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153 #TODO: find a better way instead of shipping the two exec files with the tool
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154 faToTwoBit = os.path.join(tool_dir, 'faToTwoBit')
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155 twoBitInfo = os.path.join(tool_dir, 'twoBitInfo')
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156 try:
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157 twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
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158 chrom_sizes = tempfile.NamedTemporaryFile(bufsize=0, suffix='.chrom.sizes', delete=False)
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159 except IOError as err:
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160 print "Cannot create tempfile err({0}): {1}".format(err.errno, err.strerror)
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161 try:
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162 subprocess.call(['faToTwoBit', reference, twoBitFile.name])
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163 except OSError as err:
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164 print "Cannot generate twoBitFile from faToTwoBit err({0}): {1}".format(err.errno, err.strerror)
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165 try:
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166 subprocess.call(['twoBitInfo', twoBitFile.name, chrom_sizes.name])
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167 except OSError as err:
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168 print "Cannot generate chrom_sizes from twoBitInfo err({0}): {1}".format(err.errno, err.strerror)
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169 return chrom_sizes
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170
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171 def sequence_region(chrom_sizes):
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172 """
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173 This function read from a chromatin size file generated by twoBitInfo and write the information to dict
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174 return a dict
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175 """
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176 f = open(chrom_sizes, 'r')
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177 sizes = f.readlines()
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178 sizes_dict = {}
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179 for line in sizes:
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180 chrom_info = line.rstrip().split('\t')
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181 sizes_dict[chrom_info[0]] = chrom_info[1]
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182 return sizes_dict
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183
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184 def child_blocks(parent_field, parent_attr, gff3, child_type):
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185 num = 0
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186 blockcount = int(parent_attr['blockcount'])
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187 chromstart = parent_attr['chromstarts'].split(',')
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188 blocksize = parent_attr['blocksizes'].split(',')
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189 parent_start = parent_field['start']
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yating-l
parents:
diff changeset
190 while num < blockcount:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
191 child_attr = OrderedDict()
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yating-l
parents:
diff changeset
192 child_field = parent_field
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yating-l
parents:
diff changeset
193 child_field['type'] = child_type
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yating-l
parents:
diff changeset
194 child_field['start'] = int(chromstart[num]) + int(parent_start)
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
195 child_field['end'] = int(child_field['start']) + int(blocksize[num]) - 1
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
196 child_attr['ID'] = parent_attr['ID'] + '_part_' + str(num+1)
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
197 child_attr['Parent'] = parent_attr['ID']
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yating-l
parents:
diff changeset
198 write_features(child_field, child_attr, gff3)
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yating-l
parents:
diff changeset
199 num = num + 1
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yating-l
parents:
diff changeset
200
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
201 def add_tracks_to_json(trackList_json, new_tracks, modify_type):
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yating-l
parents:
diff changeset
202 """
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
203 Add to track configuration (trackList.json)
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
204 # modify_type = 'add_tracks': add a new track like bam or bigwig, new_track = dict()
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
205 # modify_type = 'add_attr': add configuration to the existing track, new_track = dict(track_name: dict())
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yating-l
parents:
diff changeset
206 """
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yating-l
parents:
diff changeset
207 with open(trackList_json, 'r+') as f:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
208 data = json.load(f)
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yating-l
parents:
diff changeset
209 if modify_type == 'add_tracks':
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yating-l
parents:
diff changeset
210 data['tracks'].append(new_tracks)
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yating-l
parents:
diff changeset
211 elif modify_type == 'add_attr':
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yating-l
parents:
diff changeset
212 for k in new_tracks:
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yating-l
parents:
diff changeset
213 for track in data['tracks']:
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yating-l
parents:
diff changeset
214 if k.lower() in track['urlTemplate'].lower():
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yating-l
parents:
diff changeset
215 attr = new_tracks[k]
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yating-l
parents:
diff changeset
216 for k, v in attr.items():
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yating-l
parents:
diff changeset
217 track[k] = v
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yating-l
parents:
diff changeset
218 f.seek(0, 0)
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yating-l
parents:
diff changeset
219 f.write(json.dumps(data, separators=(',' , ':'), indent=4))
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yating-l
parents:
diff changeset
220 f.truncate()
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
221 f.close()
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yating-l
parents:
diff changeset
222
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yating-l
parents:
diff changeset
223
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yating-l
parents:
diff changeset
224 def createBamIndex(bamfile):
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yating-l
parents:
diff changeset
225 subprocess.call(['samtools', 'index', bamfile])
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yating-l
parents:
diff changeset
226 filename = bamfile + '.bai'
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yating-l
parents:
diff changeset
227 if os.path.exists(filename):
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yating-l
parents:
diff changeset
228 return filename
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yating-l
parents:
diff changeset
229 else:
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yating-l
parents:
diff changeset
230 raise ValueError('Did not find bai file')
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yating-l
parents:
diff changeset
231
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yating-l
parents:
diff changeset
232 def flatfile_to_json(inputFile, dataType, trackType, trackLabel, outputFolder, options=None, compress=True):
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yating-l
parents:
diff changeset
233 if "bed" in dataType:
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yating-l
parents:
diff changeset
234 fileType = "--bed"
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yating-l
parents:
diff changeset
235 elif "gff" in dataType:
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yating-l
parents:
diff changeset
236 fileType = "--gff"
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yating-l
parents:
diff changeset
237 else:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
238 raise ValueError("%s is not a valid filetype for flatfile_to_json" % dataType)
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yating-l
parents:
diff changeset
239
