Mercurial > repos > dfornika > blast_xml_to_tabular

annotate blast_xml_to_tabular.py @ 0:efe0c7b8fb78 draft

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planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
author dfornika
date Mon, 09 Sep 2019 17:17:09 -0400
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efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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1 #!/usr/bin/env python
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2
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3 """Convert a BLAST XML file to 12 column tabular output
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4
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5 Takes three command line options, input BLAST XML filename, output tabular
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6 BLAST filename, output format (std for standard 12 columns, or ext for the
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7 extended 24 columns offered in the BLAST+ wrappers).
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8
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9 The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart
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10 qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which
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11 mean:
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12
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13 ====== ========= ============================================
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14 Column NCBI name Description
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15 ------ --------- --------------------------------------------
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16 1 qseqid Query Seq-id (ID of your sequence)
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17 2 sseqid Subject Seq-id (ID of the database hit)
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18 3 pident Percentage of identical matches
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19 4 length Alignment length
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20 5 mismatch Number of mismatches
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21 6 gapopen Number of gap openings
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22 7 qstart Start of alignment in query
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23 8 qend End of alignment in query
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24 9 sstart Start of alignment in subject (database hit)
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25 10 send End of alignment in subject (database hit)
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26 11 evalue Expectation value (E-value)
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27 12 bitscore Bit score
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28 ====== ========= ============================================
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30 The additional columns offered in the Galaxy BLAST+ wrappers are:
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31
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32 ====== ============= ===========================================
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33 Column NCBI name Description
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34 ------ ------------- -------------------------------------------
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35 13 sallseqid All subject Seq-id(s), separated by a ';'
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36 14 score Raw score
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37 15 nident Number of identical matches
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38 16 positive Number of positive-scoring matches
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39 17 gaps Total number of gaps
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40 18 ppos Percentage of positive-scoring matches
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41 19 qframe Query frame
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42 20 sframe Subject frame
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43 21 qseq Aligned part of query sequence
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44 22 sseq Aligned part of subject sequence
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45 23 qlen Query sequence length
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46 24 slen Subject sequence length
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47 ====== ============= ===========================================
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48
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49 Most of these fields are given explicitly in the XML file, others some like
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50 the percentage identity and the number of gap openings must be calculated.
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51
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52 Be aware that the sequence in the extended tabular output or XML direct from
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53 BLAST+ may or may not use XXXX masking on regions of low complexity. This
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54 can throw the off the calculation of percentage identity and gap openings.
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55 [In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard,
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56 with these numbers changing depending on whether or not the low complexity
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57 filter is used.]
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58
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59 This script attempts to produce identical output to what BLAST+ would have done.
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60 However, check this with "diff -b ..." since BLAST+ sometimes includes an extra
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61 space character (probably a bug).
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62
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63 python blast_xml_parser.py in_file out_file out_format
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64 """
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65
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66 import sys
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67 import re
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68
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69 import xml.etree.cElementTree as ElementTree
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70
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71 def stop_err( msg ):
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72 sys.stderr.write("%s\n" % msg)
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73 sys.exit(1)
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74
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75 #Parse Command Line
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76 try:
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77 in_file, out_file, out_fmt = sys.argv[1:]
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78 except:
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79 stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, out format (std or ext)")
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80
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81 if out_fmt == "std":
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82 extended = False
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83 elif out_fmt == "x22":
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84 stop_err("Format argument x22 has been replaced with ext (extended 24 columns)")
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85 elif out_fmt == "ext" or out_fmt == "ext+":
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86 extended = True
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87 else:
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88 stop_err("Format argument should be std (12 column) or ext (extended 24 columns) or ext+ (extended 26 columns)")
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89
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90 extended_plus = False
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91 if '+' in out_fmt:
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92 extended_plus = True
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93
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94 # get an iterable
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95 try:
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96 context = ElementTree.iterparse(in_file, events=("start", "end"))
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97 except:
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98 stop_err("Invalid data format.")
