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1 #!/usr/bin/env python3
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2
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3 import argparse
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4 import time
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5 import os
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10
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6 import textwrap
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7 from collections import defaultdict
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8 from Bio import SeqIO
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9 import configuration
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17
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10 from dante_gff_output_filtering import parse_gff_line
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11 t_nt_seqs_extraction = time.time()
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12
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13
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14 def str2bool(v):
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15 if v.lower() in ('yes', 'true', 't', 'y', '1'):
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16 return True
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17 elif v.lower() in ('no', 'false', 'f', 'n', '0'):
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18 return False
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19 else:
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20 raise argparse.ArgumentTypeError('Boolean value expected')
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21
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22
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23 def check_file_start(gff_file):
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24 count_comment = 0
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25 with open(gff_file, "r") as gff_all:
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26 line = gff_all.readline()
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27 while line.startswith("#"):
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28 line = gff_all.readline()
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29 count_comment += 1
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30 return count_comment, line
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31
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32
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33 def extract_nt_seqs(DNA_SEQ, DOM_GFF, OUT_DIR, CLASS_TBL, EXTENDED):
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34 ''' Extract nucleotide sequences of protein domains found by DANTE from input DNA seq.
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35 Sequences are saved in fasta files separately for each transposon lineage.
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36 Sequences extraction is based on position of Best_Hit alignment reported by LASTAL.
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37 The positions can be extended (optional) based on what part of database domain was aligned
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38 (Best_Hit_DB_Pos attribute).
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39 The strand orientation needs to be considered in extending and extracting the sequence itself
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40 '''
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41 [count_comment, first_line] = check_file_start(DOM_GFF)
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42 unique_classes = get_unique_classes(CLASS_TBL)
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43 files_dict = defaultdict(str)
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44 domains_counts_dict = defaultdict(int)
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45 allSeqs = SeqIO.to_dict(SeqIO.parse(DNA_SEQ, 'fasta'))
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46 with open(DOM_GFF, "r") as domains:
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47 for comment_idx in range(count_comment):
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48 next(domains)
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49 seq_id_stored = first_line.split("\t")[0]
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50 allSeqs = SeqIO.to_dict(SeqIO.parse(DNA_SEQ, 'fasta'))
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51 seq_nt = allSeqs[seq_id_stored]
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52 for line in domains:
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53 gff_line = parse_gff_line(line)
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54 elem_type = gff_line['attributes']['Final_Classification']
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55 if elem_type == configuration.AMBIGUOUS_TAG:
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56 continue # skip ambiguous classification
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57 seq_id = gff_line['seqid']
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58 dom_type = gff_line['attributes']['Name']
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59 strand = gff_line['strand']
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60 align_nt_start = int(gff_line['attributes']['Best_Hit'].split(":")[
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61 -1].split("-")[0])
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62 align_nt_end = int(gff_line['attributes']['Best_Hit'].split(":")[
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63 -1].split("-")[1].split("[")[0])
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64 if seq_id != seq_id_stored:
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65 seq_id_stored = seq_id
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66 seq_nt = allSeqs[seq_id_stored]
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67 if EXTENDED:
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68 ## which part of database sequence was aligned
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69 db_part = gff_line['attributes']['Best_Hit_DB_Pos']
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70 ## db_part = line.split("\t")[8].split(";")[4].split("=")[1]
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71 ## datatabse seq length
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72 dom_len = int(db_part.split("of")[1])
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73 ## start of alignment on database seq
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74 db_start = int(db_part.split("of")[0].split(":")[0])
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75 ## end of alignment on database seq
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76 db_end = int(db_part.split("of")[0].split(":")[1])
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77 ## number of nucleotides missing in the beginning
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78 dom_nt_prefix = (db_start - 1) * 3
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79 ## number of nucleotides missing in the end
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80 dom_nt_suffix = (dom_len - db_end) * 3
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81 if strand == "+":
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82 dom_nt_start = align_nt_start - dom_nt_prefix
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83 dom_nt_end = align_nt_end + dom_nt_suffix
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84 ## reverse extending for - strand
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85 else:
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86 dom_nt_start = align_nt_start - dom_nt_suffix
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87 dom_nt_end = align_nt_end + dom_nt_prefix
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88 ## correction for domain after extending having negative starting positon
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89 dom_nt_start = max(1, dom_nt_start)
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90 else:
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91 dom_nt_start = align_nt_start
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92 dom_nt_end = align_nt_end
