Mercurial > repos > yating-l > jbrowsearchivecreator

annotate util/subtools.py @ 38:d17f629f5486 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
author yating-l
date Fri, 06 Apr 2018 13:44:56 -0400
parents 68466f5064ce
children 4a69515eed63
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1 #!/usr/bin/env python
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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
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7 import json
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8 import subprocess
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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 shutil
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13 import logging
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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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29 def _handleExceptionAndCheckCall(array_call, **kwargs):
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30 """
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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:
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33 See https://docs.python.org/2/library/subprocess.html#subprocess.check_call
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34 """
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35 stdout = kwargs.get('stdout', subprocess.PIPE)
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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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40 cmd = array_call[0]
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42 output = None
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43 error = None
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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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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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55 # TODO: Change this because of possible memory issues => https://docs.python.org/2/library/subprocess.html#subprocess.Popen.communicate
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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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190 while num < blockcount:
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191 child_attr = OrderedDict()
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192 child_field = parent_field
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193 child_field['type'] = child_type
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194 child_field['start'] = int(chromstart[num]) + int(parent_start)
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195 child_field['end'] = int(child_field['start']) + int(blocksize[num]) - 1
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196 child_attr['ID'] = parent_attr['ID'] + '_part_' + str(num+1)
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197 child_attr['Parent'] = parent_attr['ID']
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198 write_features(child_field, child_attr, gff3)
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199 num = num + 1
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200
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201 def add_tracks_to_json(trackList_json, new_tracks, modify_type):
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202 """
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203 Add to track configuration (trackList.json)
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204 # modify_type = 'add_tracks': add a new track like bam or bigwig, new_track = dict()
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205 # modify_type = 'add_attr': add configuration to the existing track, new_track = dict(track_name: dict())
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206 """
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207 with open(trackList_json, 'r+') as f:
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208 data = json.load(f)
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209 if modify_type == 'add_tracks':
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210 data['tracks'].append(new_tracks)
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211 elif modify_type == 'add_attr':
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212 for k in new_tracks:
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213 for track in data['tracks']:
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214 if k.lower() in track['urlTemplate'].lower():
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215 attr = new_tracks[k]
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216 for k, v in attr.items():
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217 track[k] = v
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218 f.seek(0, 0)
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219 f.write(json.dumps(data, separators=(',' , ':'), indent=4))
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220 f.truncate()
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221 f.close()
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222
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223
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224 def createBamIndex(bamfile):
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225 subprocess.call(['samtools', 'index', bamfile])
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226 filename = bamfile + '.bai'
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227 if os.path.exists(filename):
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228 return filename
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229 else:
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230 raise ValueError('Did not find bai file')
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231
38
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232 def createFastaIndex(fastaFile):
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233 subprocess.call(['samtools', 'faidx', fastaFile])
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234 filename = fastaFile + '.fai'
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235 if os.path.exists(filename):
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236 return filename
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237 else:
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238 raise ValueError('Did not find fai file')
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239
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240 def gff3sort(inputFile, outputFile, precise=False):
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241 array_call = ['gff3sort.pl', inputFile, '>', outputFile]
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diff changeset
242 if precise:
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diff changeset
243 array_call.append('--precise')
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244 p = _handleExceptionAndCheckCall(array_call)
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diff changeset
245 return p
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diff changeset
246
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247 def bedSort(inputFile, outputFile):
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248 array_call = ['sort', '-k1,1', '-k2,2n', '-k6,6', inputFile, '>', outputFile]
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249 p = _handleExceptionAndCheckCall(array_call)
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250 return p
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251
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252 def bgzip(inputFile):
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253 subprocess.call(['bgzip', inputFile])
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254 filename = inputFile + '.gz'
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255 if os.path.exists(filename):
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256 return filename
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diff changeset
257 else:
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258 raise ValueError('Did not find gz file')
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259
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diff changeset
260 def createTabix(inputFile, dataType):
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261 subprocess.call(['tabix', '-p', dataType, inputFile])
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diff changeset
262 filename = inputFile + '.tbi'
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diff changeset
263 if os.path.exists(filename):
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264 return filename
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diff changeset
265 else:
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266 raise ValueError('Did not find tbi file')
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267
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268 def generate_tabix_indexed_track(inputFile, dataType, outputFolder):
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269 if "bed" in dataType:
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270 fileType = 'bed'
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271 sortedFile = tempfile.NamedTemporaryFile(bufsize=0)
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272 bedSort(inputFile, sortedFile.name)
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273 elif "gff" in dataType:
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274 fileType = 'gff'
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275 sortedFile = tempfile.NamedTemporaryFile(bufsize=0)
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276 gff3sort(inputFile, sortedFile.name)
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277 compressedFile = bgzip(sortedFile)
