Mercurial > repos > cpt > cpt_gff_to_gbk

annotate gff2gb.py @ 3:c8fcb7246ac3 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:44:32 +0000
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3
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1 #!/usr/bin/env python
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2 """Convert a GFF and associated FASTA file into GenBank format.
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3
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4 Usage:
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5 gff_to_genbank.py <GFF annotation file> <FASTA sequence file>
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6 """
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7 import argparse
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8 import sys
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9 import re
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10 import copy
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11 import itertools
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12 import logging
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13 from Bio import SeqIO
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14
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15 # from Bio.Alphabet import generic_dna
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16 from Bio.SeqFeature import CompoundLocation, FeatureLocation
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17 from CPT_GFFParser import gffParse, gffWrite
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18 from gff3 import (
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19 feature_lambda,
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20 wa_unified_product_name,
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21 is_uuid,
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22 feature_test_type,
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23 fsort,
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24 feature_test_true,
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25 feature_test_quals,
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26 )
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27
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28 default_name = re.compile(r"^gene_(\d+)$")
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29 logging.basicConfig(level=logging.INFO)
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30
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31
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32 def rename_key(ds, k_f, k_t):
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33 """Rename a key in a dictionary and return it, FP style"""
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34 # If they key is not in the dictionary, just return immediately
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35 if k_f not in ds:
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36 return ds
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37
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38 # Otherwise, we check if the target key is in there
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39 if k_t in ds:
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40 # If it is, we need to append
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41 ds[k_t] += ds[k_f]
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42 else:
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43 # if not, we can just set.
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44 ds[k_t] = ds[k_f]
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45
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46 # Remove source
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47 del ds[k_f]
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48 return ds
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49
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50
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51 def gff3_to_genbank(gff_file, fasta_file, transltbl):
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52 fasta_input = SeqIO.to_dict(SeqIO.parse(fasta_file, "fasta")) # , generic_dna))
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53 gff_iter = gffParse(gff_file, fasta_input)
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54
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55 for record in gff_iter:
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56 yield handle_record(record, transltbl)
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57
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58
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59 def handle_non_gene_features(features):
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60 # These are NON-GENE features (maybe terminators? etc?)
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61 for feature in feature_lambda(
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62 features,
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63 feature_test_type,
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64 {"type": "gene"},
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65 subfeatures=False,
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66 invert=True,
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67 recurse=True, # used to catch RBS from new apollo runs (used to be False)
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68 ):
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69 if feature.type in (
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70 "terminator",
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71 "tRNA",
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72 "Shine_Dalgarno_sequence",
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73 "sequence_feature",
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74 "recombination_feature",
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75 "sequence_alteration",
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76 "binding_site",
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77 ):
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78 yield feature
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79 elif feature.type in ("CDS",):
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80 pass
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81 else:
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82 yield feature
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83
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84
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85 def fminmax(feature):
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86 fmin = None
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87 fmax = None
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88 for sf in feature_lambda([feature], feature_test_true, {}, subfeatures=True):
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89 if fmin is None:
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90 fmin = sf.location.start
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91 fmax = sf.location.end
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92 if sf.location.start < fmin:
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93 fmin = sf.location.start
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94 if sf.location.end > fmax:
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95 fmax = sf.location.end
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96 return fmin, fmax
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97
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98
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99 def fix_gene_boundaries(feature):
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100 # There is a frustrating bug in apollo whereby we have created gene
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101 # features which are LARGER than expected, but we cannot see this.
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102 # We only see a perfect sized gene + great SD together.
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103 #
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104 # So, we have this awful hack to clamp the location of the gene
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105 # feature to the contained mRNAs. This is good enough for now.
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106 fmin, fmax = fminmax(feature)
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107 if feature.location.strand > 0:
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108 feature.location = FeatureLocation(fmin, fmax, strand=1)
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109 else:
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110 feature.location = FeatureLocation(fmin, fmax, strand=-1)
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111 return feature
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112
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113
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114 def fix_gene_qualifiers(name, feature, fid):
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115 for mRNA in feature.sub_features:
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116 mRNA.qualifiers["locus_tag"] = "CPT_%s_%03d" % (name, fid)
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117 # And some exons below that
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118 sf_replacement = []
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119 for sf in mRNA.sub_features:
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120 # We set a locus_tag on ALL sub features
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121 sf.qualifiers["locus_tag"] = "CPT_%s_%03d" % (name, fid)
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122 # Remove Names which are UUIDs
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123 # NOT GOOD PRACTICE
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diff changeset
124 try:
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125 if is_uuid(sf.qualifiers["Name"][0]):
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126 del sf.qualifiers["Name"]
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127 except KeyError:
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128 continue # might should go back to pass, I have not put thought into this still
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129
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130 # If it is the RBS exon (mis-labelled by apollo as 'exon')
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131 if sf.type == "exon" and len(sf) < 10:
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132 sf.type = "Shine_Dalgarno_sequence"
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133 sf_replacement.append(sf)
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134 # and if it is the CDS
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135 elif sf.type == "CDS":
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136 # Update CDS qualifiers with all info that was on parent
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137 sf.qualifiers.update(feature.qualifiers)
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138 sf_replacement.append(sf)
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139 else:
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140 sf_replacement.append(sf)
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141 if mRNA.type == "tRNA":
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142 mRNA.qualifiers["product"] = mRNA.qualifiers["Name"]
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143 # Handle multiple child CDS features by merging them.
