Mercurial > repos > cpt > cpt_putative_isp

annotate cpt.py @ 1:4e02e6e9e77d draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:51:35 +0000
parents
children 08499fbf8697
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1
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1 #!/usr/bin/env python
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2 from Bio.Seq import Seq, reverse_complement, translate
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3 from Bio.SeqRecord import SeqRecord
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4 from Bio import SeqIO
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5 from Bio.Data import CodonTable
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6 import logging
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7
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8 logging.basicConfig()
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9 log = logging.getLogger()
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10
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11 PHAGE_IN_MIDDLE = re.compile("^(?P<host>.*)\s*phage (?P<phage>.*)$")
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12 BACTERIOPHAGE_IN_MIDDLE = re.compile("^(?P<host>.*)\s*bacteriophage (?P<phage>.*)$")
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13 STARTS_WITH_PHAGE = re.compile(
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14 "^(bacterio|vibrio|Bacterio|Vibrio|)?[Pp]hage (?P<phage>.*)$"
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15 )
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16 NEW_STYLE_NAMES = re.compile("(?P<phage>v[A-Z]_[A-Z][a-z]{2}_.*)")
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17
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18
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19 def phage_name_parser(name):
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20 host = None
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21 phage = None
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22 name = name.replace(", complete genome.", "")
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23 name = name.replace(", complete genome", "")
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24
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25 m = BACTERIOPHAGE_IN_MIDDLE.match(name)
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26 if m:
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27 host = m.group("host")
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28 phage = m.group("phage")
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29 return (host, phage)
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30
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31 m = PHAGE_IN_MIDDLE.match(name)
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32 if m:
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33 host = m.group("host")
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34 phage = m.group("phage")
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35 return (host, phage)
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36
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37 m = STARTS_WITH_PHAGE.match(name)
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38 if m:
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39 phage = m.group("phage")
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40 return (host, phage)
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41
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42 m = NEW_STYLE_NAMES.match(name)
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43 if m:
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44 phage = m.group("phage")
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45 return (host, phage)
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46
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47 return (host, phage)
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48
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49
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50 class OrfFinder(object):
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51 def __init__(self, table, ftype, ends, min_len, strand):
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52 self.table = table
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53 self.table_obj = CodonTable.ambiguous_generic_by_id[table]
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54 self.ends = ends
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55 self.ftype = ftype
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56 self.min_len = min_len
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57 self.starts = sorted(self.table_obj.start_codons)
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58 self.stops = sorted(self.table_obj.stop_codons)
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59 self.re_starts = re.compile("|".join(self.starts))
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60 self.re_stops = re.compile("|".join(self.stops))
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61 self.strand = strand
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62
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63 def locate(self, fasta_file, out_nuc, out_prot, out_bed, out_gff3):
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64 seq_format = "fasta"
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65 log.debug("Genetic code table %i" % self.table)
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66 log.debug("Minimum length %i aa" % self.min_len)
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67
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68 out_count = 0
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69
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70 out_gff3.write("##gff-version 3\n")
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71
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72 for idx, record in enumerate(SeqIO.parse(fasta_file, seq_format)):
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73 for i, (f_start, f_end, f_strand, n, t) in enumerate(
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74 self.get_all_peptides(str(record.seq).upper())
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75 ):
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76 out_count += 1
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77
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78 descr = "length %i aa, %i bp, from %s..%s[%s] of %s" % (
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79 len(t),
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80 len(n),
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81 f_start,
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82 f_end,
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83 f_strand,
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84 record.description,
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85 )
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86 fid = record.id + "|%s%i" % (self.ftype, i + 1)
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87
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88 r = SeqRecord(Seq(n), id=fid, name="", description=descr)
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89 t = SeqRecord(Seq(t), id=fid, name="", description=descr)
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90
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91 SeqIO.write(r, out_nuc, "fasta")
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92 SeqIO.write(t, out_prot, "fasta")
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93
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94 nice_strand = "+" if f_strand == +1 else "-"
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95
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96 out_bed.write(
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97 "\t".join(
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98 map(str, [record.id, f_start, f_end, fid, 0, nice_strand])
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99 )
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100 + "\n"
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101 )
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102
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103 out_gff3.write(
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104 "\t".join(
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105 map(
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106 str,
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107 [
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108 record.id,
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109 "getOrfsOrCds",
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110 "CDS",
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111 f_start + 1,
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112 f_end,
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113 ".",
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114 nice_strand,
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115 0,
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116 "ID=%s.%s.%s" % (self.ftype, idx, i + 1),
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117 ],
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118 )
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119 )
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120 + "\n"
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121 )
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122 log.info("Found %i %ss", out_count, self.ftype)
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123
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124 def start_chop_and_trans(self, s, strict=True):
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125 """Returns offset, trimmed nuc, protein."""
