Mercurial > repos > cpt > cpt_blast_to_xmfa

annotate blast2pxmfa.py @ 2:1623f46fdd2e draft default tip

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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:49:10 +0000
parents c66d6978a5f8
children
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1 #!/usr/bin/env python
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2 import os
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3 import argparse
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4 from CPT_GFFParser import gffParse, gffWrite
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5 from Bio import SeqIO
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6 from Bio.SeqRecord import SeqRecord
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7 from gff3 import feature_lambda, feature_test_true
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8 from Bio.Align.Applications import ClustalwCommandline
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9 from Bio import AlignIO
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10 import tempfile
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11 import logging
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12
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13 log = logging.getLogger()
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14 log.setLevel(logging.DEBUG)
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15
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16
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17 def parse_gff3(annotations, genome):
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18 annotations.seek(0)
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19 genome.seek(0)
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20
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21 data = {}
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22 seq_dict = SeqIO.to_dict(SeqIO.parse(genome, "fasta"))
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23 for record in gffParse(annotations, base_dict=seq_dict):
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24 for feature in feature_lambda(
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25 record.features, feature_test_true, {}, subfeatures=False
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26 ):
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27 data[feature.id] = {
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28 "rec": record.id,
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29 "loc": feature.location,
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30 "seq": feature.extract(record).seq.translate(table=11, cds=False)[0:-1],
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31 }
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32 return data
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33
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34
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35 def get_seqids(genome):
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36 genome.seek(0)
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37 recids = []
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38 for record in SeqIO.parse(genome, "fasta"):
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39 recids.append(record.id)
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40 return recids
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41
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42
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43 def gen_relationships(blast):
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44 for row in blast:
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45 line = row.split("\t")
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46 yield {"from": line[0], "to": line[1], "pident": line[2], "evalue": line[10]}
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47
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48
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49 def cluster_relationships(data):
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50 generated_clusters_ids = []
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51
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52 for relationship in data:
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53 hit = False
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54 relationship_set = set((relationship["from"], relationship["to"]))
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55 for idx, cluster in enumerate(generated_clusters_ids):
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56 if relationship["from"] in cluster or relationship["to"] in cluster:
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57 generated_clusters_ids[idx] = cluster.__or__(relationship_set)
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58 hit = True
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59 break
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60
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61 if not hit:
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62 generated_clusters_ids.append(relationship_set)
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63 return generated_clusters_ids
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64
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65
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66 def align_sequences(SequenceList):
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67 # No sense in aligning one sequence.
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68 if len(SequenceList) < 2:
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69 return None
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70
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71 # Clustal mangles IDs. Fricking Clustal. Specifically it truncates them
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72 # meaning we have to RE-ID every single sequence that goes into it. Lovely.
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73 id_map = {}
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74 for idx, seq in enumerate(SequenceList):
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75 id_map[str(idx)] = seq.id
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76 seq.id = str(idx)
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77
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78 t_fa = tempfile.NamedTemporaryFile(prefix="blastxmfa.", delete=False)
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79 t_aln = tempfile.NamedTemporaryFile(prefix="blastxmfa.", delete=False)
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80 # Write fasta to file
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81 SeqIO.write(SequenceList, str.encode(t_fa.name), "fasta")
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82 # Flush & close
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83 t_fa.flush()
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84 t_fa.close()
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85 t_aln.close()
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86
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87 # Build clustal CLI
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88 d = ClustalwCommandline(infile=t_fa.name, outfile=t_aln.name)
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89 logging.debug(d)
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90 # Call clustal
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91 d()
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92 # Get our alignment back
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93 try:
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94 aln = AlignIO.read(t_aln.name, "clustal")
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95 # Now we replace the IDs with the correct, full length ones
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96 for a in aln:
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97 a.id = id_map[a.id]
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98 # Cleanup
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99 os.unlink(t_fa.name)
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100 os.unlink(t_aln.name)
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101 return aln
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102 except Exception as e:
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103 logging.error("%s, %s", e, t_fa.name)
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104 os.unlink(t_aln.name)
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105 return None
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106
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107
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108 def split_by_n(seq, n):
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109 """A generator to divide a sequence into chunks of n units."""
