Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate scripts/ReMatCh/modules/rematch_module.py @ 3:0cbed1c0a762 draft default tip

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
parents 965517909457
children
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1 import os.path
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2 import multiprocessing
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3 import functools
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4 import sys
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5 import pickle
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6
3
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7 # https://chrisyeh96.github.io/2017/08/08/definitive-guide-python-imports.html#case-2-syspath-could-change
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8 sys.path.insert(0, os.path.dirname(os.path.realpath(__file__)))
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9 import utils
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11
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12 def index_fasta_samtools(fasta, region_none, region_outfile_none, print_comand_true):
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13 command = ['samtools', 'faidx', fasta, '', '', '']
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14 shell_true = False
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15 if region_none is not None:
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16 command[3] = region_none
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17 if region_outfile_none is not None:
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18 command[4] = '>'
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19 command[5] = region_outfile_none
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20 shell_true = True
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21 run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, shell_true, None, print_comand_true)
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22 return run_successfully, stdout
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23
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25 # Indexing reference file using Bowtie2
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26 def index_sequence_bowtie2(reference_file, threads):
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27 if os.path.isfile(str(reference_file + '.1.bt2')):
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28 run_successfully = True
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29 else:
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30 command = ['bowtie2-build', '--threads', str(threads), reference_file, reference_file]
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31 run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, True)
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32 return run_successfully
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33
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34
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35 # Mapping with Bowtie2
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36 def mapping_bowtie2(fastq_files, reference_file, threads, outdir, num_map_loc,
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37 bowtie_algorithm='--very-sensitive-local', bowtie_opt=None):
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38 sam_file = os.path.join(outdir, str('alignment.sam'))
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39
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40 # Index reference file
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41 run_successfully = index_sequence_bowtie2(reference_file, threads)
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42
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43 if run_successfully:
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44 command = ['bowtie2', '', '', '-q', bowtie_algorithm, '--threads', str(threads), '-x',
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45 reference_file, '', '--no-unal', '', '-S', sam_file]
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46
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47 if num_map_loc is not None and num_map_loc > 1:
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48 command[1] = '-k'
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49 command[2] = str(num_map_loc)
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50
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51 if len(fastq_files) == 1:
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52 command[9] = '-U ' + fastq_files[0]
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53 elif len(fastq_files) == 2:
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54 command[9] = '-1 ' + fastq_files[0] + ' -2 ' + fastq_files[1]
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55 else:
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56 return False, None
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57
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58 if bowtie_opt is not None:
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59 command[11] = bowtie_opt
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60
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61 run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, True)
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62
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63 if not run_successfully:
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64 sam_file = None
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65
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66 return run_successfully, sam_file
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67
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68
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69 def split_cigar(cigar):
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70 cigars = ['M', 'I', 'D', 'N', 'S', 'H', 'P', '=', 'X']
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71
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72 splited_cigars = []
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73 numbers = ''
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74 for char in cigar:
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75 if char not in cigars:
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76 numbers += char
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77 else:
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78 splited_cigars.append([int(numbers), char])
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79 numbers = ''
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80
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81 return splited_cigars
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82
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83
3
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84 def recode_cigar_based_on_base_quality(cigar, bases_quality, soft_clip_base_quality, mapping_position,
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85 direct_strand_true, soft_clip_cigar_flag_recode):
0
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86 cigar = split_cigar(cigar)
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87 soft_left = []
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88 soft_right = []
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89 cigar_flags_for_reads_length = ('M', 'I', 'S', '=', 'X')
3
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90 read_length_without_right_s = sum([cigar_part[0] for cigar_part in cigar if
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91 cigar_part[1] in cigar_flags_for_reads_length]) - \
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92 (cigar[len(cigar) - 1][0] if cigar[len(cigar) - 1][1] == 'S' else 0)
0
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93 for x, base in enumerate(bases_quality):
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94 if ord(base) - 33 >= soft_clip_base_quality:
0
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95 if x <= cigar[0][0] - 1:
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96 if cigar[0][1] == 'S':
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97 soft_left.append(x)
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98 elif x > read_length_without_right_s - 1:
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99 if cigar[len(cigar) - 1][1] == 'S':
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100 soft_right.append(x)
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101
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102 left_changed = (False, 0)
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103 if len(soft_left) > 0:
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104 soft_left = min(soft_left) + 1
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105 if soft_left == 1:
3
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106 cigar = [[cigar[0][0], soft_clip_cigar_flag_recode]] + cigar[1:]
0
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107 left_changed = (True, cigar[0][0])
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108 elif cigar[0][0] - soft_left > 0:
3
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109 cigar = [[soft_left, 'S']] + [[cigar[0][0] - soft_left, soft_clip_cigar_flag_recode]] + cigar[1:]
0
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110 left_changed = (True, cigar[0][0] - soft_left)
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111
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112 right_changed = (False, 0)
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113 if len(soft_right) > 0:
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114 soft_right = max(soft_right) + 1
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115 cigar = cigar[:-1]
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116 if soft_right - read_length_without_right_s > 0:
3
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117 cigar.append([soft_right - read_length_without_right_s, soft_clip_cigar_flag_recode])
0
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118 right_changed = (True, soft_right - read_length_without_right_s)
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119 if len(bases_quality) - soft_right > 0:
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120 cigar.append([len(bases_quality) - soft_right, 'S'])
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121
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122 if left_changed[0]:
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123 # if direct_strand_true:
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124 mapping_position = mapping_position - left_changed[1]
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125 # if right_changed[0]:
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126 # if not direct_strand_true:
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127 # mapping_position = mapping_position + right_changed[1]
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128
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129 return ''.join([str(cigar_part[0]) + cigar_part[1] for cigar_part in cigar]), str(mapping_position)
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130
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131
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132 def verify_is_forward_read(sam_flag_bit):
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133 # 64 = 1000000
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134 forward_read = False
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135 bit = format(sam_flag_bit, 'b').zfill(7)
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136 if bit[-7] == '1':
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137 forward_read = True
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138 return forward_read
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139
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140
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141 def verify_mapped_direct_strand(sam_flag_bit):
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142 # 16 = 10000 -> mapped in reverse strand
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143 direct_strand = False
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144 bit = format(sam_flag_bit, 'b').zfill(5)
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145 if bit[-5] == '0':
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146 direct_strand = True
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147 return direct_strand
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148
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149
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150 def verify_mapped_tip(reference_length, mapping_position, cigar):
0
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151 tip = False
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152 if 'S' in cigar:
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153 cigar = split_cigar(cigar)