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99 # turn it into an iterator
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100 context = iter(context)
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101 # get the root element
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102 try:
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103 event, root = context.next()
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104 except:
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105 stop_err( "Invalid data format." )
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106
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107 re_default_query_id = re.compile("^Query_\d+$")
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108 assert re_default_query_id.match("Query_101")
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109 assert not re_default_query_id.match("Query_101a")
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110 assert not re_default_query_id.match("MyQuery_101")
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111 re_default_subject_id = re.compile("^Subject_\d+$")
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112 assert re_default_subject_id.match("Subject_1")
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113 assert not re_default_subject_id.match("Subject_")
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114 assert not re_default_subject_id.match("Subject_12a")
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115 assert not re_default_subject_id.match("TheSubject_1")
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116
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117 outfile = open(out_file, 'w')
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118 blast_program = None
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119 for event, elem in context:
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120 if event == "end" and elem.tag == "BlastOutput_program":
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121 blast_program = elem.text
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122 # for every <Iteration> tag
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123 if event == "end" and elem.tag == "Iteration":
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124 #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
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125 # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
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126 # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
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127 # <Iteration_query-len>406</Iteration_query-len>
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128 # <Iteration_hits></Iteration_hits>
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129 #
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130 #Or, from BLAST 2.2.24+ run online
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131 # <Iteration_query-ID>Query_1</Iteration_query-ID>
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132 # <Iteration_query-def>Sample</Iteration_query-def>
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133 # <Iteration_query-len>516</Iteration_query-len>
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134 # <Iteration_hits>...
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135 qseqid = elem.findtext("Iteration_query-ID")
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136 if re_default_query_id.match(qseqid):
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137 #Place holder ID, take the first word of the query definition
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138 qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
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139 qlen = int(elem.findtext("Iteration_query-len"))
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140
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141 # for every <Hit> within <Iteration>
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142 for hit in elem.findall("Iteration_hits/Hit"):
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143 #Expecting either this,
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144 # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
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145 # <Hit_def>RecName: Full=Rhodopsin</Hit_def>
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146 # <Hit_accession>P56514</Hit_accession>
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147 #or,
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148 # <Hit_id>Subject_1</Hit_id>
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149 # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>
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150 # <Hit_accession>Subject_1</Hit_accession>
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151 #
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152 #apparently depending on the parse_deflines switch
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153 sseqid = hit.findtext("Hit_id").split(None,1)[0]
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154 hit_def = sseqid + " " + hit.findtext("Hit_def")
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155 if re_default_subject_id.match(sseqid) \
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156 and sseqid == hit.findtext("Hit_accession"):
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157 #Place holder ID, take the first word of the subject definition
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158 hit_def = hit.findtext("Hit_def")
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159 sseqid = hit_def.split(None,1)[0]
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160 # for every <Hsp> within <Hit>
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parents:
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161 for hsp in hit.findall("Hit_hsps/Hsp"):
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parents:
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162 nident = hsp.findtext("Hsp_identity")
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parents:
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163 length = hsp.findtext("Hsp_align-len")
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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parents:
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164 pident = "%0.2f" % (100*float(nident)/float(length))
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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165
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parents:
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166 q_seq = hsp.findtext("Hsp_qseq")
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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parents:
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167 h_seq = hsp.findtext("Hsp_hseq")
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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parents:
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168 m_seq = hsp.findtext("Hsp_midline")
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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parents:
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169 assert len(q_seq) == len(h_seq) == len(m_seq) == int(length)
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parents:
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170 gapopen = str(len(q_seq.replace('-', ' ').split())-1 + \
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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171 len(h_seq.replace('-', ' ').split())-1)
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parents:
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172
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173 mismatch = m_seq.count(' ') + m_seq.count('+') \
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174 - q_seq.count('-') - h_seq.count('-')
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parents:
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175 #TODO - Remove this alternative mismatch calculation and test
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176 #once satisifed there are no problems
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177 expected_mismatch = len(q_seq) \
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178 - sum(1 for q,h in zip(q_seq, h_seq) \
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179 if q == h or q == "-" or h == "-")
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180 xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X")
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181 if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx):
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182 stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \
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183 % (qseqid, sseqid, expected_mismatch - q_seq.count("X"),
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184 int(mismatch), expected_mismatch))
