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annotate blastxml_to_gapped_gff3.py @ 35:3235aeb45c22 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
author iuc
date Wed, 18 Dec 2019 10:46:52 -0500
parents ff11d442feed
children
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1 #!/usr/bin/env python
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2 import argparse
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3 import copy
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4 import logging
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5 import re
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6 import sys
8
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7
1
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8 from BCBio import GFF
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9 logging.basicConfig(level=logging.INFO)
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10 log = logging.getLogger(name='blastxml2gff3')
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12 __doc__ = """
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13 BlastXML files, when transformed to GFF3, do not normally show gaps in the
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14 blast hits. This tool aims to fill that "gap".
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15 """
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17
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18 def blastxml2gff3(blastxml, min_gap=3, trim=False, trim_end=False, include_seq=False):
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19 from Bio.Blast import NCBIXML
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20 from Bio.Seq import Seq
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21 from Bio.SeqRecord import SeqRecord
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22 from Bio.SeqFeature import SeqFeature, FeatureLocation
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24 blast_records = NCBIXML.parse(blastxml)
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25 for idx_record, record in enumerate(blast_records):
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26 # http://www.sequenceontology.org/browser/release_2.4/term/SO:0000343
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27 match_type = { # Currently we can only handle BLASTN, BLASTP
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28 'BLASTN': 'nucleotide_match',
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29 'BLASTP': 'protein_match',
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30 }.get(record.application, 'match')
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31
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32 recid = record.query
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33 if ' ' in recid:
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34 recid = recid[0:recid.index(' ')]
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36 rec = SeqRecord(Seq("ACTG"), id=recid)
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37 for idx_hit, hit in enumerate(record.alignments):
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38 for idx_hsp, hsp in enumerate(hit.hsps):
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39 qualifiers = {
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40 "ID": 'b2g.%s.%s.%s' % (idx_record, idx_hit, idx_hsp),
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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 if include_seq:
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49 qualifiers.update({
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50 'blast_qseq': hsp.query,
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51 'blast_sseq': hsp.sbjct,
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52 'blast_mseq': hsp.match,
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53 })
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54
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55 for prop in ('score', 'bits', 'identities', 'positives',
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56 'gaps', 'align_length', 'strand', 'frame',
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57 'query_start', 'query_end', 'sbjct_start',
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58 'sbjct_end'):
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59 qualifiers['blast_' + prop] = getattr(hsp, prop, None)
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60
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61 desc = hit.title.split(' >')[0]
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62 qualifiers['description'] = desc[desc.index(' '):]
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63
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64 # This required a fair bit of sketching out/match to figure out
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65 # the first time.
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66 #
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67 # the match_start location must account for queries and
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68 # subjecst that start at locations other than 1
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69 parent_match_start = hsp.query_start - hsp.sbjct_start
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70 # The end is the start + hit.length because the match itself
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71 # may be longer than the parent feature, so we use the supplied
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72 # subject/hit length to calculate the real ending of the target
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73 # protein.
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74 parent_match_end = hsp.query_start + hit.length + hsp.query.count('-')
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75
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76 # If we trim the left end, we need to trim without losing information.
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77 used_parent_match_start = parent_match_start
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78 if trim:
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79 if parent_match_start < 1:
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80 used_parent_match_start = 0
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81
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82 if trim or trim_end:
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83 if parent_match_end > hsp.query_end:
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84 parent_match_end = hsp.query_end + 1
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85
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86 # The ``match`` feature will hold one or more ``match_part``s
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87 top_feature = SeqFeature(
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88 FeatureLocation(used_parent_match_start, parent_match_end),
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89 type=match_type, strand=0,
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90 qualifiers=qualifiers
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91 )
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92
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93 # Unlike the parent feature, ``match_part``s have sources.
