Mercurial > repos > iss > eurl_vtec_wgs_pt
annotate scripts/ReMatCh/utils/strip_alignment.py @ 0:c6bab5103a14 draft
"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
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date | Mon, 21 Mar 2022 15:23:09 +0000 |
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1 #!/usr/bin/env python3 |
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2 |
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3 # -*- coding: utf-8 -*- |
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4 |
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5 """ |
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6 strip_alignment.py - Strip alignment positions containing gaps, |
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7 missing data and invariable positions |
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8 <https://github.com/B-UMMI/ReMatCh/> |
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9 |
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10 Copyright (C) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt> |
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11 |
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12 Last modified: October 15, 2018 |
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13 |
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14 This program is free software: you can redistribute it and/or modify |
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15 it under the terms of the GNU General Public License as published by |
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16 the Free Software Foundation, either version 3 of the License, or |
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17 (at your option) any later version. |
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18 |
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19 This program is distributed in the hope that it will be useful, |
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20 but WITHOUT ANY WARRANTY; without even the implied warranty of |
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21 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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22 GNU General Public License for more details. |
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23 |
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24 You should have received a copy of the GNU General Public License |
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25 along with this program. If not, see <http://www.gnu.org/licenses/>. |
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26 """ |
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27 |
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28 from Bio import SeqIO |
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29 import os |
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30 import argparse |
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31 import sys |
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32 |
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33 |
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34 version = '0.2' |
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35 |
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36 |
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37 def get_sequences(infile): |
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38 print('Getting sequences') |
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39 sequences_seq_io = list(SeqIO.parse(infile, 'fasta')) |
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40 |
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41 sequence_length = None |
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42 sequences_dict = {} |
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43 all_executed_printed = False |
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44 for x, sequence in enumerate(sequences_seq_io): |
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45 if sequence_length is None: |
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46 sequence_length = len(sequence.seq) |
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47 if sequence_length != len(sequence.seq): |
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48 sys.exit('Sequences with different length!') |
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49 sequences_dict[sequence.id] = list(sequence.seq) |
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50 |
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51 if (x + 1) % 10 == 0: |
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52 print('\n' + str(round((float(x + 1) / len(sequences_seq_io)) * 100, 2)) + '% of sequences already processed (getting sequences)') |
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53 if x + 1 == len(sequences_seq_io): |
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54 all_executed_printed = True |
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55 if not all_executed_printed: |
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56 print('\n' + str(round((float(x + 1) / len(sequences_seq_io)) * 100, 2)) + '% of sequences already processed (getting sequences)') |
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57 |
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58 return sequences_dict, sequence_length |
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59 |
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60 |
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61 def positions_type(sequences_dict, sequence_length, not_gaps, not_missing, not_invariable): |
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62 print('Determining positions type') |
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63 positions_2_keep = [] |
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64 invariable = [] |
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65 missing = [] |
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66 gaps = [] |
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67 gaps_missing = 0 |
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68 all_executed_printed = False |
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69 for i in range(0, sequence_length): |
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70 data = [] |
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71 for sample in sequences_dict: |
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72 data.append(sequences_dict[sample][i]) |
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73 possibilities = set(data) |
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74 if len(possibilities) == 1: |
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75 invariable.append(i) |
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76 if len(possibilities.intersection(set(['N']))) > 0: |
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77 missing.append(i) |
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78 if len(possibilities.intersection(set(['-']))) > 0: |
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79 gaps.append(i) |
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80 if len(possibilities.intersection(set(['N', '-']))) > 0: |
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81 gaps_missing += 1 |
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82 if len(possibilities) > 1 and len(possibilities.intersection(set(['N', '-']))) == 0: |
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83 positions_2_keep.append(i) |
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84 |
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85 if (i + 1) % 10000 == 0: |
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86 print('\n' + str(round((float(i + 1) / sequence_length) * 100, 2)) + '% of positions already' |
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87 ' processed (determining positions' |
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88 ' type)') |
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89 if i + 1 == len(sequences_dict): |
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90 all_executed_printed = True |
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91 if not all_executed_printed: |
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92 print('\n' + str(round((float(i + 1) / sequence_length) * 100, 2)) + '% of positions already' |
