Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate scripts/ReMatCh/utils/strip_alignment.py @ 0:965517909457 draft

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Wed, 22 Jan 2020 08:41:44 -0500
parents
children 0cbed1c0a762
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0
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1 #!/usr/bin/env python
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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) 2017 Miguel Machado <mpmachado@medicina.ulisboa.pt>
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11
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12 Last modified: March 20, 2017
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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 = '0.1'
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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_SeqIO = 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_SeqIO):
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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_SeqIO)) * 100, 2)) + '% of sequences already processed (getting sequences)'
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53 if x + 1 == len(sequences_SeqIO):
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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_SeqIO)) * 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, notGAPs, notMissing, notInvariable):
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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 processed (determining positions type)'
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87 if i + 1 == len(sequences_dict):
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88 all_executed_printed = True
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89 if not all_executed_printed:
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90 print '\n' + str(round((float(i + 1) / sequence_length) * 100, 2)) + '% of positions already processed (determining positions type)'
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91
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92 print 'Positions to keep (no matter): ' + str(len(positions_2_keep))
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93 print 'Invariable sites: ' + str(len(invariable))
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94 print 'Positions with missing data ("N"): ' + str(len(missing))
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95 print 'Positions with GAPs ("-"): ' + str(len(gaps))
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96 print 'Positions with GAPs or missing data: ' + str(gaps_missing)
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97
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98 if notGAPs:
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99 positions_2_keep.extend(gaps)
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100 if notMissing:
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101 positions_2_keep.extend(missing)
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102 if notInvariable:
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103 positions_2_keep.extend(invariable)
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104
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105 positions_2_keep = sorted(set(positions_2_keep))
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106
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107 print 'Positions to keep (final): ' + str(len(positions_2_keep))
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108
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109 return positions_2_keep
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110
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111
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112 def chunkstring(string, length):
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113 return (string[0 + i:length + i] for i in range(0, len(string), length))
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114
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115
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116 def write_fasta(sequences_dict, positions_2_keep, outfile):
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117 print 'Writing stripped sequences'
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118 all_executed_printed = False
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119 with open(outfile, 'wt') as writer:
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120 for x, sample in enumerate(sequences_dict):
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121 writer.write('>' + sample + '\n')
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122 fasta_sequence_lines = chunkstring(''.join([sequences_dict[sample][i] for i in positions_2_keep]), 80)
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123 for line in fasta_sequence_lines:
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124 writer.write(line + '\n')
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125
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126 if (x + 1) % 100 == 0:
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127 print '\n' + str(round((float(x + 1) / len(sequences_dict)) * 100, 2)) + '% of sequences already processed (writing stripped sequences)'
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128 if x + 1 == len(sequences_dict):
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129 all_executed_printed = True
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130 if not all_executed_printed:
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131 print '\n' + str(round((float(x + 1) / len(sequences_dict)) * 100, 2)) + '% of sequences already processed (writing stripped sequences)'
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132
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133
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134 def strip_alignment(args):
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135 outdir = os.path.dirname(os.path.abspath(args.outfile))
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136 if not os.path.isdir(outdir):
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137 os.makedirs(outdir)
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138
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139 outfile = os.path.abspath(args.outfile)
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140
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141 infile = os.path.abspath(args.infile.name)
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142
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143 sequences_dict, sequence_length = get_sequences(infile)
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144 positions_2_keep = positions_type(sequences_dict, sequence_length, args.notGAPs, args.notMissing, args.notInvariable)
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145 write_fasta(sequences_dict, positions_2_keep, outfile)
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146
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147
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148 def main():
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149 parser = argparse.ArgumentParser(prog='strip_alignment.py', description='Strip alignment positions containing gaps, missing data and invariable positions', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
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150 parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
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151
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152 parser_required = parser.add_argument_group('Required options')
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153 parser_required.add_argument('-i', '--infile', type=argparse.FileType('r'), metavar='/path/to/aligned/input/file.fasta', help='Path to the aligned fasta file', required=True)
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154 parser_required.add_argument('-o', '--outfile', type=str, metavar='/path/to/stripped/output/file.fasta', help='Stripped output fasta file', required=True, default='alignment_stripped.fasta')
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155
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156 parser_optional_general = parser.add_argument_group('General facultative options')
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157 parser_optional_general.add_argument('--notGAPs', action='store_true', help='Not strip positions with GAPs')
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158 parser_optional_general.add_argument('--notMissing', action='store_true', help='Not strip positions with missing data')
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159 parser_optional_general.add_argument('--notInvariable', action='store_true', help='Not strip invariable sites')
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160
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161 args = parser.parse_args()
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162
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163 strip_alignment(args)
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164
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165
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166 if __name__ == "__main__":
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167 main()