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110 # http://stackoverflow.com/questions/9475241/split-python-string-every-nth-character
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111 while seq:
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112 yield seq[:n]
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113 seq = seq[n:]
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114
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115
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116 def larger_than_one(it):
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117 for item in it:
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118 if len(item) > 1:
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119 yield item
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120
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121
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122 def smaller_than_3n(x, it):
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123 THRESH = 3 * x
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124 for item in it:
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125 if len(item) <= THRESH:
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126 yield item
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127 else:
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128 log.warn(
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129 "Cluster with %s (>%s) members, seems excessive", len(item), THRESH
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130 )
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131
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132
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133 class XmfaWriter(object):
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134 HEADER_TPL = "> {seqnum}:{start}-{end} {strand} {file} # {realname}\n"
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135
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136 def __init__(self, handle):
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137 self.output = handle
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138 self.output.write("#FormatVersion Mauve1\n")
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139
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140 def write(self, seqnum, start, end, strand, file, realname, sequence):
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141 self.output.write(
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142 self.HEADER_TPL.format(
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143 seqnum=seqnum,
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144 start=start,
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145 end=end,
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146 strand=strand,
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147 file=file,
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148 realname=realname,
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149 )
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150 )
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151
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152 for line in split_by_n(sequence, 80):
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153 self.output.write(line + "\n")
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154
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155 def end(self):
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156 self.output.write("=\n")
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157
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158
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159 def blast2pxmfa(blast, fasta, gff3, output, genomic=False):
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160 logging.info("Parsing sequence")
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161 locations = parse_gff3(gff3, fasta)
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162 logging.info("Parsed locations, clustering")
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163 recids = get_seqids(fasta)
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164 logging.info("Found %s records in fasta", len(recids))
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165
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166 xmw = XmfaWriter(output)
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167
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168 # First let's generate some blastclust style clusters.
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169 clusters = list(
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170 smaller_than_3n(
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171 len(recids),
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172 larger_than_one(cluster_relationships(gen_relationships(blast))),
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173 )
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174 )
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175 logging.debug("%s clusters generated", len(clusters))
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176
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177 def sortIndexForFeatId(element):
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178 # Will not work correctly if genome length is >1mb
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179 general = recids.index(locations[element]["rec"]) * 1000000
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180 specific = locations[element]["loc"].start
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181 return general + specific
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182
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183 for idx, cluster in enumerate(clusters):
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184 logging.debug("Cluster %s/%s, size=%s", idx + 1, len(clusters), len(cluster))
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185 # We're considering 1 LCB :: 1 cluster
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186 seqs = []
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187 for element in cluster:
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188 if element not in locations:
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189 logging.warning("Could not find this feature %s", element)
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190 continue
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191
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192 sr = SeqRecord(
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193 locations[element]["seq"],
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194 id=element,
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195 description="[{0.start}:{0.end}:{0.strand}]".format(
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196 locations[element]["loc"]
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197 ),
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198 )
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199 seqs.append(sr)
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200
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201 aligned_seqs = align_sequences(seqs)
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202 if aligned_seqs is None:
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203 logging.error("Error aligning cluster [%s]", "".join(cluster))
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204 continue
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205
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206 sortedCluster = sorted(cluster, key=lambda x: sortIndexForFeatId(x))
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207 sortedAligned = sorted(aligned_seqs, key=lambda x: sortIndexForFeatId(x.id))
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208 # print(sortedCluster, [x.id for x in sortedAligned])
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209
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210 # Pre-check the asserts.
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211 goodToGo = all(
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212 [
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213 element == aligned_seq.id
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214 for (element, aligned_seq) in zip(sortedCluster, sortedAligned)
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215 ]
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216 )
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217 if not goodToGo:
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218 logging.info(
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219 "Skipping one grouping: %s != %s",
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220 ",".join(sortedCluster),
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221 ",".join([x.id for x in sortedAligned]),
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222 )
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223 # Skip this look
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224 continue
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225 # print(aligned_seqs)
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226 for element, aligned_seq in zip(sortedCluster, sortedAligned):
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227 if element not in locations:
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228 logging.warning("Could not find this feature %s", element)
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229 continue
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230
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231 eloc = locations[element]
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232 xmw.write(
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233 seqnum=recids.index(eloc["rec"]) + 1,
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234 start=eloc["loc"].start,
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235 end=eloc["loc"].end,
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236 strand="+" if eloc["loc"].strand == 1 else "-",
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237 file=eloc["rec"] + ".fa",
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238 realname=element,
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239 sequence=str(aligned_seq.seq),
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240 )
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241 xmw.end()
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242
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243
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244 if __name__ == "__main__":
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245 parser = argparse.ArgumentParser(
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246 description="Convert Blast TSV to protein XMFA", epilog=""
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247 )
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248 parser.add_argument("blast", type=argparse.FileType("r"), help="Blast TSV Output")
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249 parser.add_argument("fasta", type=argparse.FileType("r"), help="Blast Input Fasta")
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250 parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 Gene Calls")
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251 parser.add_argument(
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252 "--genomic",
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253 action="store_true",
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254 help="Further reduce protein results into genomic-level results.",
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255 )
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256 parser.add_argument(
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257 "output", type=argparse.FileType("w"), help="Output file or - for stdout"
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258 )
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259 args = parser.parse_args()
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260
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261 blast2pxmfa(**vars(args))