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126 if strict:
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127 assert s[-3:] in self.stops, s
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128 assert len(s) % 3 == 0
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129 for match in self.re_starts.finditer(s, overlapped=True):
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130 # Must check the start is in frame
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131 start = match.start()
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132 if start % 3 == 0:
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133 n = s[start:]
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134 assert len(n) % 3 == 0, "%s is len %i" % (n, len(n))
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135 if strict:
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136 t = translate(n, self.table)
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137 else:
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138 # Use when missing stop codon,
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139 t = "M" + translate(n[3:], self.table, to_stop=True)
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140 yield start, n, t # Edited by CPT to be a generator
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141
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142 def break_up_frame(self, s):
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143 """Returns offset, nuc, protein."""
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144 start = 0
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145 for match in self.re_stops.finditer(s, overlapped=True):
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146 index = match.start() + 3
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147 if index % 3 != 0:
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148 continue
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149 n = s[start:index]
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150 for (offset, n, t) in self.start_chop_and_trans(n):
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151 if n and len(t) >= self.min_len:
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152 yield start + offset, n, t
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153 start = index
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154
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155 def putative_genes_in_sequence(self, nuc_seq):
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156 """Returns start, end, strand, nucleotides, protein.
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157 Co-ordinates are Python style zero-based.
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158 """
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159 nuc_seq = nuc_seq.upper()
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160 # TODO - Refactor to use a generator function (in start order)
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161 # rather than making a list and sorting?
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162 answer = []
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163 full_len = len(nuc_seq)
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164
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165 for frame in range(0, 3):
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166 for offset, n, t in self.break_up_frame(nuc_seq[frame:]):
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167 start = frame + offset # zero based
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168 answer.append((start, start + len(n), +1, n, t))
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169
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170 rc = reverse_complement(nuc_seq)
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171 for frame in range(0, 3):
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172 for offset, n, t in self.break_up_frame(rc[frame:]):
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173 start = full_len - frame - offset # zero based
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174 answer.append((start, start - len(n), -1, n, t))
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175 answer.sort()
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176 return answer
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177
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178 def get_all_peptides(self, nuc_seq):
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179 """Returns start, end, strand, nucleotides, protein.
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180
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181 Co-ordinates are Python style zero-based.
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182 """
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183 # Refactored into generator by CPT
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184 full_len = len(nuc_seq)
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185 if self.strand != "reverse":
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186 for frame in range(0, 3):
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187 for offset, n, t in self.break_up_frame(nuc_seq[frame:]):
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188 start = frame + offset # zero based
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189 yield (start, start + len(n), +1, n, t)
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190 if self.strand != "forward":
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191 rc = reverse_complement(nuc_seq)
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192 for frame in range(0, 3):
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193 for offset, n, t in self.break_up_frame(rc[frame:]):
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194 start = full_len - frame - offset # zero based
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195 yield (start - len(n), start, -1, n, t)
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196
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197
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198 class MGAFinder(object):
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199 def __init__(self, table, ftype, ends, min_len):
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200 self.table = table
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201 self.table_obj = CodonTable.ambiguous_generic_by_id[table]
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202 self.ends = ends
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203 self.ftype = ftype
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204 self.min_len = min_len
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205 self.starts = sorted(self.table_obj.start_codons)
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206 self.stops = sorted(self.table_obj.stop_codons)
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207 self.re_starts = re.compile("|".join(self.starts))
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208 self.re_stops = re.compile("|".join(self.stops))
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209
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210 def locate(self, fasta_file, out_nuc, out_prot, out_bed, out_gff3):
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211 seq_format = "fasta"
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212 log.debug("Genetic code table %i" % self.table)
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213 log.debug("Minimum length %i aa" % self.min_len)
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214
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215 out_count = 0
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216
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217 out_gff3.write("##gff-version 3\n")
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218
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219 for idx, record in enumerate(SeqIO.parse(fasta_file, seq_format)):
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220 for i, (f_start, f_end, f_strand, n, t) in enumerate(
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221 self.get_all_peptides(str(record.seq).upper())
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222 ):
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223 out_count += 1
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224
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225 descr = "length %i aa, %i bp, from %s..%s[%s] of %s" % (
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226 len(t),
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227 len(n),
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228 f_start,
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229 f_end,
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230 f_strand,
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231 record.description,
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parents:
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232 )
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233 fid = record.id + "|%s%i" % (self.ftype, i + 1)
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parents:
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234
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235 r = SeqRecord(Seq(n), id=fid, name="", description=descr)
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236 t = SeqRecord(Seq(t), id=fid, name="", description=descr)
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237
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238 SeqIO.write(r, out_nuc, "fasta")
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239 SeqIO.write(t, out_prot, "fasta")
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240
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241 nice_strand = "+" if f_strand == +1 else "-"
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242
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243 out_bed.write(
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parents:
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244 "\t".join(
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245 map(str, [record.id, f_start, f_end, fid, 0, nice_strand])
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246 )
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247 + "\n"
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parents:
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248 )
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parents:
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249
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250 out_gff3.write(
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parents:
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251 "\t".join(
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252 map(
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parents:
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253 str,
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parents:
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254 [
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255 record.id,
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parents:
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256 "getOrfsOrCds",
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257 "CDS",
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parents:
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258 f_start + 1,
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259 f_end,
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260 ".",
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261 nice_strand,
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262 0,
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263 "ID=%s.%s.%s" % (self.ftype, idx, i + 1),
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parents:
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264 ],
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parents:
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265 )
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parents:
diff changeset
266 )
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267 + "\n"
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parents:
diff changeset
268 )
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269 log.info("Found %i %ss", out_count, self.ftype)
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270
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271 def start_chop_and_trans(self, s, strict=True):
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272 """Returns offset, trimmed nuc, protein."""
