Mercurial > repos > fubar > jbrowse2

annotate GFFOutput.py @ 18:2e6c48910819 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a572525c0f1d7b4dbae1c3aaa4e748aa019d8347
author fubar
date Mon, 29 Jan 2024 02:34:43 +0000
parents 4c201a3d4755
children
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17
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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1 """Output Biopython SeqRecords and SeqFeatures to GFF3 format.
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2
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3 The target format is GFF3, the current GFF standard:
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4 http://www.sequenceontology.org/gff3.shtml
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5 """
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6 from six.moves import urllib
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7
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8 from Bio import SeqIO
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9
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10
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11 class _IdHandler:
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12 """Generate IDs for GFF3 Parent/Child
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13 relationships where they don't exist."""
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14
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15 def __init__(self):
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16 self._prefix = "biopygen"
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17 self._counter = 1
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18 self._seen_ids = []
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19
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20 def _generate_id(self, quals):
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21 """Generate a unique ID not present in our existing IDs."""
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22 gen_id = self._get_standard_id(quals)
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23 if gen_id is None:
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24 while 1:
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25 gen_id = "%s%s" % (self._prefix, self._counter)
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26 if gen_id not in self._seen_ids:
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27 break
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28 self._counter += 1
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29 return gen_id
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30
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31 def _get_standard_id(self, quals):
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32 """Retrieve standardized IDs from other sources like NCBI GenBank.
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33
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34 This tries to find IDs from known key/values when stored differently
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35 than GFF3 specifications.
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36 """
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37 possible_keys = ["transcript_id", "protein_id"]
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38 for test_key in possible_keys:
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39 if test_key in quals:
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40 cur_id = quals[test_key]
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41 if isinstance(cur_id, tuple) or isinstance(cur_id, list):
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42 return cur_id[0]
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43 else:
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44 return cur_id
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45 return None
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46
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47 def update_quals(self, quals, has_children):
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48 """Update a set of qualifiers, adding an ID if necessary."""
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49 cur_id = quals.get("ID", None)
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50 # if we have an ID, record it
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51 if cur_id:
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52 if not isinstance(cur_id, list) and not isinstance(cur_id, tuple):
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53 cur_id = [cur_id]
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54 for add_id in cur_id:
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55 self._seen_ids.append(add_id)
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56 # if we need one and don't have it, create a new one
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57 elif has_children:
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58 new_id = self._generate_id(quals)
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59 self._seen_ids.append(new_id)
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60 quals["ID"] = [new_id]
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61 return quals
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62
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63
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64 class GFF3Writer:
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65 """Write GFF3 files starting with standard Biopython objects."""
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66
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67 def __init__(self):
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68 pass
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69
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70 def write(self, recs, out_handle, include_fasta=False):
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71 """Write the provided records to the given handle in GFF3 format."""
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72 id_handler = _IdHandler()
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73 self._write_header(out_handle)
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74 fasta_recs = []
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75 try:
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76 recs = iter(recs)
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77 except TypeError:
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78 recs = [recs]
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79 for rec in recs:
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80 self._write_rec(rec, out_handle)
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81 self._write_annotations(rec.annotations, rec.id, len(rec.seq), out_handle)
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82 for sf in rec.features:
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83 sf = self._clean_feature(sf)
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84 id_handler = self._write_feature(sf, rec.id, out_handle, id_handler)
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85 if include_fasta and len(rec.seq) > 0:
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86 fasta_recs.append(rec)
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87 if len(fasta_recs) > 0:
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88 self._write_fasta(fasta_recs, out_handle)
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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89
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90 def _clean_feature(self, feature):
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91 quals = {}
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92 for key, val in feature.qualifiers.items():
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93 if not isinstance(val, (list, tuple)):
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94 val = [val]
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95 val = [str(x) for x in val]
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96 quals[key] = val
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97 feature.qualifiers = quals
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98 # Support for Biopython 1.68 and above, which removed sub_features
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99 if not hasattr(feature, "sub_features"):
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100 feature.sub_features = []
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101 clean_sub = [self._clean_feature(f) for f in feature.sub_features]
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102 feature.sub_features = clean_sub
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103 return feature
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104
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105 def _write_rec(self, rec, out_handle):
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106 # if we have a SeqRecord, write out optional directive
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107 if len(rec.seq) > 0:
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108 out_handle.write("##sequence-region %s 1 %s\n" % (rec.id, len(rec.seq)))
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109
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110 def _get_phase(self, feature):
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111 if "phase" in feature.qualifiers:
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112 phase = feature.qualifiers["phase"][0]
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113 elif feature.type == "CDS":
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114 phase = int(feature.qualifiers.get("codon_start", [1])[0]) - 1
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115 else:
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116 phase = "."
