Mercurial > repos > iuc > jbrowse

annotate blastxml_to_gapped_gff3.py @ 10:1a6d882d340d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
author iuc
date Fri, 02 Dec 2016 17:58:54 -0500
parents ad4b9d7eae6a
children db5fe5a3176a
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1 #!/usr/bin/perl
8
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2 import argparse
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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3 import copy
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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4 import logging
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5 import re
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6 import sys
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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8 from BCBio import GFF
8
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9
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10 logging.basicConfig(level=logging.INFO)
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11 log = logging.getLogger(name='blastxml2gff3')
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12
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13 __author__ = "Eric Rasche"
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14 __version__ = "0.4.0"
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15 __maintainer__ = "Eric Rasche"
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16 __email__ = "esr@tamu.edu"
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18 __doc__ = """
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19 BlastXML files, when transformed to GFF3, do not normally show gaps in the
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20 blast hits. This tool aims to fill that "gap".
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21 """
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24 def blastxml2gff3(blastxml, min_gap=3, trim=False, trim_end=False):
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25 from Bio.Blast import NCBIXML
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26 from Bio.Seq import Seq
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27 from Bio.SeqRecord import SeqRecord
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28 from Bio.SeqFeature import SeqFeature, FeatureLocation
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29
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30 blast_records = NCBIXML.parse(blastxml)
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31 records = []
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32 for record in blast_records:
3
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33 # http://www.sequenceontology.org/browser/release_2.4/term/SO:0000343
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34 match_type = { # Currently we can only handle BLASTN, BLASTP
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35 'BLASTN': 'nucleotide_match',
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36 'BLASTP': 'protein_match',
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37 }.get(record.application, 'match')
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38
1
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39 rec = SeqRecord(Seq("ACTG"), id=record.query)
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40 for hit in record.alignments:
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41 for hsp in hit.hsps:
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42 qualifiers = {
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43 "source": "blast",
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44 "score": hsp.expect,
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45 "accession": hit.accession,
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46 "hit_id": hit.hit_id,
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47 "length": hit.length,
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48 "hit_titles": hit.title.split(' >')
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49 }
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50 desc = hit.title.split(' >')[0]
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51 qualifiers['description'] = desc[desc.index(' '):]
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52
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53 # This required a fair bit of sketching out/match to figure out
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54 # the first time.
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55 #
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56 # the match_start location must account for queries and
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57 # subjecst that start at locations other than 1
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58 parent_match_start = hsp.query_start - hsp.sbjct_start
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59 # The end is the start + hit.length because the match itself
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60 # may be longer than the parent feature, so we use the supplied
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61 # subject/hit length to calculate the real ending of the target
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62 # protein.
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63 parent_match_end = hsp.query_start + hit.length + hsp.query.count('-')
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64
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65 # However, if the user requests that we trim the feature, then
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66 # we need to cut the ``match`` start to 0 to match the parent feature.
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67 # We'll also need to cut the end to match the query's end. It (maybe)
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68 # should be the feature end? But we don't have access to that data, so
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69 # We settle for this.
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70 if trim:
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71 if parent_match_start < 1:
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72 parent_match_start = 0
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73
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74 if trim or trim_end:
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75 if parent_match_end > hsp.query_end:
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76 parent_match_end = hsp.query_end + 1
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77
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78 # The ``match`` feature will hold one or more ``match_part``s
1
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79 top_feature = SeqFeature(
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80 FeatureLocation(parent_match_start, parent_match_end),
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81 type=match_type, strand=0,
1
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82 qualifiers=qualifiers
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83 )
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84
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85 # Unlike the parent feature, ``match_part``s have sources.