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185
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dfornika
parents:
diff changeset
186 #TODO - Remove this alternative identity calculation and test
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
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187 #once satisifed there are no problems
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parents:
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188 expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h)
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parents:
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189 if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")):
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parents:
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190 stop_err("%s vs %s identities, expected %i <= %i <= %i" \
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parents:
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191 % (qseqid, sseqid, expected_identity, int(nident),
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parents:
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192 expected_identity + q_seq.count("X")))
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193
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parents:
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194 evalue = hsp.findtext("Hsp_evalue")
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parents:
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195 if evalue == "0":
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parents:
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196 evalue = "0.0"
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197 else:
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parents:
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198 evalue = "%0.0e" % float(evalue)
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199
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dfornika
parents:
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200 bitscore = float(hsp.findtext("Hsp_bit-score"))
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dfornika
parents:
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201 if bitscore < 100:
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dfornika
parents:
diff changeset
202 #Seems to show one decimal place for lower scores
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dfornika
parents:
diff changeset
203 bitscore = "%0.1f" % bitscore
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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parents:
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204 else:
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parents:
diff changeset
205 #Note BLAST does not round to nearest int, it truncates
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dfornika
parents:
diff changeset
206 bitscore = "%i" % bitscore
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207
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parents:
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208 qstart = hsp.findtext("Hsp_query-from")
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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parents:
diff changeset
209 qend = hsp.findtext("Hsp_query-to")
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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parents:
diff changeset
210 values = [qseqid,
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parents:
diff changeset
211 sseqid,
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parents:
diff changeset
212 pident,
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parents:
diff changeset
213 length, #hsp.findtext("Hsp_align-len")
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parents:
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214 str(mismatch),
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parents:
diff changeset
215 gapopen,
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parents:
diff changeset
216 #hsp.findtext("Hsp_query-from"), #qstart,
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diff changeset
217 #hsp.findtext("Hsp_query-to"), #qend,
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parents:
diff changeset
218 qstart,
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parents:
diff changeset
219 qend,
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parents:
diff changeset
220 hsp.findtext("Hsp_hit-from"), #sstart,
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parents:
diff changeset
221 hsp.findtext("Hsp_hit-to"), #send,
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parents:
diff changeset
222 evalue, #hsp.findtext("Hsp_evalue") in scientific notation
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parents:
diff changeset
223 bitscore, #hsp.findtext("Hsp_bit-score") rounded
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parents:
diff changeset
224 ]
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225
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parents:
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226 if extended:
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parents:
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227 sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(">"))
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parents:
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228 #print hit_def, "-->", sallseqid
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parents:
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229 positive = hsp.findtext("Hsp_positive")
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parents:
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230 ppos = "%0.2f" % (100*float(positive)/float(length))
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parents:
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231 qframe = hsp.findtext("Hsp_query-frame")
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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parents:
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232 sframe = hsp.findtext("Hsp_hit-frame")
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parents:
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233 if blast_program == "blastp":
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parents:
diff changeset
234 #Probably a bug in BLASTP that they use 0 or 1 depending on format
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parents:
diff changeset
235 if qframe == "0": qframe = "1"
efe0c7b8fb78 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_xml_to_tabular commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
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parents:
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236 if sframe == "0": sframe = "1"
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parents:
diff changeset
237 slen = int(hit.findtext("Hit_len"))
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parents:
diff changeset
238 values.extend([sallseqid,
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parents:
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239 hsp.findtext("Hsp_score"), #score,
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240 nident,
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241 positive,
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242 hsp.findtext("Hsp_gaps"), #gaps,
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243 ppos,
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244 qframe,
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245 sframe,
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246 #NOTE - for blastp, XML shows original seq, tabular uses XXX masking
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247 q_seq,
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248 h_seq,
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249 str(qlen),
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250 str(slen)
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251 ])
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252
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253 if extended_plus:
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254 pcov = "%0.2f" % (float(int(qend) - int(qstart) + 1)/qlen * 100)
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255 sallseqdescr = ";".join(name.split(None,1)[1] for name in hit_def.split(">"))
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256 values.extend([pcov, sallseqdescr])
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257
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258 #print "\t".join(values)
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259 outfile.write("\t".join(values) + "\n")
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260 # prevents ElementTree from growing large datastructure
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261 root.clear()
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262 elem.clear()
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263 outfile.close()