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144 # Replace the subfeatures on the mRNA
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145 mRNA.sub_features = merge_multi_cds(sf_replacement)
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146 return feature
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147
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148
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149 def fix_frameshifted(features):
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150 logging.info("Fixing Frameshifted group: [%s]", str(features))
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151 genes = features
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152 # Find all mRNAs (plus reduce nested list into flattened one)
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153 mRNAs = sum([f.sub_features for f in genes], [])
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154 # Find all CDSs (plus reduce nested list into flattened one)
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155 cdss = sum([m.sub_features for m in mRNAs], [])
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156 # List to store the RBSs which we'll break apart + re-attach later.
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157 rbss = []
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158 # List to store all of the CDSs (i.e. cdss - rbss)
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159 cdss2 = []
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160 # Copy genes + clean out subfeatures. We'll re-use these constructs.
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161 fixed_features = copy.deepcopy(genes)
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162 for f in fixed_features:
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163 f.sub_features = []
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164 # Copy / empty out mRNAs
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165 fixed_mrnas = copy.deepcopy(mRNAs)
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166 for f in fixed_mrnas:
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167 f.sub_features = []
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168 f.qualifiers = {}
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169 # Fill rbss + cdss2
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170 for cds in cdss:
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171 if "frameshift" in cds.qualifiers:
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172 del cds.qualifiers["frameshift"]
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173 # Ignore short features, as those are RBSs
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174 if len(cds) < 15:
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175 rbss.append(cds)
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176 continue
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177 # Otherwise cdss.
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178 else:
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179 cdss2.append(cds)
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180 # Ok, now have cdss2 to deal with.
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181 other = []
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182 # Find the two with least value for distance between end / start (strand aware).
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183 # For every possible pair, we'll check their distance
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184 match_data = {}
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185 for (a, b) in itertools.permutations(cdss2, 2):
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186 if a.location.start < b.location.start:
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187 # A is downstream of B
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cpt
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188 match_data[(a, b)] = b.location.start - a.location.end
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189 else:
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parents:
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190 match_data[(a, b)] = a.location.start - b.location.end
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cpt
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191
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192 # Now we'll find the features which are closest in terms of start/end
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193 ((merge_a, merge_b), value) = max(match_data.items(), key=lambda kv: kv[1])
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194 # And get the non-matching features into other
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195 for f in cdss2:
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cpt
parents:
diff changeset
196 if f != merge_a and f != merge_b:
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parents:
diff changeset
197 other.append(f)
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198 # Back to the merge_a/b
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diff changeset
199 # With those, we'll merge them into one feature, and discard the other.
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cpt
parents:
diff changeset
200 merge_a.location = CompoundLocation([merge_a.location, merge_b.location])
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cpt
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diff changeset
201 # The gene + RBSs should be identical and two/two.
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cpt
parents:
diff changeset
202 assert len(fixed_features) == 2
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cpt
parents:
diff changeset
203 # If not, we can just duplicate the RBS, doesn't matter.
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cpt
parents:
diff changeset
204 noRBS = len(rbss) == 0
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cpt
parents:
diff changeset
205 if len(rbss) != 2 and not noRBS:
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cpt
parents:
diff changeset
206 rbss = [rbss[0], copy.deepcopy(rbss[0])]
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cpt
parents:
diff changeset
207 # Now re-construct.
