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annotate blast.py @ 13:e96b515847dd draft

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v0.0.21 - Updated citation information with GigaScience paper
author peterjc
date Fri, 04 Sep 2015 07:09:45 -0400
parents da92fef90117
children 623a3fbe5340
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1 """
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2 BlastXml class
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3 """
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4
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5 from galaxy.datatypes.data import get_file_peek
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6 from galaxy.datatypes.data import Text, Data, GenericAsn1
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7 from galaxy.datatypes.xml import GenericXml
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8 from galaxy.datatypes.metadata import MetadataElement
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9
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10 from time import sleep
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11 import os
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12 import logging
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13
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14 log = logging.getLogger(__name__)
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15
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16 class BlastXml( GenericXml ):
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17 """NCBI Blast XML Output data"""
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18 file_ext = "blastxml"
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19
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20 def set_peek( self, dataset, is_multi_byte=False ):
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21 """Set the peek and blurb text"""
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22 if not dataset.dataset.purged:
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23 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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24 dataset.blurb = 'NCBI Blast XML data'
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25 else:
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26 dataset.peek = 'file does not exist'
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27 dataset.blurb = 'file purged from disk'
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28
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29 def sniff( self, filename ):
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30 """
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31 Determines whether the file is blastxml
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32
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33 >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' )
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34 >>> BlastXml().sniff( fname )
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35 True
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36 >>> fname = get_test_fname( 'tblastn_four_human_vs_rhodopsin.xml' )
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37 >>> BlastXml().sniff( fname )
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38 True
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39 >>> fname = get_test_fname( 'interval.interval' )
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40 >>> BlastXml().sniff( fname )
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41 False
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42 """
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43 #TODO - Use a context manager on Python 2.5+ to close handle
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44 handle = open(filename)
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45 line = handle.readline()
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46 if line.strip() != '<?xml version="1.0"?>':
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47 handle.close()
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48 return False
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49 line = handle.readline()
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50 if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
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51 '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
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52 handle.close()
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53 return False
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54 line = handle.readline()
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55 if line.strip() != '<BlastOutput>':
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56 handle.close()
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57 return False
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58 handle.close()
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59 return True
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60
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61 def merge(split_files, output_file):
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62 """Merging multiple XML files is non-trivial and must be done in subclasses."""
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63 if len(split_files) == 1:
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64 #For one file only, use base class method (move/copy)
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65 return Text.merge(split_files, output_file)
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66 if not split_files:
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67 raise ValueError("Given no BLAST XML files, %r, to merge into %s" \
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68 % (split_files, output_file))
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69 out = open(output_file, "w")
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70 h = None
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71 for f in split_files:
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72 if not os.path.isfile(f):
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73 log.warning("BLAST XML file %s missing, retry in 1s..." % f)
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74 sleep(1)
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75 if not os.path.isfile(f):
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76 log.error("BLAST XML file %s missing" % f)
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77 raise ValueError("BLAST XML file %s missing" % f)
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78 h = open(f)
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79 header = h.readline()
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80 if not header:
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81 out.close()
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82 h.close()
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83 #Retry, could be transient error with networked file system...
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84 log.warning("BLAST XML file %s empty, retry in 1s..." % f)
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85 sleep(1)
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86 h = open(f)
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87 header = h.readline()
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88 if not header:
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89 log.error("BLAST XML file %s was empty" % f)
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90 raise ValueError("BLAST XML file %s was empty" % f)
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91 if header.strip() != '<?xml version="1.0"?>':
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92 out.write(header) #for diagnosis
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93 out.close()
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94 h.close()
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95 raise ValueError("%s is not an XML file!" % f)
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96 line = h.readline()
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97 header += line
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98 if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
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99 '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
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100 out.write(header) #for diagnosis
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101 out.close()
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102 h.close()
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103 raise ValueError("%s is not a BLAST XML file!" % f)
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104 while True:
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105 line = h.readline()
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106 if not line:
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107 out.write(header) #for diagnosis
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108 out.close()
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109 h.close()
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110 raise ValueError("BLAST XML file %s ended prematurely" % f)
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111 header += line
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112 if "<Iteration>" in line:
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113 break
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114 if len(header) > 10000:
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115 #Something has gone wrong, don't load too much into memory!