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154 if cigar[0][1] == 'S':
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155 if mapping_position - cigar[0][0] < 0:
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156 tip = True
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157 if cigar[len(cigar) - 1][1] == 'S':
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158 if mapping_position + cigar[len(cigar) - 1][0] > reference_length:
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159 tip = True
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160 return tip
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161
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162
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163 def change_sam_flag_bit_mapped_reverse_strand_2_direct_strand(sam_flag_bit):
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164 bit = list(format(sam_flag_bit, 'b').zfill(5))
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165 bit[-5] = '0'
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166 return int(''.join(bit), 2)
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167
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168
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169 def change_sam_flag_bit_mate_reverse_strand_2_direct_strand(sam_flag_bit):
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170 bit = list(format(sam_flag_bit, 'b').zfill(6))
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171 bit[-6] = '0'
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172 return int(''.join(bit), 2)
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173
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174
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175 def move_read_mapped_reverse_strand_2_direct_strand(seq, bases_quality, sam_flag_bit, cigar):
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176 seq = utils.reverse_complement(seq)
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177 bases_quality = ''.join(reversed(list(bases_quality)))
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178 sam_flag_bit = change_sam_flag_bit_mapped_reverse_strand_2_direct_strand(sam_flag_bit)
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179 cigar = ''.join([str(cigar_part[0]) + cigar_part[1] for cigar_part in reversed(split_cigar(cigar))])
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180 return seq, bases_quality, str(sam_flag_bit), cigar
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181
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182
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183 @utils.trace_unhandled_exceptions
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184 def parallelized_recode_soft_clipping(line_collection, pickle_file, soft_clip_base_quality, sequences_length,
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185 soft_clip_cigar_flag_recode):
0
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186 lines_sam = []
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187 for line in line_collection:
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188 line = line.rstrip('\r\n')
0
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189 if len(line) > 0:
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190 if line.startswith('@'):
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191 lines_sam.append(line)
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192 else:
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193 line = line.split('\t')
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194 if not verify_mapped_tip(sequences_length[line[2]], int(line[3]), line[5]):
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195 line[5], line[3] = recode_cigar_based_on_base_quality(line[5], line[10], soft_clip_base_quality,
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196 int(line[3]),
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197 verify_mapped_direct_strand(int(line[1])),
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198 soft_clip_cigar_flag_recode)
0
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199 lines_sam.append('\t'.join(line))
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200 with open(pickle_file, 'wb') as writer:
0
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201 pickle.dump(lines_sam, writer)
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202
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203
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204 def recode_soft_clipping_from_sam(sam_file, outdir, threads, soft_clip_base_quality, reference_dict,
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205 soft_clip_cigar_flag_recode):
0
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206 pickle_files = []
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207 sequences_length = {}
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208 for x, seq_info in list(reference_dict.items()):
0
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209 sequences_length[seq_info['header']] = seq_info['length']
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210
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211 with open(sam_file, 'rtU') as reader:
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212 pool = multiprocessing.Pool(processes=threads)
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213 line_collection = []
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214 x = 0
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215 for x, line in enumerate(reader):
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216 line_collection.append(line)
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217 if x % 10000 == 0:
3
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218 pickle_file = os.path.join(outdir, 'remove_soft_clipping.' + str(x) + '.pkl')
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219 pickle_files.append(pickle_file)
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220 pool.apply_async(parallelized_recode_soft_clipping, args=(line_collection, pickle_file,
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221 soft_clip_base_quality, sequences_length,
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222 soft_clip_cigar_flag_recode,))
0
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223 line_collection = []
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224 if len(line_collection) > 0:
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225 pickle_file = os.path.join(outdir, 'remove_soft_clipping.' + str(x) + '.pkl')
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226 pickle_files.append(pickle_file)
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227 pool.apply_async(parallelized_recode_soft_clipping, args=(line_collection, pickle_file,
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228 soft_clip_base_quality, sequences_length,
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229 soft_clip_cigar_flag_recode,))
0
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230 pool.close()
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231 pool.join()
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232
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233 os.remove(sam_file)
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234
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235 new_sam_file = os.path.join(outdir, 'alignment_with_soft_clipping_recoded.sam')
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236 with open(new_sam_file, 'wt') as writer:
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237 for pickle_file in pickle_files:
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238 if os.path.isfile(pickle_file):
0
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239 lines_sam = None
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240 with open(pickle_file, 'rb') as reader:
0
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241 lines_sam = pickle.load(reader)
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242 if lines_sam is not None:
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243 for line in lines_sam:
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244 writer.write(line + '\n')
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245 os.remove(pickle_file)
0
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246
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247 return new_sam_file
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248
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249
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250 # Sort alignment file
3
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251 def sort_alignment(alignment_file, output_file, sort_by_name_true, threads):
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252 out_format_string = os.path.splitext(output_file)[1][1:].lower()
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253 command = ['samtools', 'sort', '-o', output_file, '-O', out_format_string, '', '-@', str(threads), alignment_file]
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254 if sort_by_name_true:
0
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255 command[6] = '-n'
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256 run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, True)
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257 if not run_successfully:
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258 output_file = None
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259 return run_successfully, output_file
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260
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261
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262 # Index alignment file
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263 def index_alignment(alignment_file):
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264 command = ['samtools', 'index', alignment_file]
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265 run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, True)
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266 return run_successfully
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267
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268
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269 def mapping_reads(fastq_files, reference_file, threads, outdir, num_map_loc, rematch_run,
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270 soft_clip_base_quality, soft_clip_recode_run, reference_dict, soft_clip_cigar_flag_recode,
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271 bowtie_algorithm, bowtie_opt, clean_run=True):
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272 # Create a symbolic link to the reference_file
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273 if clean_run:
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274 reference_link = os.path.join(outdir, os.path.basename(reference_file))
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275 if os.path.islink(reference_link):
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276 os.unlink(reference_link)
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277 os.symlink(reference_file, reference_link)
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278 reference_file = reference_link
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279
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280 bam_file = None
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281 # Mapping reads using Bowtie2
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282 run_successfully, sam_file = mapping_bowtie2(fastq_files=fastq_files, reference_file=reference_file,
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283 threads=threads, outdir=outdir, num_map_loc=num_map_loc,
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284 bowtie_algorithm=bowtie_algorithm, bowtie_opt=bowtie_opt)
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285
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286 if run_successfully:
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287 # Remove soft clipping
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288 if rematch_run == soft_clip_recode_run or soft_clip_recode_run == 'both':
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289 print('Recoding soft clipped regions')
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290 sam_file = recode_soft_clipping_from_sam(sam_file, outdir, threads, soft_clip_base_quality, reference_dict,
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291 soft_clip_cigar_flag_recode)
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292
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293 # Convert sam to bam and sort bam
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294 run_successfully, bam_file = sort_alignment(sam_file, str(os.path.splitext(sam_file)[0] + '.bam'), False,
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295 threads)
0
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296