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cpt
parents:
diff changeset
208 gene_0 = fixed_features[0]
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cpt
parents:
diff changeset
209 gene_1 = fixed_features[1]
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cpt
parents:
diff changeset
210 mRNA_0 = fixed_mrnas[0]
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cpt
parents:
diff changeset
211 mRNA_1 = fixed_mrnas[1]
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cpt
parents:
diff changeset
212
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cpt
parents:
diff changeset
213 if not noRBS:
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cpt
parents:
diff changeset
214 mRNA_0.sub_features = [rbss[0], merge_a]
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cpt
parents:
diff changeset
215 mRNA_1.sub_features = other + [rbss[1]]
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cpt
parents:
diff changeset
216 else:
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parents:
diff changeset
217 mRNA_0.sub_features = [merge_a]
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cpt
parents:
diff changeset
218 mRNA_1.sub_features = other
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cpt
parents:
diff changeset
219 mRNA_0 = fix_gene_boundaries(mRNA_0)
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cpt
parents:
diff changeset
220 mRNA_1 = fix_gene_boundaries(mRNA_1)
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cpt
parents:
diff changeset
221
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parents:
diff changeset
222 gene_0.sub_features = [mRNA_0]
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cpt
parents:
diff changeset
223 gene_1.sub_features = [mRNA_1]
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cpt
parents:
diff changeset
224 gene_0 = fix_gene_boundaries(gene_0)
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cpt
parents:
diff changeset
225 gene_1 = fix_gene_boundaries(gene_1)
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cpt
parents:
diff changeset
226
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cpt
parents:
diff changeset
227 return fixed_features
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cpt
parents:
diff changeset
228
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cpt
parents:
diff changeset
229
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parents:
diff changeset
230 def fix_frameshifts(features):
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cpt
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diff changeset
231 # Collect all gene features where at least one subfeature has a
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cpt
parents:
diff changeset
232 # frameshift=??? annotation.
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cpt
parents:
diff changeset
233 def has_frameshift_qual(f):
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cpt
parents:
diff changeset
234 return (
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cpt
parents:
diff changeset
235 len(
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cpt
parents:
diff changeset
236 list(
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cpt
parents:
diff changeset
237 feature_lambda(
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cpt
parents:
diff changeset
238 f.sub_features, feature_test_quals, {"frameshift": None}
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cpt
parents:
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239 )
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240 )
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241 )
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242 > 0
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243 )
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244
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245 def has_frameshift_qual_val(f, val):
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246 return (
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247 len(
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248 list(
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249 feature_lambda(
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250 f.sub_features, feature_test_quals, {"frameshift": val}
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251 )
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252 )
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253 )
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254 > 0
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255 )
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256
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257 def get_frameshift_qual(f):
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258 for f in feature_lambda(
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259 f.sub_features, feature_test_quals, {"frameshift": None}
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260 ):
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261 return f.qualifiers["frameshift"]
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262
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263 to_frameshift = [x for x in features if x.type == "gene" and has_frameshift_qual(x)]
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264 fixed = [x for x in features if x not in to_frameshift]
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265
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266 frameshift_keys = set(sum(map(get_frameshift_qual, to_frameshift), []))
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267 for key in frameshift_keys:
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268 # Get features matching that key
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269 current = [x for x in to_frameshift if has_frameshift_qual_val(x, key)]
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270 # Fix them and append them
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271 fixed += fix_frameshifted(current)
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272
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273 return fixed
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274
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275
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276 def remove_useless_features(features):
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277 # Drop mRNAs, apollo crap, useless CDSs
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278 for f in features:
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279 if f.type in (
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280 "non_canonical_three_prime_splice_site",
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281 "non_canonical_five_prime_splice_site",
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282 "stop_codon_read_through",
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283 "mRNA",
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284 "exon",
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285 ):
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286 continue
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287 else:
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288 if f.type == "CDS" and len(f) < 10:
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289 # Another RBS mistake
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290 continue
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291 # We use the full GO term, but it should be less than that.
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292 if f.type == "Shine_Dalgarno_sequence":
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293 f.type = "RBS"
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294
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295 if f.type == "sequence_feature":
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296 f.type = "misc_feature"
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297
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298 if f.type == "recombination_feature":
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299 f.type = "misc_recomb"
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300
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301 if f.type == "sequence_alteration":
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302 f.type = "variation"
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303
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304 if f.type == "binding_site":
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305 f.type = "misc_binding"
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306
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307 yield f
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308
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309
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310 def merge_multi_cds(mRNA_sf):
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311 cdss = [x for x in mRNA_sf if x.type == "CDS"]
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312 non_cdss = [x for x in mRNA_sf if x.type != "CDS"]
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313 if len(cdss) <= 1:
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314 return non_cdss + cdss
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315 else:
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316 # Grab all locations, and sort them so we can work with them rationally.
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317 locations = sorted([x.location for x in cdss], key=lambda y: y.start)
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318 # Pick randomly a main CDS
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319 main_cds = cdss[0]
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320 # We'll merge the other CDSs into this one.