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yating-l
parents:
diff changeset
240
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yating-l
parents:
diff changeset
241 array_call = ['flatfile-to-json.pl',
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
242 fileType, inputFile,
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yating-l
parents:
diff changeset
243 '--trackType', trackType,
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yating-l
parents:
diff changeset
244 '--trackLabel', trackLabel,
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yating-l
parents:
diff changeset
245 '--out', outputFolder]
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yating-l
parents:
diff changeset
246 if compress:
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yating-l
parents:
diff changeset
247 array_call.append('--compress')
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yating-l
parents:
diff changeset
248 if options:
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yating-l
parents:
diff changeset
249 config = options.get("config")
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yating-l
parents:
diff changeset
250 clientConfig = options.get("clientConfig")
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yating-l
parents:
diff changeset
251 renderClassName = options.get('renderClassName')
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yating-l
parents:
diff changeset
252 subfeatureClasses = options.get('subfeatureClasses')
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yating-l
parents:
diff changeset
253 load_type = options.get("type")
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yating-l
parents:
diff changeset
254 if clientConfig:
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yating-l
parents:
diff changeset
255 array_call.append('--clientConfig')
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
256 array_call.append(clientConfig)
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yating-l
parents:
diff changeset
257 if config:
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yating-l
parents:
diff changeset
258 array_call.append('--config')
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yating-l
parents:
diff changeset
259 array_call.append(config)
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yating-l
parents:
diff changeset
260 if load_type:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
261 array_call.append('--type')
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
262 array_call.append(load_type)
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yating-l
parents:
diff changeset
263 if renderClassName:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
264 array_call.append('--renderClassName')
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
265 array_call.append(renderClassName)
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yating-l
parents:
diff changeset
266 if subfeatureClasses:
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yating-l
parents:
diff changeset
267 array_call.append('--subfeatureClasses')
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
parents:
diff changeset
268 array_call.append(json.dumps(subfeatureClasses))
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yating-l
parents:
diff changeset
269
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yating-l
parents:
diff changeset
270 p = _handleExceptionAndCheckCall(array_call)
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yating-l
parents:
diff changeset
271 return p
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yating-l
parents:
diff changeset
272
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yating-l
parents:
diff changeset
273 def bam_to_json(inputFile, trackLabel, outputFolder, options=None, compress=False):
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yating-l
parents:
diff changeset
274
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yating-l
parents:
diff changeset
275 array_call = ['bam-to-json.pl',
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yating-l
parents:
diff changeset
276 '--bam', inputFile,
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yating-l
parents:
diff changeset
277 '--trackLabel', trackLabel,
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yating-l
parents:
diff changeset
278 '--out', outputFolder]
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yating-l
parents:
diff changeset
279 if compress:
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yating-l
parents:
diff changeset
280 array_call.append('--compress')
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yating-l
parents:
diff changeset
281 if options:
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yating-l
parents:
diff changeset
282 config = options.get('config')
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yating-l
parents:
diff changeset
283 clientConfig = options.get('clientConfig')
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yating-l
parents:
diff changeset
284 if clientConfig:
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yating-l
parents:
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285 array_call.append('--clientConfig')
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286 array_call.append(clientConfig)
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287 if config:
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288 array_call.append('--config')
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289 array_call.append(config)
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290
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291 p = _handleExceptionAndCheckCall(array_call)
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292 return p
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293
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294 def add_track_json(trackList, track_json):
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295 track_json = json.dumps(track_json)
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296 new_track = subprocess.Popen(['echo', track_json], stdout=subprocess.PIPE)
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297 p = subprocess.call(['add-track-json.pl', trackList], stdin=new_track.stdout)
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298 return p
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299
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300 def prepare_refseqs(fasta_file_name, outputFolder):
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301 array_call = ['prepare-refseqs.pl', '--fasta', fasta_file_name, '--out', outputFolder]
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302 p = _handleExceptionAndCheckCall(array_call)
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303 return p
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304
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305 def generate_names(outputFolder):
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306 array_call = ['generate-names.pl', '-v', '--out', outputFolder]
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307 p = _handleExceptionAndCheckCall(array_call)
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308 return p
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309
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310 def validateFiles(input_file, chrom_sizes_file_name, file_type, options=None):
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311 """
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312 Call validateFiles on input_file, using chrom_sizes_file_name and file_type
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313 :param input_file:
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314 :param chrom_sizes_file_name:
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315 :param file_type:
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316 :return:
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317 """
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318
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319 array_call = ['validateFiles', '-chromInfo=' + chrom_sizes_file_name, '-type='+ file_type, input_file]
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320 if options:
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321 tab = options.get("tab")
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322 autoSql = options.get("autoSql")
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323 logging.debug("tab: {0}".format(tab))
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324 logging.debug("autoSql: {0}".format(autoSql))
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325 if autoSql:
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326 autoSql = ''.join(['-as=', autoSql])
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327 array_call.append(autoSql)
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328 if tab:
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329 array_call.append('-tab')
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330 p = _handleExceptionAndCheckCall(array_call)
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331 return p
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332