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1 #!/usr/bin/env python
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2 """Convert a BLAST XML file to tabular output.
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3
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4 Takes three command line options, input BLAST XML filename, output tabular
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5 BLAST filename, output format (std for standard 12 columns, or ext for the
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6 extended 24 columns offered in the BLAST+ wrappers).
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7
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8 The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart
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9 qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which
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10 mean:
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11
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12 ====== ========= ============================================
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13 Column NCBI name Description
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14 ------ --------- --------------------------------------------
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15 1 qseqid Query Seq-id (ID of your sequence)
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16 2 sseqid Subject Seq-id (ID of the database hit)
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17 3 pident Percentage of identical matches
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18 4 length Alignment length
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19 5 mismatch Number of mismatches
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20 6 gapopen Number of gap openings
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21 7 qstart Start of alignment in query
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22 8 qend End of alignment in query
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23 9 sstart Start of alignment in subject (database hit)
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24 10 send End of alignment in subject (database hit)
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25 11 evalue Expectation value (E-value)
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26 12 bitscore Bit score
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27 ====== ========= ============================================
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28
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29 The additional columns offered in the Galaxy BLAST+ wrappers are:
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30
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31 ====== ============= ===========================================
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32 Column NCBI name Description
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33 ------ ------------- -------------------------------------------
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34 13 sallseqid All subject Seq-id(s), separated by a ';'
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35 14 score Raw score
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36 15 nident Number of identical matches
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37 16 positive Number of positive-scoring matches
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38 17 gaps Total number of gaps
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39 18 ppos Percentage of positive-scoring matches
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40 19 qframe Query frame
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41 20 sframe Subject frame
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42 21 qseq Aligned part of query sequence
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43 22 sseq Aligned part of subject sequence
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44 23 qlen Query sequence length
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45 24 slen Subject sequence length
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46 ====== ============= ===========================================
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47
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48 Most of these fields are given explicitly in the XML file, others some like
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49 the percentage identity and the number of gap openings must be calculated.
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50
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51 Be aware that the sequence in the extended tabular output or XML direct from
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52 BLAST+ may or may not use XXXX masking on regions of low complexity. This
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53 can throw the off the calculation of percentage identity and gap openings.
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54 [In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard,
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55 with these numbers changing depending on whether or not the low complexity
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56 filter is used.]
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57
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58 This script attempts to produce identical output to what BLAST+ would have done.
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59 However, check this with "diff -b ..." since BLAST+ sometimes includes an extra
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60 space character (probably a bug).
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61 """
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62 import sys
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63 import re
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64
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65 if "-v" in sys.argv or "--version" in sys.argv:
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66 print "v0.0.12"
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67 sys.exit(0)
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68
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69 if sys.version_info[:2] >= ( 2, 5 ):
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70 try:
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71 from xml.etree import cElementTree as ElementTree
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72 except ImportError:
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73 from xml.etree import ElementTree as ElementTree
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74 else:
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75 from galaxy import eggs
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76 import pkg_resources; pkg_resources.require( "elementtree" )
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77 from elementtree import ElementTree
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78
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79 def stop_err( msg ):
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80 sys.stderr.write("%s\n" % msg)
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81 sys.exit(1)
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82
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83 #Parse Command Line
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84 try:
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85 in_file, out_file, out_fmt = sys.argv[1:]
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86 except:
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87 stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, out format (std or ext)")
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88
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89 if out_fmt == "std":
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90 extended = False
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91 elif out_fmt == "x22":
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92 stop_err("Format argument x22 has been replaced with ext (extended 24 columns)")
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93 elif out_fmt == "ext":
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94 extended = True
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95 else:
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96 stop_err("Format argument should be std (12 column) or ext (extended 24 columns)")
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97
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98
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99 # get an iterable
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100 try:
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101 context = ElementTree.iterparse(in_file, events=("start", "end"))
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102 except:
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103 stop_err("Invalid data format.")
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104 # turn it into an iterator
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105 context = iter(context)
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106 # get the root element
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107 try:
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108 event, root = context.next()
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109 except:
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110 stop_err( "Invalid data format." )
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111
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112
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113 re_default_query_id = re.compile("^Query_\d+$")
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114 assert re_default_query_id.match("Query_101")
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115 assert not re_default_query_id.match("Query_101a")
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116 assert not re_default_query_id.match("MyQuery_101")
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117 re_default_subject_id = re.compile("^Subject_\d+$")
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118 assert re_default_subject_id.match("Subject_1")
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119 assert not re_default_subject_id.match("Subject_")
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120 assert not re_default_subject_id.match("Subject_12a")
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121 assert not re_default_subject_id.match("TheSubject_1")
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122
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123
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124 outfile = open(out_file, 'w')
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125 blast_program = None
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126 for event, elem in context:
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127 if event == "end" and elem.tag == "BlastOutput_program":
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128 blast_program = elem.text
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129 # for every <Iteration> tag
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130 if event == "end" and elem.tag == "Iteration":
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131 #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
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132 # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
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133 # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
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134 # <Iteration_query-len>406</Iteration_query-len>
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135 # <Iteration_hits></Iteration_hits>
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136 #
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137 #Or, from BLAST 2.2.24+ run online
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138 # <Iteration_query-ID>Query_1</Iteration_query-ID>
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139 # <Iteration_query-def>Sample</Iteration_query-def>
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140 # <Iteration_query-len>516</Iteration_query-len>
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141 # <Iteration_hits>...