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321 main_cds.location = CompoundLocation(locations)
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322 return non_cdss + [main_cds]
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323
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324
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325 def handle_record(record, transltbl):
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326 full_feats = []
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327 for feature in fsort(record.features):
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328 if (
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329 feature.type == "region"
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330 and "source" in feature.qualifiers
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331 and "GenBank" in feature.qualifiers["source"]
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332 ):
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333 feature.type = "source"
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334
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335 if "comment1" in feature.qualifiers:
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336 del feature.qualifiers["comment1"]
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337
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338 if "Note" in feature.qualifiers:
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339 record.annotations = feature.qualifiers
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340 if len(feature.qualifiers["Note"]) > 1:
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341 record.annotations["comment"] = feature.qualifiers["Note"][1]
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342 del feature.qualifiers["Note"]
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343
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344 if "comment" in feature.qualifiers:
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345 del feature.qualifiers["comment"]
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346
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347 # We'll work on a separate copy of features to avoid modifying a list
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348 # we're iterating over
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349 replacement_feats = []
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350 replacement_feats += list(handle_non_gene_features(record.features))
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351
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352 # Renumbering requires sorting
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353 fid = 0
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354 for feature in fsort(
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355 feature_lambda(
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356 record.features, feature_test_type, {"type": "gene"}, subfeatures=True
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357 )
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358 ):
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359 # Our modifications only involve genes
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360 fid += 1
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361
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362 feature = fix_gene_boundaries(feature)
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363 # Which have mRNAs we'll drop later
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364 feature = fix_gene_qualifiers(record.id, feature, fid)
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365
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366 # Wipe out the parent gene's data, leaving only a locus_tag
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367 feature.qualifiers = {"locus_tag": "CPT_%s_%03d" % (record.id, fid)}
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368
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369 # Patch our features back in (even if they're non-gene features)
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370 replacement_feats.append(feature)
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371
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372 replacement_feats = fix_frameshifts(replacement_feats)
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373 # exit(0)
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374 flat_features = feature_lambda(
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375 replacement_feats, lambda x: True, {}, subfeatures=True
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376 )
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377
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378 flat_features = remove_useless_features(flat_features)
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379
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380 # Meat of our modifications
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381 for flat_feat in flat_features:
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382 # Try and figure out a name. We gave conflicting instructions, so
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383 # this isn't as trivial as it should be.
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384 protein_product = wa_unified_product_name(flat_feat)
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385
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386 for x in (
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387 "source",
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388 "phase",
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389 "Parent",
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390 "ID",
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391 "owner",
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392 "date_creation",
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393 "date_last_modified",
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394 "datasetSource",
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395 ):
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396 if x in flat_feat.qualifiers:
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397 if x == "ID":
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398 flat_feat._ID = flat_feat.qualifiers["ID"]
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399 del flat_feat.qualifiers[x]
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400
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401 # Add product tag
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402 if flat_feat.type == "CDS":
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403 flat_feat.qualifiers["product"] = [protein_product]
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404 flat_feat.qualifiers["transl_table"] = [transltbl]
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405 if "Product" in flat_feat.qualifiers:
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406 del flat_feat.qualifiers["Product"]
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407 elif flat_feat.type == "RBS":
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408 if "locus_tag" not in flat_feat.qualifiers.keys():
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409 continue
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410
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411 elif flat_feat.type == "terminator":
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412 flat_feat.type = "regulatory"
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413 flat_feat.qualifiers = {"regulatory_class": "terminator"}
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414
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415 # In genbank format, note is lower case.
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416 flat_feat.qualifiers = rename_key(flat_feat.qualifiers, "Note", "note")
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417 flat_feat.qualifiers = rename_key(flat_feat.qualifiers, "description", "note")
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418 flat_feat.qualifiers = rename_key(flat_feat.qualifiers, "protein", "note")
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419 flat_feat.qualifiers = rename_key(flat_feat.qualifiers, "Dbxref", "db_xref")
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420 if "Name" in flat_feat.qualifiers:
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421 del flat_feat.qualifiers["Name"]
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422
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423 # more apollo nonsense
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424 if "Manually set translation start" in flat_feat.qualifiers.get("note", []):
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425 flat_feat.qualifiers["note"].remove("Manually set translation start")
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426
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427 # Append the feature
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428 full_feats.append(flat_feat)
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429
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430 # Update our features
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431 record.features = fsort(full_feats)
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432 # Strip off record names that would cause crashes.
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433 record.name = record.name[0:16]
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434 return record
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435
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436
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437 if __name__ == "__main__":
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438 # Grab all of the filters from our plugin loader
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439 parser = argparse.ArgumentParser(description="Convert gff3 to gbk")
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440 parser.add_argument("gff_file", type=argparse.FileType("r"), help="GFF3 file")
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441 parser.add_argument("fasta_file", type=argparse.FileType("r"), help="Fasta Input")
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442 parser.add_argument(
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443 "--transltbl",
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444 type=int,
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445 default=11,
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446 help="Translation Table choice for CDS tag, default 11",
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447 )
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448 args = parser.parse_args()
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449
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450 for record in gff3_to_genbank(**vars(args)):
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451 record.annotations["molecule_type"] = "DNA"
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452 # record.seq.alphabet = generic_dna
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453 SeqIO.write([record], sys.stdout, "genbank")