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116 #Write what we have to the merged file for diagnostics
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117 out.write(header)
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118 out.close()
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119 h.close()
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120 raise ValueError("BLAST XML file %s has too long a header!" % f)
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121 if "<BlastOutput>" not in header:
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122 out.close()
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123 h.close()
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124 raise ValueError("%s is not a BLAST XML file:\n%s\n..." % (f, header))
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125 if f == split_files[0]:
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126 out.write(header)
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127 old_header = header
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128 elif old_header[:300] != header[:300]:
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129 #Enough to check <BlastOutput_program> and <BlastOutput_version> match
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130 out.close()
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131 h.close()
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132 raise ValueError("BLAST XML headers don't match for %s and %s - have:\n%s\n...\n\nAnd:\n%s\n...\n" \
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133 % (split_files[0], f, old_header[:300], header[:300]))
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134 else:
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135 out.write(" <Iteration>\n")
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136 for line in h:
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137 if "</BlastOutput_iterations>" in line:
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138 break
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139 #TODO - Increment <Iteration_iter-num> and if required automatic query names
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140 #like <Iteration_query-ID>Query_3</Iteration_query-ID> to be increasing?
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141 out.write(line)
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142 h.close()
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143 out.write(" </BlastOutput_iterations>\n")
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144 out.write("</BlastOutput>\n")
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145 out.close()
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146 merge = staticmethod(merge)
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147
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148
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149 class _BlastDb(object):
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150 """Base class for BLAST database datatype."""
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151
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152 def set_peek( self, dataset, is_multi_byte=False ):
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153 """Set the peek and blurb text."""
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154 if not dataset.dataset.purged:
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155 dataset.peek = "BLAST database (multiple files)"
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156 dataset.blurb = "BLAST database (multiple files)"
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157 else:
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158 dataset.peek = 'file does not exist'
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159 dataset.blurb = 'file purged from disk'
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160
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161 def display_peek( self, dataset ):
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162 """Create HTML content, used for displaying peek."""
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163 try:
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164 return dataset.peek
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165 except:
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166 return "BLAST database (multiple files)"
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167
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168 def display_data(self, trans, data, preview=False, filename=None,
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169 to_ext=None, size=None, offset=None, **kwd):
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170 """Documented as an old display method, but still gets called via tests etc
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171
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172 This allows us to format the data shown in the central pane via the "eye" icon.
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173 """
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174 if filename is not None and filename != "index":
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175 #Change nothing - important for the unit tests to access child files:
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176 return Data.display_data(self, trans, data, preview, filename,
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177 to_ext, size, offset, **kwd)
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178 if self.file_ext == "blastdbn":
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179 title = "This is a nucleotide BLAST database"
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180 elif self.file_ext =="blastdbp":
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181 title = "This is a protein BLAST database"
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182 elif self.file_ext =="blastdbd":
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183 title = "This is a domain BLAST database"
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184 else:
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185 #Error?
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186 title = "This is a BLAST database."
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187 msg = ""
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188 try:
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189 #Try to use any text recorded in the dummy index file:
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190 handle = open(data.file_name, "rU")
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191 msg = handle.read().strip()
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192 handle.close()
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193 except Exception, err:
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194 #msg = str(err)
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195 pass
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196 if not msg:
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197 msg = title
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198 #Galaxy assumes HTML for the display of composite datatypes,
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199 return "<html><head><title>%s</title></head><body><pre>%s</pre></body></html>" % (title, msg)
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200
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201 def merge(split_files, output_file):
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202 """Merge BLAST databases (not implemented for now)."""
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203 raise NotImplementedError("Merging BLAST databases is non-trivial (do this via makeblastdb?)")
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204
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205 def split( cls, input_datasets, subdir_generator_function, split_params):
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206 """Split a BLAST database (not implemented for now)."""
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207 if split_params is None:
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208 return None
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209 raise NotImplementedError("Can't split BLAST databases")
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210
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211
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212 class BlastNucDb( _BlastDb, Data ):
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213 """Class for nucleotide BLAST database files."""
