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annotate blastxml_to_gapped_gff3.py @ 7:1e74f16adaa1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
author iuc
date Sun, 26 Jun 2016 10:50:15 -0400
parents 7342f467507b
children ad4b9d7eae6a
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1 #!/usr/bin/perl
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2 import re
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3 import sys
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4 import copy
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5 import argparse
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6 from BCBio import GFF
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7 import logging
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8 logging.basicConfig(level=logging.INFO)
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9 log = logging.getLogger(name='blastxml2gff3')
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10
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11 __author__ = "Eric Rasche"
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12 __version__ = "0.4.0"
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13 __maintainer__ = "Eric Rasche"
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14 __email__ = "esr@tamu.edu"
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16 __doc__ = """
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17 BlastXML files, when transformed to GFF3, do not normally show gaps in the
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18 blast hits. This tool aims to fill that "gap".
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19 """
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22 def blastxml2gff3(blastxml, min_gap=3, trim=False, trim_end=False):
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23 from Bio.Blast import NCBIXML
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24 from Bio.Seq import Seq
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25 from Bio.SeqRecord import SeqRecord
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26 from Bio.SeqFeature import SeqFeature, FeatureLocation
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27
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28 blast_records = NCBIXML.parse(blastxml)
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29 records = []
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30 for record in blast_records:
3
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31 # http://www.sequenceontology.org/browser/release_2.4/term/SO:0000343
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32 match_type = { # Currently we can only handle BLASTN, BLASTP
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33 'BLASTN': 'nucleotide_match',
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34 'BLASTP': 'protein_match',
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35 }.get(record.application, 'match')
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36
1
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37 rec = SeqRecord(Seq("ACTG"), id=record.query)
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38 for hit in record.alignments:
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39 for hsp in hit.hsps:
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40 qualifiers = {
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41 "source": "blast",
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42 "score": hsp.expect,
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43 "accession": hit.accession,
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44 "hit_id": hit.hit_id,
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45 "length": hit.length,
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46 "hit_titles": hit.title.split(' >')
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47 }
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48 desc = hit.title.split(' >')[0]
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49 qualifiers['description'] = desc[desc.index(' '):]
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50
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51 # This required a fair bit of sketching out/match to figure out
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52 # the first time.
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53 #
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54 # the match_start location must account for queries and
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55 # subjecst that start at locations other than 1
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56 parent_match_start = hsp.query_start - hsp.sbjct_start
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57 # The end is the start + hit.length because the match itself
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58 # may be longer than the parent feature, so we use the supplied
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59 # subject/hit length to calculate the real ending of the target
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60 # protein.
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61 parent_match_end = hsp.query_start + hit.length + hsp.query.count('-')
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62
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63 # However, if the user requests that we trim the feature, then
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64 # we need to cut the ``match`` start to 0 to match the parent feature.
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65 # We'll also need to cut the end to match the query's end. It (maybe)
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66 # should be the feature end? But we don't have access to that data, so
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67 # We settle for this.
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68 if trim:
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69 if parent_match_start < 1:
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70 parent_match_start = 0
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71
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72 if trim or trim_end:
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73 if parent_match_end > hsp.query_end:
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74 parent_match_end = hsp.query_end + 1
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75
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76 # The ``match`` feature will hold one or more ``match_part``s
1
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77 top_feature = SeqFeature(
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78 FeatureLocation(parent_match_start, parent_match_end),
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79 type=match_type, strand=0,
1
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80 qualifiers=qualifiers
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81 )
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82
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83 # Unlike the parent feature, ``match_part``s have sources.