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297 if run_successfully:
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298 os.remove(sam_file)
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299 # Index bam
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300 run_successfully = index_alignment(bam_file)
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301
3
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302 return run_successfully, bam_file, reference_file
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303
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304
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305 def create_vcf(bam_file, sequence_to_analyse, outdir, counter, reference_file):
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306 gene_vcf = os.path.join(outdir, 'samtools_mpileup.sequence_' + str(counter) + '.vcf')
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307
3
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308 command = ['samtools', 'mpileup', '--count-orphans', '--no-BAQ', '--min-BQ', '0', '--min-MQ', str(7), '--fasta-ref',
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309 reference_file, '--region', sequence_to_analyse, '--output', gene_vcf, '--VCF', '--uncompressed',
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310 '--output-tags', 'INFO/AD,AD,DP', bam_file]
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311
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312 run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, False)
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313 if not run_successfully:
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314 gene_vcf = None
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315 return run_successfully, gene_vcf
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316
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317
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318 # Read vcf file
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319 class Vcf:
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320 def __init__(self, vcf_file, encoding=None, newline=None):
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321 try:
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322 self.vcf = open(vcf_file, 'rt', encoding=encoding, newline=newline)
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323 except TypeError:
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324 self.vcf = open(vcf_file, 'rt')
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325 self.line_read = self.vcf.readline()
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326 self.contigs_info_dict = {}
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327 while self.line_read.startswith('#'):
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328 if self.line_read.startswith('##contig=<ID='):
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329 seq = self.line_read.split('=')[2].split(',')[0]
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330 seq_len = self.line_read.split('=')[3].split('>')[0]
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331 self.contigs_info_dict[seq] = int(seq_len)
0
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332 self.line_read = self.vcf.readline()
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333 self.line = self.line_read
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334
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335 def readline(self):
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336 line_stored = self.line
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337 self.line = self.vcf.readline()
3
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338 return line_stored
0
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339
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340 def close(self):
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341 self.vcf.close()
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342
3
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343 def get_contig_legth(self, contig):
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344 return self.contigs_info_dict[contig]
0
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345
3
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346
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347 def get_variants(gene_vcf, seq_name, encoding=None, newline=None):
0
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348 variants = {}
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349
3
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350 vfc_file = Vcf(vcf_file=gene_vcf, encoding=encoding, newline=newline)
0
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351 line = vfc_file.readline()
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352 counter = 1
0
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353 while len(line) > 0:
3
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354 fields = line.rstrip('\r\n').split('\t')
0
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355 if len(fields) > 0:
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356 fields[1] = int(fields[1])
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357
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358 info_field = {}
3
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359 try:
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360 for i in fields[7].split(';'):
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361 i = i.split('=')
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362 if len(i) > 1:
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363 info_field[i[0]] = i[1]
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364 else:
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365 info_field[i[0]] = None
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366 except IndexError:
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367 if counter > vfc_file.get_contig_legth(contig=seq_name):
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368 break
0
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369 else:
3
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370 raise IndexError
0
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371
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372 format_field = {}
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373 format_field_name = fields[8].split(':')
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cstrittmatter
parents:
diff changeset
374 format_data = fields[9].split(':')
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cstrittmatter
parents:
diff changeset
375
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cstrittmatter
parents:
diff changeset
376 for i in range(0, len(format_data)):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
377 format_field[format_field_name[i]] = format_data[i].split(',')
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cstrittmatter
parents:
diff changeset
378
3
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cstrittmatter
parents: 0
diff changeset
379 fields_to_store = {'REF': fields[3], 'ALT': fields[4].split(','), 'info': info_field,
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cstrittmatter
parents: 0
diff changeset
380 'format': format_field}
0
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cstrittmatter
parents:
diff changeset
381 if fields[1] in variants:
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cstrittmatter
parents:
diff changeset
382 variants[fields[1]][len(variants[fields[1]])] = fields_to_store
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cstrittmatter
parents:
diff changeset
383 else:
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cstrittmatter
parents:
diff changeset
384 variants[fields[1]] = {0: fields_to_store}
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cstrittmatter
parents:
diff changeset
385
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
386 try:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
387 line = vfc_file.readline()
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cstrittmatter
parents: 0
diff changeset
388 except UnicodeDecodeError:
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cstrittmatter
parents: 0
diff changeset
389 if counter + 1 > vfc_file.get_contig_legth(contig=seq_name):
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cstrittmatter
parents: 0
diff changeset
390 break
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cstrittmatter
parents: 0
diff changeset
391 else:
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cstrittmatter
parents: 0
diff changeset
392 raise UnicodeDecodeError
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cstrittmatter
parents: 0
diff changeset
393
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cstrittmatter
parents: 0
diff changeset
394 counter += 1
0
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cstrittmatter
parents:
diff changeset
395 vfc_file.close()
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cstrittmatter
parents:
diff changeset
396
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cstrittmatter
parents:
diff changeset
397 return variants
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cstrittmatter
parents:
diff changeset
398
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cstrittmatter
parents:
diff changeset
399
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cstrittmatter
parents:
diff changeset
400 def indel_entry(variant_position):
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cstrittmatter
parents:
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401 entry_with_indel = []
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cstrittmatter
parents:
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402 entry_with_snp = None
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cstrittmatter
parents:
diff changeset
403 for i in variant_position:
3
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cstrittmatter
parents: 0
diff changeset
404 keys = list(variant_position[i]['info'].keys())
0
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cstrittmatter
parents:
diff changeset
405 if 'INDEL' in keys:
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cstrittmatter
parents:
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406 entry_with_indel.append(i)
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cstrittmatter
parents:
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407 else:
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cstrittmatter
parents:
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408 entry_with_snp = i
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cstrittmatter
parents:
diff changeset
409
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cstrittmatter
parents:
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410 return entry_with_indel, entry_with_snp
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cstrittmatter
parents:
diff changeset
411
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cstrittmatter
parents:
diff changeset
412
3
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cstrittmatter
parents: 0
diff changeset
413 def get_alt_no_matter(variant_position, indel_true):
0
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cstrittmatter
parents:
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414 dp = sum(map(int, variant_position['format']['AD']))
3
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cstrittmatter
parents: 0
diff changeset
415 index_alleles_sorted_position = sorted(zip(list(map(int, variant_position['format']['AD'])),
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
416 list(range(0, len(variant_position['format']['AD'])))),
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
417 reverse=True)
0
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parents:
diff changeset
418 index_dominant_allele = None
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cstrittmatter
parents:
diff changeset
419 if not indel_true:
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cstrittmatter
parents:
diff changeset
420 ad_idv = index_alleles_sorted_position[0][0]
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cstrittmatter
parents:
diff changeset
421
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cstrittmatter
parents:
diff changeset
422 if len([x for x in index_alleles_sorted_position if x[0] == ad_idv]) > 1:
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cstrittmatter
parents:
diff changeset
423 index_alleles_sorted_position = sorted([x for x in index_alleles_sorted_position if x[0] == ad_idv])
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cstrittmatter
parents:
diff changeset
424
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cstrittmatter
parents:
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425 index_dominant_allele = index_alleles_sorted_position[0][1]
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cstrittmatter
parents:
diff changeset
426 if index_dominant_allele == 0:
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cstrittmatter
parents:
diff changeset
427 alt = '.'