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214 file_ext = 'blastdbn'
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215 allow_datatype_change = False
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216 composite_type = 'basic'
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217
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218 def __init__(self, **kwd):
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219 Data.__init__(self, **kwd)
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220 self.add_composite_file('blastdb.nhr', is_binary=True) # sequence headers
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221 self.add_composite_file('blastdb.nin', is_binary=True) # index file
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222 self.add_composite_file('blastdb.nsq', is_binary=True) # nucleotide sequences
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223 self.add_composite_file('blastdb.nal', is_binary=False, optional=True) # alias ( -gi_mask option of makeblastdb)
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224 self.add_composite_file('blastdb.nhd', is_binary=True, optional=True) # sorted sequence hash values ( -hash_index option of makeblastdb)
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225 self.add_composite_file('blastdb.nhi', is_binary=True, optional=True) # index of sequence hash values ( -hash_index option of makeblastdb)
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226 self.add_composite_file('blastdb.nnd', is_binary=True, optional=True) # sorted GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
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227 self.add_composite_file('blastdb.nni', is_binary=True, optional=True) # index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
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228 self.add_composite_file('blastdb.nog', is_binary=True, optional=True) # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb)
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229 self.add_composite_file('blastdb.nsd', is_binary=True, optional=True) # sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
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230 self.add_composite_file('blastdb.nsi', is_binary=True, optional=True) # index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
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231 # self.add_composite_file('blastdb.00.idx', is_binary=True, optional=True) # first volume of the MegaBLAST index generated by makembindex
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232 # The previous line should be repeated for each index volume, with filename extensions like '.01.idx', '.02.idx', etc.
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233 self.add_composite_file('blastdb.shd', is_binary=True, optional=True) # MegaBLAST index superheader (-old_style_index false option of makembindex)
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234 # self.add_composite_file('blastdb.naa', is_binary=True, optional=True) # index of a WriteDB column for e.g. mask data
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235 # self.add_composite_file('blastdb.nab', is_binary=True, optional=True) # data of a WriteDB column
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236 # self.add_composite_file('blastdb.nac', is_binary=True, optional=True) # multiple byte order for a WriteDB column
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237 # The previous 3 lines should be repeated for each WriteDB column, with filename extensions like ('.nba', '.nbb', '.nbc'), ('.nca', '.ncb', '.ncc'), etc.
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238
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239
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240 class BlastProtDb( _BlastDb, Data ):
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241 """Class for protein BLAST database files."""
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242 file_ext = 'blastdbp'
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243 allow_datatype_change = False
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244 composite_type = 'basic'
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245
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246 def __init__(self, **kwd):
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247 Data.__init__(self, **kwd)
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248 # Component file comments are as in BlastNucDb except where noted
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249 self.add_composite_file('blastdb.phr', is_binary=True)
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250 self.add_composite_file('blastdb.pin', is_binary=True)
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251 self.add_composite_file('blastdb.psq', is_binary=True) # protein sequences
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252 self.add_composite_file('blastdb.phd', is_binary=True, optional=True)
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253 self.add_composite_file('blastdb.phi', is_binary=True, optional=True)
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254 self.add_composite_file('blastdb.pnd', is_binary=True, optional=True)
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255 self.add_composite_file('blastdb.pni', is_binary=True, optional=True)
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256 self.add_composite_file('blastdb.pog', is_binary=True, optional=True)
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257 self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
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258 self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
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259 # self.add_composite_file('blastdb.paa', is_binary=True, optional=True)
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260 # self.add_composite_file('blastdb.pab', is_binary=True, optional=True)
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261 # self.add_composite_file('blastdb.pac', is_binary=True, optional=True)
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262 # The last 3 lines should be repeated for each WriteDB column, with filename extensions like ('.pba', '.pbb', '.pbc'), ('.pca', '.pcb', '.pcc'), etc.
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263
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264
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265 class BlastDomainDb( _BlastDb, Data ):
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266 """Class for domain BLAST database files."""
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267 file_ext = 'blastdbd'
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268 allow_datatype_change = False
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269 composite_type = 'basic'
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270
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271 def __init__(self, **kwd):
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272 Data.__init__(self, **kwd)
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273 self.add_composite_file('blastdb.phr', is_binary=True)
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274 self.add_composite_file('blastdb.pin', is_binary=True)
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275 self.add_composite_file('blastdb.psq', is_binary=True)
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276 self.add_composite_file('blastdb.freq', is_binary=True, optional=True)
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277 self.add_composite_file('blastdb.loo', is_binary=True, optional=True)
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278 self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
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279 self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
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280 self.add_composite_file('blastdb.rps', is_binary=True, optional=True)
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281 self.add_composite_file('blastdb.aux', is_binary=True, optional=True)