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142 qseqid = elem.findtext("Iteration_query-ID")
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143 if re_default_query_id.match(qseqid):
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144 #Place holder ID, take the first word of the query definition
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145 qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
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146 qlen = int(elem.findtext("Iteration_query-len"))
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147
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148 # for every <Hit> within <Iteration>
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149 for hit in elem.findall("Iteration_hits/Hit"):
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150 #Expecting either this,
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151 # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
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152 # <Hit_def>RecName: Full=Rhodopsin</Hit_def>
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153 # <Hit_accession>P56514</Hit_accession>
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154 #or,
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155 # <Hit_id>Subject_1</Hit_id>
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156 # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>
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157 # <Hit_accession>Subject_1</Hit_accession>
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158 #
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159 #apparently depending on the parse_deflines switch
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160 sseqid = hit.findtext("Hit_id").split(None,1)[0]
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161 hit_def = sseqid + " " + hit.findtext("Hit_def")
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162 if re_default_subject_id.match(sseqid) \
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163 and sseqid == hit.findtext("Hit_accession"):
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164 #Place holder ID, take the first word of the subject definition
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165 hit_def = hit.findtext("Hit_def")
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166 sseqid = hit_def.split(None,1)[0]
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167 # for every <Hsp> within <Hit>
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168 for hsp in hit.findall("Hit_hsps/Hsp"):
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169 nident = hsp.findtext("Hsp_identity")
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170 length = hsp.findtext("Hsp_align-len")
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171 pident = "%0.2f" % (100*float(nident)/float(length))
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172
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173 q_seq = hsp.findtext("Hsp_qseq")
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174 h_seq = hsp.findtext("Hsp_hseq")
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175 m_seq = hsp.findtext("Hsp_midline")
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176 assert len(q_seq) == len(h_seq) == len(m_seq) == int(length)
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177 gapopen = str(len(q_seq.replace('-', ' ').split())-1 + \
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178 len(h_seq.replace('-', ' ').split())-1)
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179
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180 mismatch = m_seq.count(' ') + m_seq.count('+') \
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181 - q_seq.count('-') - h_seq.count('-')
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182 #TODO - Remove this alternative mismatch calculation and test
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183 #once satisifed there are no problems
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184 expected_mismatch = len(q_seq) \
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185 - sum(1 for q,h in zip(q_seq, h_seq) \
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186 if q == h or q == "-" or h == "-")
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187 xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X")
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188 if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx):
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189 stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \
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190 % (qseqid, sseqid, expected_mismatch - q_seq.count("X"),
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191 int(mismatch), expected_mismatch))
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192
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193 #TODO - Remove this alternative identity calculation and test
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194 #once satisifed there are no problems
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195 expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h)
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196 if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")):
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197 stop_err("%s vs %s identities, expected %i <= %i <= %i" \
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198 % (qseqid, sseqid, expected_identity, int(nident),
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199 expected_identity + q_seq.count("X")))
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200
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201
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202 evalue = hsp.findtext("Hsp_evalue")
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203 if evalue == "0":
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204 evalue = "0.0"
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205 else:
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206 evalue = "%0.0e" % float(evalue)
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207
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208 bitscore = float(hsp.findtext("Hsp_bit-score"))
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209 if bitscore < 100:
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210 #Seems to show one decimal place for lower scores
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211 bitscore = "%0.1f" % bitscore
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212 else:
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213 #Note BLAST does not round to nearest int, it truncates
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214 bitscore = "%i" % bitscore
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215
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216 values = [qseqid,
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217 sseqid,
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218 pident,
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219 length, #hsp.findtext("Hsp_align-len")
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220 str(mismatch),
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221 gapopen,
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222 hsp.findtext("Hsp_query-from"), #qstart,
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223 hsp.findtext("Hsp_query-to"), #qend,
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224 hsp.findtext("Hsp_hit-from"), #sstart,
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225 hsp.findtext("Hsp_hit-to"), #send,
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226 evalue, #hsp.findtext("Hsp_evalue") in scientific notation
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227 bitscore, #hsp.findtext("Hsp_bit-score") rounded
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228 ]
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229
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230 if extended:
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231 sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(">"))
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232 #print hit_def, "-->", sallseqid
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233 positive = hsp.findtext("Hsp_positive")
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234 ppos = "%0.2f" % (100*float(positive)/float(length))
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235 qframe = hsp.findtext("Hsp_query-frame")
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236 sframe = hsp.findtext("Hsp_hit-frame")
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237 if blast_program == "blastp":
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238 #Probably a bug in BLASTP that they use 0 or 1 depending on format
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239 if qframe == "0": qframe = "1"
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240 if sframe == "0": sframe = "1"
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241 slen = int(hit.findtext("Hit_len"))
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242 values.extend([sallseqid,
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243 hsp.findtext("Hsp_score"), #score,
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244 nident,
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245 positive,
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246 hsp.findtext("Hsp_gaps"), #gaps,
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247 ppos,
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248 qframe,
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249 sframe,
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250 #NOTE - for blastp, XML shows original seq, tabular uses XXX masking
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251 q_seq,
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252 h_seq,
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253 str(qlen),
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254 str(slen),
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255 ])
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256 #print "\t".join(values)
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257 outfile.write("\t".join(values) + "\n")
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258 # prevents ElementTree from growing large datastructure
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259 root.clear()
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260 elem.clear()
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261 outfile.close()
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