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86 part_qualifiers = {
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87 "source": "blast",
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88 }
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89 top_feature.sub_features = []
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90 for start, end, cigar in generate_parts(hsp.query, hsp.match,
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91 hsp.sbjct,
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92 ignore_under=min_gap):
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93 part_qualifiers['Gap'] = cigar
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94 part_qualifiers['ID'] = hit.hit_id
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95
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96 if trim:
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97 # If trimming, then we start relative to the
3
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98 # match's start
1
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99 match_part_start = parent_match_start + start
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100 else:
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101 # Otherwise, we have to account for the subject start's location
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102 match_part_start = parent_match_start + hsp.sbjct_start + start - 1
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103
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104 # We used to use hsp.align_length here, but that includes
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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105 # gaps in the parent sequence
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106 #
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107 # Furthermore align_length will give calculation errors in weird places
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108 # So we just use (end-start) for simplicity
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109 match_part_end = match_part_start + (end - start)
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110
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111 top_feature.sub_features.append(
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112 SeqFeature(
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113 FeatureLocation(match_part_start, match_part_end),
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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114 type="match_part", strand=0,
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115 qualifiers=copy.deepcopy(part_qualifiers))
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116 )
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117
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118 rec.features.append(top_feature)
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119 rec.annotations = {}
1
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120 records.append(rec)
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121 return records
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122
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123
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124 def __remove_query_gaps(query, match, subject):
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125 """remove positions in all three based on gaps in query
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126
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127 In order to simplify math and calculations...we remove all of the gaps
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128 based on gap locations in the query sequence::
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129
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130 Q:ACTG-ACTGACTG
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131 S:ACTGAAC---CTG
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132
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133 will become::
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134
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135 Q:ACTGACTGACTG
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136 S:ACTGAC---CTG
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137
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138 which greatly simplifies the process of identifying the correct location
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139 for a match_part
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140 """
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141 prev = 0
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142 fq = ''
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143 fm = ''
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144 fs = ''
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145 for position in re.finditer('-', query):
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146 fq += query[prev:position.start()]
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147 fm += match[prev:position.start()]
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148 fs += subject[prev:position.start()]
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149 prev = position.start() + 1
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150 fq += query[prev:]
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151 fm += match[prev:]
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152 fs += subject[prev:]
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153
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154 return (fq, fm, fs)
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155
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156
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157 def generate_parts(query, match, subject, ignore_under=3):
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158 region_q = []
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159 region_m = []
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160 region_s = []
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161
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162 (query, match, subject) = __remove_query_gaps(query, match, subject)
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163
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164 region_start = -1
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165 region_end = -1
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166 mismatch_count = 0
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167 for i, (q, m, s) in enumerate(zip(query, match, subject)):
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168
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169 # If we have a match
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170 if m != ' ' or m == '+':
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171 if region_start == -1:
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172 region_start = i
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173 # It's a new region, we need to reset or it's pre-seeded with
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174 # spaces
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175 region_q = []
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176 region_m = []
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177 region_s = []
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178 region_end = i
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179 mismatch_count = 0
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180 else:
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181 mismatch_count += 1
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182
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183 region_q.append(q)
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184 region_m.append(m)
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185 region_s.append(s)
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186
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187 if mismatch_count >= ignore_under and region_start != -1 and region_end != -1:
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188 region_q = region_q[0:-ignore_under]
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189 region_m = region_m[0:-ignore_under]
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190 region_s = region_s[0:-ignore_under]
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191 yield region_start, region_end + 1, \
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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192 cigar_from_string(region_q, region_m, region_s, strict_m=True)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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193 region_q = []
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194 region_m = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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195 region_s = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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196
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197 region_start = -1
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198 region_end = -1
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199 mismatch_count = 0
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200
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201 yield region_start, region_end + 1, \
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202 cigar_from_string(region_q, region_m, region_s, strict_m=True)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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203
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204
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205 def _qms_to_matches(query, match, subject, strict_m=True):
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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206 matchline = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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207
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208 for (q, m, s) in zip(query, match, subject):
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209 ret = ''
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210
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211 if m != ' ' or m == '+':
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212 ret = '='
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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213 elif m == ' ':
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214 if q == '-':
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215 ret = 'D'
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216 elif s == '-':
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iuc
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217 ret = 'I'
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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218 else:
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219 ret = 'X'
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220 else:
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221 log.warn("Bad data: \n\t%s\n\t%s\n\t%s\n" % (query, match, subject))
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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222
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223 if strict_m:
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224 if ret == '=' or ret == 'X':
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225 ret = 'M'
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226
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227 matchline.append(ret)
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228 return matchline
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229
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230
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231 def _matchline_to_cigar(matchline):
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232 cigar_line = []
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233 last_char = matchline[0]
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234 count = 0
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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235 for char in matchline:
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236 if char == last_char:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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237 count += 1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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238 else:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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239 cigar_line.append("%s%s" % (last_char, count))
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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240 count = 1
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241 last_char = char
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242 cigar_line.append("%s%s" % (last_char, count))
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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243 return ' '.join(cigar_line)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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244
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245
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246 def cigar_from_string(query, match, subject, strict_m=True):
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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247 matchline = _qms_to_matches(query, match, subject, strict_m=strict_m)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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248 if len(matchline) > 0:
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249 return _matchline_to_cigar(matchline)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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250 else:
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251 return ""
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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252
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253
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254 if __name__ == '__main__':
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255 parser = argparse.ArgumentParser(description='Convert Blast XML to gapped GFF3', epilog='')
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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256 parser.add_argument('blastxml', type=file, help='Blast XML Output')
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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257 parser.add_argument('--min_gap', type=int, help='Maximum gap size before generating a new match_part', default=3)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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258 parser.add_argument('--trim', action='store_true', help='Trim blast hits to be only as long as the parent feature')
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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259 parser.add_argument('--trim_end', action='store_true', help='Cut blast results off at end of gene')
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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260 args = parser.parse_args()
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261
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262 result = blastxml2gff3(**vars(args))
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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263 GFF.write(result, sys.stdout)