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94 part_qualifiers = {
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95 "source": "blast",
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96 }
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97 top_feature.sub_features = []
17
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98 for idx_part, (start, end, cigar) in \
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99 enumerate(generate_parts(hsp.query, hsp.match,
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100 hsp.sbjct,
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101 ignore_under=min_gap)):
1
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102 part_qualifiers['Gap'] = cigar
17
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103 part_qualifiers['ID'] = qualifiers['ID'] + ('.%s' % idx_part)
1
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104
17
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105 # Otherwise, we have to account for the subject start's location
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106 match_part_start = parent_match_start + hsp.sbjct_start + start - 1
1
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107
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108 # We used to use hsp.align_length here, but that includes
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109 # gaps in the parent sequence
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110 #
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111 # Furthermore align_length will give calculation errors in weird places
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112 # So we just use (end-start) for simplicity
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113 match_part_end = match_part_start + (end - start)
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114
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115 top_feature.sub_features.append(
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116 SeqFeature(
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117 FeatureLocation(match_part_start, match_part_end),
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118 type="match_part", strand=0,
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119 qualifiers=copy.deepcopy(part_qualifiers))
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120 )
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121
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122 rec.features.append(top_feature)
3
7342f467507b Uploaded v0.4 of JBrowse
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123 rec.annotations = {}
17
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124 yield rec
1
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125
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126
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127 def __remove_query_gaps(query, match, subject):
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128 """remove positions in all three based on gaps in query
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129
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130 In order to simplify math and calculations...we remove all of the gaps
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131 based on gap locations in the query sequence::
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132
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133 Q:ACTG-ACTGACTG
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134 S:ACTGAAC---CTG
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135
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136 will become::
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137
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138 Q:ACTGACTGACTG
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139 S:ACTGAC---CTG
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140
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141 which greatly simplifies the process of identifying the correct location
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142 for a match_part
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143 """
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144 prev = 0
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145 fq = ''
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146 fm = ''
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147 fs = ''
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148 for position in re.finditer('-', query):
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149 fq += query[prev:position.start()]
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150 fm += match[prev:position.start()]
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151 fs += subject[prev:position.start()]
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152 prev = position.start() + 1
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153 fq += query[prev:]
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154 fm += match[prev:]
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155 fs += subject[prev:]
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156
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157 return (fq, fm, fs)
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158
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159
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160 def generate_parts(query, match, subject, ignore_under=3):
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161 region_q = []
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162 region_m = []
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163 region_s = []
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164
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165 (query, match, subject) = __remove_query_gaps(query, match, subject)
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166
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167 region_start = -1
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168 region_end = -1
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169 mismatch_count = 0
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170 for i, (q, m, s) in enumerate(zip(query, match, subject)):
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171
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172 # If we have a match
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173 if m != ' ' or m == '+':
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174 if region_start == -1:
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175 region_start = i
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176 # It's a new region, we need to reset or it's pre-seeded with
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177 # spaces
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178 region_q = []
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179 region_m = []
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180 region_s = []
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181 region_end = i
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182 mismatch_count = 0
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183 else:
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184 mismatch_count += 1
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185
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186 region_q.append(q)
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187 region_m.append(m)
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188 region_s.append(s)
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189
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190 if mismatch_count >= ignore_under and region_start != -1 and region_end != -1:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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191 region_q = region_q[0:-ignore_under]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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192 region_m = region_m[0:-ignore_under]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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193 region_s = region_s[0:-ignore_under]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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194 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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195 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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196 region_q = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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197 region_m = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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198 region_s = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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199
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200 region_start = -1
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201 region_end = -1
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202 mismatch_count = 0
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 yield region_start, region_end + 1, \
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205 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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206
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207
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208 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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209 matchline = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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210
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211 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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212 ret = ''
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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213
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214 if m != ' ' or m == '+':
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iuc
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215 ret = '='
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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216 elif m == ' ':
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217 if q == '-':
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iuc
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218 ret = 'D'
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219 elif s == '-':
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iuc
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220 ret = 'I'
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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221 else:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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222 ret = 'X'
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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223 else:
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diff changeset
224 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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225
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226 if strict_m:
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227 if ret == '=' or ret == 'X':
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iuc
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228 ret = 'M'
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229
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230 matchline.append(ret)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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231 return matchline
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232
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233
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234 def _matchline_to_cigar(matchline):
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235 cigar_line = []
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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236 last_char = matchline[0]
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237 count = 0
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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238 for char in matchline:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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239 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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240 count += 1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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241 else:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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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
iuc
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diff changeset
243 count = 1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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244 last_char = char
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245 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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246 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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247
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248
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249 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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250 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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251 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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252 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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253 else:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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254 return ""
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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255
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256
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257 if __name__ == '__main__':
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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258 parser = argparse.ArgumentParser(description='Convert Blast XML to gapped GFF3', epilog='')
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
259 parser.add_argument('blastxml', type=argparse.FileType("r"), help='Blast XML Output')
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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260 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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261 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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262 parser.add_argument('--trim_end', action='store_true', help='Cut blast results off at end of gene')
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
263 parser.add_argument('--include_seq', action='store_true', help='Include sequence')
1
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264 args = parser.parse_args()
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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265
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
266 for rec in blastxml2gff3(**vars(args)):
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
267 if len(rec.features):
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
268 GFF.write([rec], sys.stdout)