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117 return str(phase)
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118
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119 def _write_feature(self, feature, rec_id, out_handle, id_handler, parent_id=None):
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120 """Write a feature with location information."""
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121 if feature.location.strand == 1:
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122 strand = "+"
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123 elif feature.location.strand == -1:
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124 strand = "-"
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125 else:
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126 strand = "."
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127 # remove any standard features from the qualifiers
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128 quals = feature.qualifiers.copy()
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129 for std_qual in ["source", "score", "phase"]:
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130 if std_qual in quals and len(quals[std_qual]) == 1:
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131 del quals[std_qual]
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132 # add a link to a parent identifier if it exists
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133 if parent_id:
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134 if "Parent" not in quals:
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135 quals["Parent"] = []
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136 quals["Parent"].append(parent_id)
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137 quals = id_handler.update_quals(quals, len(feature.sub_features) > 0)
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138 if feature.type:
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139 ftype = feature.type
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140 else:
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141 ftype = "sequence_feature"
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142 parts = [
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143 str(rec_id),
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144 feature.qualifiers.get("source", ["feature"])[0],
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145 ftype,
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146 str(feature.location.start + 1), # 1-based indexing
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147 str(feature.location.end),
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148 feature.qualifiers.get("score", ["."])[0],
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149 strand,
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150 self._get_phase(feature),
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151 self._format_keyvals(quals),
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152 ]
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153 out_handle.write("\t".join(parts) + "\n")
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154 for sub_feature in feature.sub_features:
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155 id_handler = self._write_feature(
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156 sub_feature,
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157 rec_id,
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158 out_handle,
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159 id_handler,
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160 quals["ID"][0],
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161 )
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162 return id_handler
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163
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164 def _format_keyvals(self, keyvals):
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165 format_kvs = []
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166 for key in sorted(keyvals.keys()):
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167 values = keyvals[key]
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168 key = key.strip()
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169 format_vals = []
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170 if not isinstance(values, list) or isinstance(values, tuple):
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171 values = [values]
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172 for val in values:
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173 val = urllib.parse.quote(str(val).strip(), safe=":/ ")
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174 if (key and val) and val not in format_vals:
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175 format_vals.append(val)
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176 format_kvs.append("%s=%s" % (key, ",".join(format_vals)))
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177 return ";".join(format_kvs)
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178
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179 def _write_annotations(self, anns, rec_id, size, out_handle):
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180 """Add annotations which refer to an entire sequence."""
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181 format_anns = self._format_keyvals(anns)
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182 if format_anns:
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183 parts = [
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184 rec_id,
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185 "annotation",
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186 "remark",
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187 "1",
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188 str(size if size > 1 else 1),
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189 ".",
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190 ".",
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191 ".",
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192 format_anns,
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193 ]
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194 out_handle.write("\t".join(parts) + "\n")
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195
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196 def _write_header(self, out_handle):
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197 """Write out standard header directives."""
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198 out_handle.write("##gff-version 3\n")
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199
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200 def _write_fasta(self, recs, out_handle):
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201 """Write sequence records using the ##FASTA directive."""
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202 out_handle.write("##FASTA\n")
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203 SeqIO.write(recs, out_handle, "fasta")
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204
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205
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206 def write(recs, out_handle, include_fasta=False):
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207 """High level interface to write GFF3 files from SeqRecords and SeqFeatures.
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208
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209 If include_fasta is True, the GFF3 file will include sequence information
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210 using the ##FASTA directive.
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211 """
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212 writer = GFF3Writer()
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213 return writer.write(recs, out_handle, include_fasta)