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cstrittmatter
parents:
diff changeset
428 else:
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cstrittmatter
parents:
diff changeset
429 alt = variant_position['ALT'][index_dominant_allele - 1]
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cstrittmatter
parents:
diff changeset
430
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cstrittmatter
parents:
diff changeset
431 else:
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cstrittmatter
parents:
diff changeset
432 ad_idv = int(variant_position['info']['IDV'])
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cstrittmatter
parents:
diff changeset
433
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cstrittmatter
parents:
diff changeset
434 if float(ad_idv) / float(dp) >= 0.5:
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cstrittmatter
parents:
diff changeset
435 if len([x for x in index_alleles_sorted_position if x[0] == index_alleles_sorted_position[0][0]]) > 1:
3
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cstrittmatter
parents: 0
diff changeset
436 index_alleles_sorted_position = sorted([x for x in index_alleles_sorted_position if
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
437 x[0] == index_alleles_sorted_position[0][0]])
0
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cstrittmatter
parents:
diff changeset
438
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cstrittmatter
parents:
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439 index_dominant_allele = index_alleles_sorted_position[0][1]
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cstrittmatter
parents:
diff changeset
440 if index_dominant_allele == 0:
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cstrittmatter
parents:
diff changeset
441 alt = '.'
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cstrittmatter
parents:
diff changeset
442 else:
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cstrittmatter
parents:
diff changeset
443 alt = variant_position['ALT'][index_dominant_allele - 1]
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cstrittmatter
parents:
diff changeset
444 else:
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cstrittmatter
parents:
diff changeset
445 ad_idv = int(variant_position['format']['AD'][0])
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cstrittmatter
parents:
diff changeset
446 alt = '.'
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cstrittmatter
parents:
diff changeset
447
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cstrittmatter
parents:
diff changeset
448 return alt, dp, ad_idv, index_dominant_allele
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cstrittmatter
parents:
diff changeset
449
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cstrittmatter
parents:
diff changeset
450
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cstrittmatter
parents:
diff changeset
451 def count_number_diferences(ref, alt):
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cstrittmatter
parents:
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452 number_diferences = 0
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cstrittmatter
parents:
diff changeset
453
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cstrittmatter
parents:
diff changeset
454 if len(ref) != len(alt):
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cstrittmatter
parents:
diff changeset
455 number_diferences += 1
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
456
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
457 for i in range(0, min(len(ref), len(alt))):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
458 if alt[i] != 'N' and ref[i] != alt[i]:
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cstrittmatter
parents:
diff changeset
459 number_diferences += 1
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cstrittmatter
parents:
diff changeset
460
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cstrittmatter
parents:
diff changeset
461 return number_diferences
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cstrittmatter
parents:
diff changeset
462
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cstrittmatter
parents:
diff changeset
463
3
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cstrittmatter
parents: 0
diff changeset
464 def get_alt_correct(variant_position, alt_no_matter, dp, ad_idv, index_dominant_allele, minimum_depth_presence,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
465 minimum_depth_call, minimum_depth_frequency_dominant_allele):
0
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cstrittmatter
parents:
diff changeset
466 alt = None
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cstrittmatter
parents:
diff changeset
467 low_coverage = False
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cstrittmatter
parents:
diff changeset
468 multiple_alleles = False
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cstrittmatter
parents:
diff changeset
469
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cstrittmatter
parents:
diff changeset
470 if dp >= minimum_depth_presence:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
471 if dp < minimum_depth_call:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
472 alt = 'N' * len(variant_position['REF'])
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
473 low_coverage = True
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
474 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
475 if ad_idv < minimum_depth_call:
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cstrittmatter
parents:
diff changeset
476 alt = 'N' * len(variant_position['REF'])
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
477 low_coverage = True
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
478 if float(ad_idv) / float(dp) < minimum_depth_frequency_dominant_allele:
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cstrittmatter
parents:
diff changeset
479 multiple_alleles = True
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
480 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
481 if float(ad_idv) / float(dp) < minimum_depth_frequency_dominant_allele:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
482 alt = 'N' * len(variant_position['REF'])
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
483 if index_dominant_allele is not None:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
484 variants_coverage = [int(variant_position['format']['AD'][i]) for i in
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
485 range(0, len(variant_position['ALT']) + 1) if i != index_dominant_allele]
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
486 if sum(variants_coverage) > 0:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
487 if float(max(variants_coverage)) / float(sum(variants_coverage)) > 0.5:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
488 multiple_alleles = True
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
489 elif float(max(variants_coverage)) / float(sum(variants_coverage)) == 0.5 and \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
490 len(variants_coverage) > 2:
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
491 multiple_alleles = True
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
492 else:
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cstrittmatter
parents:
diff changeset
493 multiple_alleles = True
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
494 else:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
495 alt = alt_no_matter
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
496 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
497 low_coverage = True
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
498
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cstrittmatter
parents:
diff changeset
499 return alt, low_coverage, multiple_alleles
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
500
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
501
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
502 def get_alt_alignment(ref, alt):
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cstrittmatter
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503 if alt is None:
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504 alt = 'N' * len(ref)
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505 else:
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506 if len(ref) != len(alt):
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507 if len(alt) < len(ref):
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508 if alt == '.':
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509 alt = ref
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510 alt += 'N' * (len(ref) - len(alt))
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511 else:
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512 if alt[:len(ref)] == ref:
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513 alt = '.'