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93 ' processed (determining positions' |
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94 ' type)') |
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95 |
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96 print('Positions to keep (no matter): ' + str(len(positions_2_keep))) |
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97 print('Invariable sites: ' + str(len(invariable))) |
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98 print('Positions with missing data ("N"): ' + str(len(missing))) |
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99 print('Positions with GAPs ("-"): ' + str(len(gaps))) |
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100 print('Positions with GAPs or missing data: ' + str(gaps_missing)) |
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101 |
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102 if not_gaps: |
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103 positions_2_keep.extend(gaps) |
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104 if not_missing: |
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105 positions_2_keep.extend(missing) |
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106 if not_invariable: |
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107 positions_2_keep.extend(invariable) |
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108 |
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109 positions_2_keep = sorted(set(positions_2_keep)) |
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110 |
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111 print('Positions to keep (final): ' + str(len(positions_2_keep))) |
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112 |
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113 return positions_2_keep |
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114 |
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115 |
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116 def chunkstring(string, length): |
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117 return (string[0 + i:length + i] for i in range(0, len(string), length)) |
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118 |
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119 |
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120 def write_fasta(sequences_dict, positions_2_keep, outfile): |
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121 print('Writing stripped sequences') |
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122 all_executed_printed = False |
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123 with open(outfile, 'wt') as writer: |
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124 for x, sample in enumerate(sequences_dict): |
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125 writer.write('>' + sample + '\n') |
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126 fasta_sequence_lines = chunkstring(''.join([sequences_dict[sample][i] for i in positions_2_keep]), 80) |
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127 for line in fasta_sequence_lines: |
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128 writer.write(line + '\n') |
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129 |
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130 if (x + 1) % 100 == 0: |
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131 print('\n' + str(round((float(x + 1) / len(sequences_dict)) * 100, 2)) + '% of sequences already' |
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132 ' processed (writing stripped' |
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133 ' sequences)') |
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134 if x + 1 == len(sequences_dict): |
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135 all_executed_printed = True |
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136 if not all_executed_printed: |
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137 print('\n' + str(round((float(x + 1) / len(sequences_dict)) * 100, 2)) + '% of sequences already' |
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138 ' processed (writing stripped' |
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139 ' sequences)') |
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140 |
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141 |
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142 def strip_alignment(args): |
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143 outdir = os.path.dirname(os.path.abspath(args.outfile)) |
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144 if not os.path.isdir(outdir): |
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145 os.makedirs(outdir) |
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146 |
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147 outfile = os.path.abspath(args.outfile) |
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148 |
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149 infile = os.path.abspath(args.infile.name) |
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150 |
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151 sequences_dict, sequence_length = get_sequences(infile) |
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152 positions_2_keep = positions_type(sequences_dict, sequence_length, args.notGAPs, args.notMissing, |
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153 args.notInvariable) |
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154 write_fasta(sequences_dict, positions_2_keep, outfile) |
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155 |
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156 |
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157 def main(): |
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158 parser = argparse.ArgumentParser(prog='strip_alignment.py', |
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159 description='Strip alignment positions containing gaps, missing data and' |
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160 ' invariable positions', |
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161 formatter_class=argparse.ArgumentDefaultsHelpFormatter) |
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162 parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version)) |
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163 |
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164 parser_required = parser.add_argument_group('Required options') |
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165 parser_required.add_argument('-i', '--infile', type=argparse.FileType('r'), |
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166 metavar='/path/to/aligned/input/file.fasta', help='Path to the aligned fasta file', |
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167 required=True) |
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168 parser_required.add_argument('-o', '--outfile', type=str, metavar='/path/to/stripped/output/file.fasta', |
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169 help='Stripped output fasta file', required=True, default='alignment_stripped.fasta') |
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170 |
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171 parser_optional_general = parser.add_argument_group('General facultative options') |
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172 parser_optional_general.add_argument('--notGAPs', action='store_true', help='Not strip positions with GAPs') |
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173 parser_optional_general.add_argument('--notMissing', action='store_true', |
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174 help='Not strip positions with missing data') |
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175 parser_optional_general.add_argument('--notInvariable', action='store_true', help='Not strip invariable sites') |
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176 |
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177 args = parser.parse_args() |
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178 |
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179 strip_alignment(args) |
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180 |
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181 |
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182 if __name__ == "__main__": |
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183 main() |