annotate jb2_GFF/GFFOutput.py @ 17:4c201a3d4755 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
author fubar
date Sun, 28 Jan 2024 06:48:52 +0000
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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(
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42 cur_id, list
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43 ):
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44 return cur_id[0]
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45 else:
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46 return cur_id
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47 return None
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48
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49 def update_quals(self, quals, has_children):
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50 """Update a set of qualifiers, adding an ID if necessary."""
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51 cur_id = quals.get("ID", None)
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52 # if we have an ID, record it
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53 if cur_id:
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54 if not isinstance(cur_id, list) and not isinstance(
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55 cur_id, tuple
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56 ):
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57 cur_id = [cur_id]
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58 for add_id in cur_id:
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59 self._seen_ids.append(add_id)
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60 # if we need one and don't have it, create a new one
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61 elif has_children:
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62 new_id = self._generate_id(quals)
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63 self._seen_ids.append(new_id)
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64 quals["ID"] = [new_id]
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65 return quals
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66
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67
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68 class GFF3Writer:
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69 """Write GFF3 files starting with standard Biopython objects."""
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70
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71 def __init__(self):
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72 pass
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73
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74 def write(self, recs, out_handle, include_fasta=False):
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75 """Write the provided records to the given handle in GFF3 format."""
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76 id_handler = _IdHandler()
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77 self._write_header(out_handle)
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78 fasta_recs = []
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79 try:
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80 recs = iter(recs)
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81 except TypeError:
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82 recs = [recs]
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83 for rec in recs:
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84 self._write_rec(rec, out_handle)
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85 self._write_annotations(
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86 rec.annotations, rec.id, len(rec.seq), out_handle
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87 )
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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88 for sf in rec.features:
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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89 sf = self._clean_feature(sf)
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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90 id_handler = self._write_feature(
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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91 sf, rec.id, out_handle, id_handler
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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92 )
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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93 if include_fasta and len(rec.seq) > 0:
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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94 fasta_recs.append(rec)
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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95 if len(fasta_recs) > 0:
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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96 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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97
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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98 def _clean_feature(self, feature):
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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99 quals = {}
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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100 for key, val in feature.qualifiers.items():
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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101 if not isinstance(val, (list, tuple)):
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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102 val = [val]
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103 val = [str(x) for x in val]
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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104 quals[key] = val
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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105 feature.qualifiers = quals
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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106 # Support for Biopython 1.68 and above, which removed sub_features
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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107 if not hasattr(feature, "sub_features"):
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108 feature.sub_features = []
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109 clean_sub = [
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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110 self._clean_feature(f) for f in feature.sub_features
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111 ]
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112 feature.sub_features = clean_sub
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113 return feature
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114
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115 def _write_rec(self, rec, out_handle):
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116 # if we have a SeqRecord, write out optional directive
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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117 if len(rec.seq) > 0:
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118 out_handle.write(
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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119 "##sequence-region %s 1 %s\n" % (rec.id, len(rec.seq))
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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120 )
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121
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122 def _get_phase(self, feature):
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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123 if "phase" in feature.qualifiers:
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124 phase = feature.qualifiers["phase"][0]
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125 elif feature.type == "CDS":
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126 phase = (
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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127 int(feature.qualifiers.get("codon_start", [1])[0]) - 1
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128 )
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129 else:
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130 phase = "."
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131 return str(phase)
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132
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133 def _write_feature(
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134 self, feature, rec_id, out_handle, id_handler, parent_id=None
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diff changeset
135 ):
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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136 """Write a feature with location information."""
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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137 if feature.location.strand == 1:
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138 strand = "+"
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139 elif feature.location.strand == -1:
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140 strand = "-"
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141 else:
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142 strand = "."
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143 # remove any standard features from the qualifiers
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144 quals = feature.qualifiers.copy()
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145 for std_qual in ["source", "score", "phase"]:
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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146 if std_qual in quals and len(quals[std_qual]) == 1:
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147 del quals[std_qual]
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148 # add a link to a parent identifier if it exists
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149 if parent_id:
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150 if "Parent" not in quals:
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151 quals["Parent"] = []
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152 quals["Parent"].append(parent_id)
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153 quals = id_handler.update_quals(
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154 quals, len(feature.sub_features) > 0
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155 )
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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156 if feature.type:
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157 ftype = feature.type
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158 else:
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159 ftype = "sequence_feature"
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160 parts = [
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161 str(rec_id),
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162 feature.qualifiers.get("source", ["feature"])[0],
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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diff changeset
163 ftype,
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164 str(feature.location.start + 1), # 1-based indexing
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165 str(feature.location.end),
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166 feature.qualifiers.get("score", ["."])[0],
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167 strand,
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168 self._get_phase(feature),
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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169 self._format_keyvals(quals),
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170 ]
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171 out_handle.write("\t".join(parts) + "\n")
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172 for sub_feature in feature.sub_features:
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173 id_handler = self._write_feature(
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174 sub_feature,
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175 rec_id,
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176 out_handle,
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177 id_handler,
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178 quals["ID"][0],
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179 )
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180 return id_handler
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181
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182 def _format_keyvals(self, keyvals):
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183 format_kvs = []
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184 for key in sorted(keyvals.keys()):
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185 values = keyvals[key]
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186 key = key.strip()
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187 format_vals = []
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188 if not isinstance(values, list) or isinstance(
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189 values, tuple
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190 ):
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191 values = [values]
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192 for val in values:
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193 val = urllib.parse.quote(str(val).strip(), safe=":/ ")
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194 if (key and val) and val not in format_vals:
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195 format_vals.append(val)
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196 format_kvs.append("%s=%s" % (key, ",".join(format_vals)))
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197 return ";".join(format_kvs)
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198
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199 def _write_annotations(self, anns, rec_id, size, out_handle):
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200 """Add annotations which refer to an entire sequence."""
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201 format_anns = self._format_keyvals(anns)
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202 if format_anns:
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203 parts = [
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204 rec_id,
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205 "annotation",
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206 "remark",
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207 "1",
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208 str(size if size > 1 else 1),
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209 ".",
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210 ".",
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211 ".",
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212 format_anns,
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213 ]
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214 out_handle.write("\t".join(parts) + "\n")
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215
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216 def _write_header(self, out_handle):
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217 """Write out standard header directives."""
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218 out_handle.write("##gff-version 3\n")
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219
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220 def _write_fasta(self, recs, out_handle):
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221 """Write sequence records using the ##FASTA directive."""
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222 out_handle.write("##FASTA\n")
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223 SeqIO.write(recs, out_handle, "fasta")
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224
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225
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226 def write(recs, out_handle, include_fasta=False):
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227 """High level interface to write GFF3 files from SeqRecords and SeqFeatures.
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228
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229 If include_fasta is True, the GFF3 file will include sequence information
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230 using the ##FASTA directive.
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231 """
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232 writer = GFF3Writer()
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233 return writer.write(recs, out_handle, include_fasta)