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278 tabixFile = createTabix(compressedFile, fileType)
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279 trackPath = os.path.join(outputFolder, inputFile)
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280 trackIndexPath = os.path.join(outputFolder, inputFile+'.tbi')
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281 shutil.copy(compressedFile, trackPath)
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282 shutil.copy(tabixFile, trackIndexPath)
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283
35
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284 def flatfile_to_json(inputFile, dataType, trackType, trackLabel, outputFolder, options=None, compress=True):
25
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285 if "bed" in dataType:
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286 fileType = "--bed"
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287 elif "gff" in dataType:
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288 fileType = "--gff"
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289 else:
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290 raise ValueError("%s is not a valid filetype for flatfile_to_json" % dataType)
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291
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292
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293 array_call = ['flatfile-to-json.pl',
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294 fileType, inputFile,
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295 '--trackType', trackType,
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296 '--trackLabel', trackLabel,
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297 '--out', outputFolder]
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298 if compress:
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299 array_call.append('--compress')
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300 if options:
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301 config = options.get("config")
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302 clientConfig = options.get("clientConfig")
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303 renderClassName = options.get('renderClassName')
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304 subfeatureClasses = options.get('subfeatureClasses')
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305 load_type = options.get("type")
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306 if clientConfig:
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307 array_call.append('--clientConfig')
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308 array_call.append(clientConfig)
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309 if config:
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310 array_call.append('--config')
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311 array_call.append(config)
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312 if load_type:
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313 array_call.append('--type')
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314 array_call.append(load_type)
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315 if renderClassName:
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316 array_call.append('--renderClassName')
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317 array_call.append(renderClassName)
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318 if subfeatureClasses:
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319 array_call.append('--subfeatureClasses')
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320 array_call.append(json.dumps(subfeatureClasses))
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321
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322 p = _handleExceptionAndCheckCall(array_call)
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323 return p
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324
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325 def bam_to_json(inputFile, trackLabel, outputFolder, options=None, compress=False):
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326
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327 array_call = ['bam-to-json.pl',
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328 '--bam', inputFile,
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329 '--trackLabel', trackLabel,
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330 '--out', outputFolder]
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331 if compress:
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332 array_call.append('--compress')
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333 if options:
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334 config = options.get('config')
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335 clientConfig = options.get('clientConfig')
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336 if clientConfig:
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337 array_call.append('--clientConfig')
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338 array_call.append(clientConfig)
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339 if config:
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340 array_call.append('--config')
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341 array_call.append(config)
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342
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343 p = _handleExceptionAndCheckCall(array_call)
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344 return p
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345
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346 def add_track_json(trackList, track_json):
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347 track_json = json.dumps(track_json)
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348 new_track = subprocess.Popen(['echo', track_json], stdout=subprocess.PIPE)
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349 p = subprocess.call(['add-track-json.pl', trackList], stdin=new_track.stdout)
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350 return p
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351
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352 def prepare_refseqs(fasta_file_name, outputFolder):
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353 array_call = ['prepare-refseqs.pl', '--fasta', fasta_file_name, '--out', outputFolder]
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354 p = _handleExceptionAndCheckCall(array_call)
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355 return p
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356
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357 def generate_names(outputFolder):
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358 array_call = ['generate-names.pl', '-v', '--out', outputFolder]
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359 p = _handleExceptionAndCheckCall(array_call)
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360 return p
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361
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362 def validateFiles(input_file, chrom_sizes_file_name, file_type, options=None):
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363 """
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364 Call validateFiles on input_file, using chrom_sizes_file_name and file_type
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365 :param input_file:
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366 :param chrom_sizes_file_name:
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367 :param file_type:
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368 :return:
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369 """
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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370
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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371 array_call = ['validateFiles', '-chromInfo=' + chrom_sizes_file_name, '-type='+ file_type, input_file]
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
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372 if options:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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373 tab = options.get("tab")
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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374 autoSql = options.get("autoSql")
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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375 logging.debug("tab: {0}".format(tab))
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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376 logging.debug("autoSql: {0}".format(autoSql))
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
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377 if autoSql:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
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378 autoSql = ''.join(['-as=', autoSql])
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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379 array_call.append(autoSql)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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380 if tab:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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381 array_call.append('-tab')
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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382 p = _handleExceptionAndCheckCall(array_call)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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383 return p
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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384