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93 full_dom_nt = seq_nt.seq[dom_nt_start - 1:dom_nt_end]
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94 ## for - strand take reverse complement of the extracted sequence
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95 if strand == "-":
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96 full_dom_nt = full_dom_nt.reverse_complement()
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97 full_dom_nt = str(full_dom_nt)
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98 ## report when domain classified to the last level and no Ns in extracted seq
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99 if elem_type in unique_classes and "N" not in full_dom_nt:
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100 # lineages reported in separate fasta files
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101 if not elem_type in files_dict:
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102 files_dict[elem_type] = os.path.join(
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103 OUT_DIR, "{}.fasta".format(elem_type.split("|")[
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104 -1].replace("/", "_")))
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105 with open(files_dict[elem_type], "a") as out_nt_seq:
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106 out_nt_seq.write(">{}:{}-{}|{}[{}]\n{}\n".format(
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107 seq_nt.id, dom_nt_start, dom_nt_end, dom_type,
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108 elem_type, textwrap.fill(full_dom_nt,
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109 configuration.FASTA_LINE)))
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110 domains_counts_dict[elem_type] += 1
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111 return domains_counts_dict
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112
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113
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114 def get_unique_classes(CLASS_TBL):
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115 ''' Get all the lineages of current domains classification table to check if domains are classified to the last level.
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116 Only the sequences of unambiguous and completely classified domains will be extracted.
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117 '''
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118 unique_classes = []
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119 with open(CLASS_TBL, "r") as class_tbl:
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120 for line in class_tbl:
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121 line_class = "|".join(line.rstrip().split("\t")[1:])
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122 if line_class not in unique_classes:
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123 unique_classes.append(line_class)
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124 return unique_classes
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125
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126
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127 def write_domains_stat(domains_counts_dict, OUT_DIR):
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128 ''' Report counts of domains for individual lineages
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129 '''
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130 total = 0
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131 with open(
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132 os.path.join(OUT_DIR,
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133 configuration.EXTRACT_DOM_STAT), "w") as dom_stat:
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134 for domain, count in domains_counts_dict.items():
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135 dom_stat.write(";{}:{}\n".format(domain, count))
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136 total += count
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137 dom_stat.write(";TOTAL:{}\n".format(total))
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138
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139
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140 def main(args):
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141
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142 DNA_SEQ = args.input_dna
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143 DOM_GFF = args.domains_gff
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144 OUT_DIR = args.out_dir
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145 CLASS_TBL = args.classification
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146 EXTENDED = args.extended
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147
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148 if not os.path.exists(OUT_DIR):
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149 os.makedirs(OUT_DIR)
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150
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151 domains_counts_dict = extract_nt_seqs(DNA_SEQ, DOM_GFF, OUT_DIR, CLASS_TBL,
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152 EXTENDED)
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153 write_domains_stat(domains_counts_dict, OUT_DIR)
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154
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155 print("ELAPSED_TIME_EXTRACTION = {} s\n".format(time.time() -
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156 t_nt_seqs_extraction))
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157
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158
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159 if __name__ == "__main__":
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160
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161 # Command line arguments
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162 parser = argparse.ArgumentParser()
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163 parser.add_argument('-i',
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164 '--input_dna',
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165 type=str,
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166 required=True,
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167 help='path to input DNA sequence')
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168 parser.add_argument('-d',
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169 '--domains_gff',
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170 type=str,
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171 required=True,
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172 help='GFF file of protein domains')
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173 parser.add_argument('-cs',
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174 '--classification',
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175 type=str,
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176 required=True,
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177 help='protein domains classification file')
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178 parser.add_argument('-out',
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179 '--out_dir',
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180 type=str,
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181 default=configuration.EXTRACT_OUT_DIR,
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182 help='output directory')
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183 parser.add_argument(
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184 '-ex',
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185 '--extended',
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186 type=str2bool,
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187 default=True,
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188 help=
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189 'extend the domains edges if not the whole datatabase sequence was aligned')
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190 args = parser.parse_args()
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191 main(args)
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