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84 part_qualifiers = {
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85 "source": "blast",
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86 }
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87 top_feature.sub_features = []
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88 for start, end, cigar in generate_parts(hsp.query, hsp.match,
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89 hsp.sbjct,
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90 ignore_under=min_gap):
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91 part_qualifiers['Gap'] = cigar
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92 part_qualifiers['ID'] = hit.hit_id
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93
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94 if trim:
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95 # If trimming, then we start relative to the
3
7342f467507b Uploaded v0.4 of JBrowse
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96 # match's start
1
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97 match_part_start = parent_match_start + start
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98 else:
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99 # Otherwise, we have to account for the subject start's location
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100 match_part_start = parent_match_start + hsp.sbjct_start + start - 1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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101
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102 # 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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103 # gaps in the parent sequence
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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104 #
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105 # Furthermore align_length will give calculation errors in weird places
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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106 # So we just use (end-start) for simplicity
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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107 match_part_end = match_part_start + (end - start)
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108
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109 top_feature.sub_features.append(
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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110 SeqFeature(
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111 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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112 type="match_part", strand=0,
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113 qualifiers=copy.deepcopy(part_qualifiers))
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114 )
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115
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116 rec.features.append(top_feature)
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117 rec.annotations = {}
1
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118 records.append(rec)
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119 return records
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120
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121
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122 def __remove_query_gaps(query, match, subject):
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123 """remove positions in all three based on gaps in query
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124
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125 In order to simplify math and calculations...we remove all of the gaps
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126 based on gap locations in the query sequence::
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127
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128 Q:ACTG-ACTGACTG
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129 S:ACTGAAC---CTG
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130
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131 will become::
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132
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133 Q:ACTGACTGACTG
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134 S:ACTGAC---CTG
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135
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136 which greatly simplifies the process of identifying the correct location
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137 for a match_part
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138 """
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139 prev = 0
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140 fq = ''
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141 fm = ''
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142 fs = ''
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143 for position in re.finditer('-', query):
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144 fq += query[prev:position.start()]
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145 fm += match[prev:position.start()]
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146 fs += subject[prev:position.start()]
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147 prev = position.start() + 1
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148 fq += query[prev:]
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149 fm += match[prev:]
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150 fs += subject[prev:]
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151
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152 return (fq, fm, fs)
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153
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154
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155 def generate_parts(query, match, subject, ignore_under=3):
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156 region_q = []
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157 region_m = []
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158 region_s = []
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159
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160 (query, match, subject) = __remove_query_gaps(query, match, subject)
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161
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162 region_start = -1
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163 region_end = -1
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164 mismatch_count = 0
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165 for i, (q, m, s) in enumerate(zip(query, match, subject)):
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166
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167 # If we have a match
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168 if m != ' ' or m == '+':
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169 if region_start == -1:
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170 region_start = i
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171 # It's a new region, we need to reset or it's pre-seeded with
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172 # spaces
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173 region_q = []
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174 region_m = []
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175 region_s = []
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176 region_end = i
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177 mismatch_count = 0
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178 else:
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179 mismatch_count += 1
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180
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181 region_q.append(q)
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182 region_m.append(m)
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183 region_s.append(s)
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184
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185 if mismatch_count >= ignore_under and region_start != -1 and region_end != -1:
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186 region_q = region_q[0:-ignore_under]
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187 region_m = region_m[0:-ignore_under]
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188 region_s = region_s[0:-ignore_under]
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189 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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190 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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191 region_q = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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192 region_m = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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193 region_s = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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194
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195 region_start = -1
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196 region_end = -1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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197 mismatch_count = 0
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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198
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199 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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200 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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201
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202
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203 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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204 matchline = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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205
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206 for (q, m, s) in zip(query, match, subject):
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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207 ret = ''
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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208
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209 if m != ' ' or m == '+':
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210 ret = '='
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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211 elif m == ' ':
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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212 if q == '-':
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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213 ret = 'D'
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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214 elif s == '-':
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iuc
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215 ret = 'I'
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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216 else:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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217 ret = 'X'
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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218 else:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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219 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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220
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221
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222 if strict_m:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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223 if ret == '=' or ret == 'X':
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224 ret = 'M'
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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225
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226 matchline.append(ret)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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227 return matchline
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228
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229
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230 def _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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231 cigar_line = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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232 last_char = matchline[0]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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233 count = 0
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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234 for char in matchline:
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235 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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236 count += 1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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237 else:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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238 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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239 count = 1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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240 last_char = char
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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241 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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242 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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243
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244
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245 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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246 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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247 if len(matchline) > 0:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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248 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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249 else:
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250 return ""
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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251
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252
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253 if __name__ == '__main__':
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254 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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255 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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256 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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257 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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258 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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259 args = parser.parse_args()
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260
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261 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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262 GFF.write(result, sys.stdout)