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514 else:
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515 alt = alt[:len(ref)]
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516
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517 return alt
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518
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519
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520 def get_indel_more_likely(variant_position, indels_entry):
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521 indel_coverage = {}
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522 for i in indels_entry:
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523 indel_coverage[i] = int(variant_position['info']['IDV'])
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524 return indel_coverage.index(str(max(indel_coverage.values())))
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525
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526
3
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527 def determine_variant(variant_position, minimum_depth_presence, minimum_depth_call,
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528 minimum_depth_frequency_dominant_allele, indel_true):
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529 alt_no_matter, dp, ad_idv, index_dominant_allele = get_alt_no_matter(variant_position, indel_true)
0
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530
3
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531 alt_correct, low_coverage, multiple_alleles = get_alt_correct(variant_position, alt_no_matter, dp, ad_idv,
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532 index_dominant_allele, minimum_depth_presence,
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533 minimum_depth_call,
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534 minimum_depth_frequency_dominant_allele)
0
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535
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536 alt_alignment = get_alt_alignment(variant_position['REF'], alt_correct)
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537
3
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parents: 0
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538 return variant_position['REF'], alt_correct, low_coverage, multiple_alleles, alt_no_matter, alt_alignment
0
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parents:
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539
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540
3
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parents: 0
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541 def confirm_nucleotides_indel(ref, alt, variants, position_start_indel, minimum_depth_presence, minimum_depth_call,
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542 minimum_depth_frequency_dominant_allele, alignment_true):
0
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543 alt = list(alt)
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544
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545 for i in range(0, len(alt) - 1):
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546 if len(alt) < len(ref):
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547 new_position = position_start_indel + len(alt) - i - 1
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548 alt_position = len(alt) - i - 1
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549 else:
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550 if i + 1 > len(ref):
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551 break
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552 new_position = position_start_indel + 1 + i
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553 alt_position = 1 + i
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554
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555 if alt[alt_position] != 'N':
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556 if new_position not in variants:
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557 if alignment_true:
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558 alt[alt_position] = 'N'
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559 else:
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560 alt = alt[: alt_position]
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561 break
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562
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563 entry_with_indel, entry_with_snp = indel_entry(variants[new_position])
3
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564 new_ref, alt_correct, low_coverage, multiple_alleles, alt_no_matter, alt_alignment = \
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565 determine_variant(variants[new_position][entry_with_snp], minimum_depth_presence, minimum_depth_call,
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566 minimum_depth_frequency_dominant_allele, False)
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567 if alt_no_matter != '.' and alt[alt_position] != alt_no_matter:
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568 alt[alt_position] = alt_no_matter
0
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569
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570 return ''.join(alt)
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571
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572
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573 def snp_indel(variants, position, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele):
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574 entry_with_indel, entry_with_snp = indel_entry(variants[position])
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575
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576 if len(entry_with_indel) == 0:
3
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577 ref, alt_correct, low_coverage, multiple_alleles, alt_no_matter, alt_alignment = \
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578 determine_variant(variants[position][entry_with_snp], minimum_depth_presence, minimum_depth_call,
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579 minimum_depth_frequency_dominant_allele, False)
0
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580 else:
3
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581 ref_snp, alt_correct_snp, low_coverage_snp, multiple_alleles_snp, alt_no_matter_snp, alt_alignment_snp = \
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diff changeset
582 determine_variant(variants[position][entry_with_snp], minimum_depth_presence, minimum_depth_call,
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583 minimum_depth_frequency_dominant_allele, False)
0
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584
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585 indel_more_likely = entry_with_indel[0]
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586 if len(entry_with_indel) > 1:
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587 indel_more_likely = get_indel_more_likely(variants[position], entry_with_indel)
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588
3
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parents: 0
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589 ref, alt_correct, low_coverage, multiple_alleles, alt_no_matter, alt_alignment = \
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diff changeset
590 determine_variant(variants[position][indel_more_likely], minimum_depth_presence, minimum_depth_call,
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591 minimum_depth_frequency_dominant_allele, True)
0
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592
3
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parents: 0
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593 if alt_no_matter == '.':
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parents: 0
diff changeset
594 ref, alt_correct, low_coverage, multiple_alleles, alt_no_matter, alt_alignment = \
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diff changeset
595 ref_snp, alt_correct_snp, low_coverage_snp, multiple_alleles_snp, alt_no_matter_snp, alt_alignment_snp
0
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596 else:
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597 if alt_correct is None and alt_correct_snp is not None:
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598 alt_correct = alt_correct_snp
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599 elif alt_correct is not None and alt_correct_snp is not None:
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600 if alt_correct_snp != '.' and alt_correct[0] != alt_correct_snp:
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601 alt_correct = alt_correct_snp + alt_correct[1:] if len(alt_correct) > 1 else alt_correct_snp
3
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parents: 0
diff changeset
602 if alt_no_matter_snp != '.' and alt_no_matter[0] != alt_no_matter_snp:
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parents: 0
diff changeset
603 alt_no_matter = alt_no_matter_snp + alt_no_matter[1:] if len(alt_no_matter) > 1 else alt_no_matter_snp
0
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604 if alt_alignment_snp != '.' and alt_alignment[0] != alt_alignment_snp:
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605 alt_alignment = alt_alignment_snp + alt_alignment[1:] if len(alt_alignment) > 1 else alt_alignment_snp
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parents:
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606
3
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cstrittmatter
parents: 0
diff changeset
607 # if alt_no_matter != '.':
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cstrittmatter
parents: 0
diff changeset
608 # alt_no_matter = confirm_nucleotides_indel(ref, alt_no_matter, variants, position, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele, False)
0
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609 # if alt_correct is not None and alt_correct != '.':
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diff changeset
610 # alt_correct = confirm_nucleotides_indel(ref, alt_correct, variants, position, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele, False)
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diff changeset
611 # if alt_alignment != '.':
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diff changeset
612 # alt_alignment = confirm_nucleotides_indel(ref, alt_alignment, variants, position, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele, True)
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parents:
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613
3
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cstrittmatter
parents: 0
diff changeset
614 return ref, alt_correct, low_coverage, multiple_alleles, alt_no_matter, alt_alignment
0
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parents:
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615
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parents:
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616
3
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diff changeset
617 def get_true_variants(variants, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele,
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618 sequence):
0
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619 variants_correct = {}
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620 variants_no_matter = {}
0
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621 variants_alignment = {}
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622
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diff changeset
623 correct_absent_positions = {}
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cstrittmatter
parents:
diff changeset
624 correct_last_absent_position = ''
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cstrittmatter
parents:
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625
3
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cstrittmatter
parents: 0
diff changeset
626 no_matter_absent_positions = {}
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cstrittmatter
parents: 0
diff changeset
627 no_matter_last_absent_position = ''
0
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cstrittmatter
parents:
diff changeset
628
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cstrittmatter
parents:
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629 multiple_alleles_found = []
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cstrittmatter
parents:
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630
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cstrittmatter
parents:
diff changeset
631 counter = 1
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cstrittmatter
parents:
diff changeset
632 while counter <= len(sequence):
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cstrittmatter
parents:
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633 if counter in variants:
3
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cstrittmatter
parents: 0
diff changeset
634 no_matter_last_absent_position = ''
0
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cstrittmatter
parents:
diff changeset
635
3
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cstrittmatter
parents: 0
diff changeset
636 ref, alt_correct, low_coverage, multiple_alleles, alt_no_matter, alt_alignment = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
637 snp_indel(variants, counter, minimum_depth_presence, minimum_depth_call,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
638 minimum_depth_frequency_dominant_allele)
0
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cstrittmatter
parents:
diff changeset
639
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cstrittmatter
parents:
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640 if alt_alignment != '.':
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cstrittmatter
parents:
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641 variants_alignment[counter] = {'REF': ref, 'ALT': alt_alignment}
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cstrittmatter
parents:
diff changeset
642
3
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cstrittmatter
parents: 0
diff changeset
643 if alt_no_matter != '.':
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cstrittmatter
parents: 0
diff changeset
644 variants_no_matter[counter] = {'REF': ref, 'ALT': alt_no_matter}
0
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cstrittmatter
parents:
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645
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
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646 if alt_correct is None:
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parents:
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647 if counter - len(correct_last_absent_position) in correct_absent_positions:
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parents:
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648 correct_absent_positions[counter - len(correct_last_absent_position)]['REF'] += ref
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parents:
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649 else:
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parents:
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650 correct_absent_positions[counter] = {'REF': ref, 'ALT': ''}
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cstrittmatter
parents:
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651 correct_last_absent_position += ref
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652 else:
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cstrittmatter
parents:
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653 if alt_correct != '.':
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cstrittmatter
parents:
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654 if len(alt_correct) < len(ref):
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parents:
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655 if len(alt_correct) == 1:
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656 correct_absent_positions[counter + 1] = {'REF': ref[1:], 'ALT': ''}
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657 else:
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658 correct_absent_positions[counter + 1] = {'REF': ref[1:], 'ALT': alt_correct[1:]}
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cstrittmatter
parents:
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659
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660 correct_last_absent_position = ref[1:]
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661 else:
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662 variants_correct[counter] = {'REF': ref, 'ALT': alt_correct}
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parents:
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663 correct_last_absent_position = ''
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parents:
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664 else:
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parents:
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665 correct_last_absent_position = ''
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cstrittmatter
parents:
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666
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cstrittmatter
parents:
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667 if multiple_alleles:
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parents:
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668 multiple_alleles_found.append(counter)
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parents:
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669
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parents:
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670 counter += len(ref)
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parents:
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671 else:
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672 variants_alignment[counter] = {'REF': sequence[counter - 1], 'ALT': 'N'}
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cstrittmatter
parents:
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673
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cstrittmatter
parents:
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674 if counter - len(correct_last_absent_position) in correct_absent_positions:
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cstrittmatter
parents:
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675 correct_absent_positions[counter - len(correct_last_absent_position)]['REF'] += sequence[counter - 1]
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parents:
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676 else:
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parents:
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677 correct_absent_positions[counter] = {'REF': sequence[counter - 1], 'ALT': ''}
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parents:
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678 correct_last_absent_position += sequence[counter - 1]
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parents:
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679
3
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cstrittmatter
parents: 0
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680 if counter - len(no_matter_last_absent_position) in no_matter_absent_positions:
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parents: 0
diff changeset
681 no_matter_absent_positions[counter - len(no_matter_last_absent_position)]['REF'] += \
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parents: 0
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682 sequence[counter - 1]
0
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parents:
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683 else:
3
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parents: 0
diff changeset
684 no_matter_absent_positions[counter] = {'REF': sequence[counter - 1], 'ALT': ''}
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cstrittmatter
parents: 0
diff changeset
685 no_matter_last_absent_position += sequence[counter - 1]
0
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parents:
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686
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cstrittmatter
parents:
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687 counter += 1
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cstrittmatter
parents:
diff changeset
688
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cstrittmatter
parents:
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689 for position in correct_absent_positions:
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cstrittmatter
parents:
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690 if position == 1:
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cstrittmatter
parents:
diff changeset
691 variants_correct[position] = {'REF': correct_absent_positions[position]['REF'], 'ALT': 'N'}
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692 else:
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parents:
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693 if position - 1 not in variants_correct:
3
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cstrittmatter
parents: 0
diff changeset
694 variants_correct[position - 1] = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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diff changeset
695 {'REF': sequence[position - 2] + correct_absent_positions[position]['REF'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
696 'ALT': sequence[position - 2] + correct_absent_positions[position]['ALT']}