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273 if strict:
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parents:
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274 assert s[-3:] in self.stops, s
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275 assert len(s) % 3 == 0
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276 for match in self.re_starts.finditer(s, overlapped=True):
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277 # Must check the start is in frame
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278 start = match.start()
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279 if start % 3 == 0:
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280 n = s[start:]
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281 assert len(n) % 3 == 0, "%s is len %i" % (n, len(n))
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282 if strict:
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283 t = translate(n, self.table)
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284 else:
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285 # Use when missing stop codon,
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parents:
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286 t = "M" + translate(n[3:], self.table, to_stop=True)
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287 yield start, n, t
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288
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parents:
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289 def break_up_frame(self, s):
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290 """Returns offset, nuc, protein."""
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291 start = 0
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292 for match in self.re_stops.finditer(s, overlapped=True):
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parents:
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293 index = match.start() + 3
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parents:
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294 if index % 3 != 0:
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parents:
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295 continue
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296 n = s[start:index]
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parents:
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297 for (offset, n, t) in self.start_chop_and_trans(n):
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parents:
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298 if n and len(t) >= self.min_len:
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parents:
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299 yield start + offset, n, t
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parents:
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300 start = index
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parents:
diff changeset
301
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302 def putative_genes_in_sequence(self, nuc_seq):
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303 """Returns start, end, strand, nucleotides, protein.
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parents:
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304 Co-ordinates are Python style zero-based.
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parents:
diff changeset
305 """
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parents:
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306 nuc_seq = nuc_seq.upper()
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cpt
parents:
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307 # TODO - Refactor to use a generator function (in start order)
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parents:
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308 # rather than making a list and sorting?
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309 answer = []
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310 full_len = len(nuc_seq)
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parents:
diff changeset
311
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parents:
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312 for frame in range(0, 3):
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parents:
diff changeset
313 for offset, n, t in self.break_up_frame(nuc_seq[frame:]):
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parents:
diff changeset
314 start = frame + offset # zero based
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parents:
diff changeset
315 answer.append((start, start + len(n), +1, n, t))
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parents:
diff changeset
316
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317 rc = reverse_complement(nuc_seq)
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parents:
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318 for frame in range(0, 3):
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parents:
diff changeset
319 for offset, n, t in self.break_up_frame(rc[frame:]):
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parents:
diff changeset
320 start = full_len - frame - offset # zero based
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parents:
diff changeset
321 answer.append((start, start - len(n), -1, n, t))
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parents:
diff changeset
322 answer.sort()
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parents:
diff changeset
323 return answer
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parents:
diff changeset
324
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parents:
diff changeset
325 def get_all_peptides(self, nuc_seq):
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parents:
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326 """Returns start, end, strand, nucleotides, protein.
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cpt
parents:
diff changeset
327
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parents:
diff changeset
328 Co-ordinates are Python style zero-based.
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parents:
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329 """
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parents:
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330 # Refactored into generator by CPT
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parents:
diff changeset
331
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parents:
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332 full_len = len(nuc_seq)
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cpt
parents:
diff changeset
333 for frame in range(0, 3):
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parents:
diff changeset
334 for offset, n, t in self.break_up_frame(nuc_seq[frame:]):
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parents:
diff changeset
335 start = frame + offset # zero based
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parents:
diff changeset
336 yield (start, start + len(n), +1, n, t)
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parents:
diff changeset
337 rc = reverse_complement(nuc_seq)
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parents:
diff changeset
338 for frame in range(0, 3):
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parents:
diff changeset
339 for offset, n, t in self.break_up_frame(rc[frame:]):
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parents:
diff changeset
340 start = full_len - frame - offset # zero based
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parents:
diff changeset
341 yield (start - len(n), start, -1, n, t)