0
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cstrittmatter
parents:
diff changeset
697 else:
3
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parents: 0
diff changeset
698 variants_correct[position - 1] = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
699 {'REF': variants_correct[position - 1]['REF'] +
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
700 correct_absent_positions[position]['REF'][len(variants_correct[position - 1]['REF']) - 1:],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
701 'ALT': variants_correct[position - 1]['ALT'] +
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cstrittmatter
parents: 0
diff changeset
702 correct_absent_positions[position]['ALT'][len(variants_correct[position - 1]['ALT']) - 1 if
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
703 len(variants_correct[position - 1]['ALT']) > 0
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
704 else 0:]}
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
705
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
706 for position in no_matter_absent_positions:
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
707 if position == 1:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
708 variants_no_matter[position] = {'REF': no_matter_absent_positions[position]['REF'], 'ALT': 'N'}
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
709 else:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
710 if position - 1 not in variants_no_matter:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
711 variants_no_matter[position - 1] = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
712 {'REF': sequence[position - 2] + no_matter_absent_positions[position]['REF'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
713 'ALT': sequence[position - 2] + no_matter_absent_positions[position]['ALT']}
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
714 else:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
715 variants_no_matter[position - 1] = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
716 {'REF': variants_no_matter[position - 1]['REF'] +
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
717 no_matter_absent_positions[position]['REF'][len(variants_no_matter[position - 1]['REF']) -
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
718 1:],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
719 'ALT': variants_no_matter[position - 1]['ALT'] +
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
720 no_matter_absent_positions[position]['ALT'][len(variants_no_matter[position - 1]['ALT']) -
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
721 1 if
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
722 len(variants_no_matter[position - 1]['ALT']) > 0
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
723 else 0:]}
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
724
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
725 return variants_correct, variants_no_matter, variants_alignment, multiple_alleles_found
0
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cstrittmatter
parents:
diff changeset
726
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
727
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
728 def clean_variant_in_extra_seq_left(variant_dict, position, length_extra_seq, multiple_alleles_found,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
729 number_multi_alleles):
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
730 number_diferences = 0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
731
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
732 if position + len(variant_dict[position]['REF']) - 1 > length_extra_seq:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
733 if multiple_alleles_found is not None and position in multiple_alleles_found:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
734 number_multi_alleles += 1
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
735
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
736 temp_variant = variant_dict[position]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
737 del variant_dict[position]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
738 variant_dict[length_extra_seq] = {}
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
739 variant_dict[length_extra_seq]['REF'] = temp_variant['REF'][length_extra_seq - position:]
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
740 variant_dict[length_extra_seq]['ALT'] = temp_variant['ALT'][length_extra_seq - position:] if \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
741 len(temp_variant['ALT']) > length_extra_seq - position else \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
742 temp_variant['REF'][length_extra_seq - position]
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
743 number_diferences = count_number_diferences(variant_dict[length_extra_seq]['REF'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
744 variant_dict[length_extra_seq]['ALT'])
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
745 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
746 del variant_dict[position]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
747
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cstrittmatter
parents:
diff changeset
748 return variant_dict, number_multi_alleles, number_diferences
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cstrittmatter
parents:
diff changeset
749
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cstrittmatter
parents:
diff changeset
750
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cstrittmatter
parents:
diff changeset
751 def clean_variant_in_extra_seq_rigth(variant_dict, position, sequence_length, length_extra_seq):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
752 if position + len(variant_dict[position]['REF']) - 1 > sequence_length - length_extra_seq:
3
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cstrittmatter
parents: 0
diff changeset
753 variant_dict[position]['REF'] = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
754 variant_dict[position]['REF'][: - (position - (sequence_length - length_extra_seq)) + 1]
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
755 variant_dict[position]['ALT'] = \
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cstrittmatter
parents: 0
diff changeset
756 variant_dict[position]['ALT'][: - (position - (sequence_length - length_extra_seq)) + 1] if \
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cstrittmatter
parents: 0
diff changeset
757 len(variant_dict[position]['ALT']) >= - (position - (sequence_length - length_extra_seq)) + 1 else \
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parents: 0
diff changeset
758 variant_dict[position]['ALT']
0
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cstrittmatter
parents:
diff changeset
759
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cstrittmatter
parents:
diff changeset
760 number_diferences = count_number_diferences(variant_dict[position]['REF'], variant_dict[position]['ALT'])
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cstrittmatter
parents:
diff changeset
761
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cstrittmatter
parents:
diff changeset
762 return variant_dict, number_diferences
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cstrittmatter
parents:
diff changeset
763
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cstrittmatter
parents:
diff changeset
764
3
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cstrittmatter
parents: 0
diff changeset
765 def cleanning_variants_extra_seq(variants_correct, variants_no_matter, variants_alignment, multiple_alleles_found,
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parents: 0
diff changeset
766 length_extra_seq, sequence_length):
0
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parents:
diff changeset
767 number_multi_alleles = 0
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parents:
diff changeset
768 number_diferences = 0
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cstrittmatter
parents:
diff changeset
769
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cstrittmatter
parents:
diff changeset
770 counter = 1
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cstrittmatter
parents:
diff changeset
771 while counter <= sequence_length:
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cstrittmatter
parents:
diff changeset
772 if counter <= length_extra_seq:
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cstrittmatter
parents:
diff changeset
773 if counter in variants_correct:
3
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cstrittmatter
parents: 0
diff changeset
774 variants_correct, number_multi_alleles, number_diferences = \
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cstrittmatter
parents: 0
diff changeset
775 clean_variant_in_extra_seq_left(variants_correct, counter, length_extra_seq, multiple_alleles_found,
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cstrittmatter
parents: 0
diff changeset
776 number_multi_alleles)
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parents: 0
diff changeset
777 if counter in variants_no_matter:
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parents: 0
diff changeset
778 variants_no_matter, ignore, ignore = \
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parents: 0
diff changeset
779 clean_variant_in_extra_seq_left(variants_no_matter, counter, length_extra_seq, None, None)
0
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cstrittmatter
parents:
diff changeset
780 if counter in variants_alignment:
3
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cstrittmatter
parents: 0
diff changeset
781 variants_alignment, ignore, ignore = \
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cstrittmatter
parents: 0
diff changeset
782 clean_variant_in_extra_seq_left(variants_alignment, counter, length_extra_seq, None, None)
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parents: 0
diff changeset
783 elif sequence_length - length_extra_seq >= counter > length_extra_seq:
0
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cstrittmatter
parents:
diff changeset
784 if counter in variants_correct:
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cstrittmatter
parents:
diff changeset
785 if counter in multiple_alleles_found:
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parents:
diff changeset
786 number_multi_alleles += 1
3
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cstrittmatter
parents: 0
diff changeset
787 variants_correct, number_diferences_found = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
788 clean_variant_in_extra_seq_rigth(variants_correct, counter, sequence_length, length_extra_seq)
0
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parents:
diff changeset
789 number_diferences += number_diferences_found
3
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cstrittmatter
parents: 0
diff changeset
790 if counter in variants_no_matter:
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cstrittmatter
parents: 0
diff changeset
791 variants_no_matter, ignore = \
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cstrittmatter
parents: 0
diff changeset
792 clean_variant_in_extra_seq_rigth(variants_no_matter, counter, sequence_length, length_extra_seq)
0
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parents:
diff changeset
793 if counter in variants_alignment:
3
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parents: 0
diff changeset
794 variants_alignment, ignore = \
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parents: 0
diff changeset
795 clean_variant_in_extra_seq_rigth(variants_alignment, counter, sequence_length, length_extra_seq)
0
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parents:
diff changeset
796 else:
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parents:
diff changeset
797 if counter in variants_correct:
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parents:
diff changeset
798 del variants_correct[counter]
3
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cstrittmatter
parents: 0
diff changeset
799 if counter in variants_no_matter:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
800 del variants_no_matter[counter]
0
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parents:
diff changeset
801 if counter in variants_alignment:
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cstrittmatter
parents:
diff changeset
802 del variants_alignment[counter]
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cstrittmatter
parents:
diff changeset
803
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cstrittmatter
parents:
diff changeset
804 counter += 1
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parents:
diff changeset
805
3
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parents: 0
diff changeset
806 return variants_correct, variants_no_matter, variants_alignment, number_multi_alleles, number_diferences
0
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cstrittmatter
parents:
diff changeset
807
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cstrittmatter
parents:
diff changeset
808
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parents:
diff changeset
809 def get_coverage(gene_coverage):
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parents:
diff changeset
810 coverage = {}
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parents:
diff changeset
811
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parents:
diff changeset
812 with open(gene_coverage, 'rtU') as reader:
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cstrittmatter
parents:
diff changeset
813 for line in reader:
3
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parents: 0
diff changeset
814 line = line.rstrip('\r\n')
0
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parents:
diff changeset
815 if len(line) > 0:
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parents:
diff changeset
816 line = line.split('\t')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents:
diff changeset
817 coverage[int(line[1])] = int(line[2])
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cstrittmatter
parents:
diff changeset
818
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cstrittmatter
parents:
diff changeset
819 return coverage
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
820
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cstrittmatter
parents:
diff changeset
821
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parents:
diff changeset
822 def get_coverage_report(coverage, sequence_length, minimum_depth_presence, minimum_depth_call, length_extra_seq):
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parents:
diff changeset
823 if len(coverage) == 0:
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cstrittmatter
parents:
diff changeset
824 return sequence_length - 2 * length_extra_seq, 100.0, 0.0
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cstrittmatter
parents:
diff changeset
825
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parents:
diff changeset
826 count_absent = 0
3
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parents: 0
diff changeset
827 count_low_coverage = 0
0
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cstrittmatter
parents:
diff changeset
828 sum_coverage = 0
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cstrittmatter
parents:
diff changeset
829
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cstrittmatter
parents:
diff changeset
830 counter = 1
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
831 while counter <= sequence_length:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
832 if sequence_length - length_extra_seq >= counter > length_extra_seq:
0
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parents:
diff changeset
833 if coverage[counter] < minimum_depth_presence:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
834 count_absent += 1
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents:
diff changeset
835 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents:
diff changeset
836 if coverage[counter] < minimum_depth_call:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
837 count_low_coverage += 1
0
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cstrittmatter
parents:
diff changeset
838 sum_coverage += coverage[counter]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
839 counter += 1
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents:
diff changeset
840
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parents:
diff changeset
841 mean_coverage = 0
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
842 percentage_low_coverage = 0
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents:
diff changeset
843 if sequence_length - 2 * length_extra_seq - count_absent > 0:
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cstrittmatter
parents:
diff changeset
844 mean_coverage = float(sum_coverage) / float(sequence_length - 2 * length_extra_seq - count_absent)
3
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cstrittmatter
parents: 0
diff changeset
845 percentage_low_coverage = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
846 float(count_low_coverage) / float(sequence_length - 2 * length_extra_seq - count_absent) * 100
0
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cstrittmatter
parents:
diff changeset
847
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
848 return count_absent, percentage_low_coverage, mean_coverage
0
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cstrittmatter
parents:
diff changeset
849
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cstrittmatter
parents:
diff changeset
850
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cstrittmatter
parents:
diff changeset
851 # Get genome coverage data
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cstrittmatter
parents:
diff changeset
852 def compute_genome_coverage_data(alignment_file, sequence_to_analyse, outdir, counter):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
853 genome_coverage_data_file = os.path.join(outdir, 'samtools_depth.sequence_' + str(counter) + '.tab')
3
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cstrittmatter
parents: 0
diff changeset
854 command = ['samtools', 'depth', '-a', '-q', '0', '-r', sequence_to_analyse, alignment_file, '>',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
855 genome_coverage_data_file]
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
856 run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, True, None, False)
0
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cstrittmatter
parents:
diff changeset
857 return run_successfully, genome_coverage_data_file
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cstrittmatter
parents:
diff changeset
858
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cstrittmatter
parents:
diff changeset
859
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
860 def write_variants_vcf(variants, outdir, sequence_to_analyse, sufix):
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cstrittmatter
parents:
diff changeset
861 vcf_file = os.path.join(outdir, str(sequence_to_analyse + '.' + sufix + '.vcf'))
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
862 with open(vcf_file, 'wt') as writer:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
863 writer.write('##fileformat=VCFv4.2' + '\n')
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
864 writer.write('#' + '\t'.join(['SEQUENCE', 'POSITION', 'ID_unused', 'REFERENCE_sequence', 'ALTERNATIVE_sequence',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
865 'QUALITY_unused', 'FILTER_unused', 'INFO_unused', 'FORMAT_unused']) + '\n')
0
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cstrittmatter
parents:
diff changeset
866 for i in sorted(variants.keys()):
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
867 writer.write('\t'.join([sequence_to_analyse, str(i), '.', variants[i]['REF'], variants[i]['ALT'], '.', '.',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
868 '.', '.']) + '\n')
0
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cstrittmatter
parents:
diff changeset
869
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870 compressed_vcf_file = vcf_file + '.gz'
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871 command = ['bcftools', 'convert', '-o', compressed_vcf_file, '-O', 'z', vcf_file]
3
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872 run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, False)
0
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873 if run_successfully:
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874 command = ['bcftools', 'index', compressed_vcf_file]
3
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875 run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, False)
0
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876
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877 if not run_successfully:
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878 compressed_vcf_file = None
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879
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880 return run_successfully, compressed_vcf_file
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881
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882
3
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883 def parse_fasta_in_memory(fasta_memory):
0
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884 fasta_memory = fasta_memory.splitlines()
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885 sequence_dict = {}
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886 for line in fasta_memory:
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887 if len(line) > 0:
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888 if line.startswith('>'):
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889 sequence_dict = {'header': line[1:], 'sequence': ''}
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890 else:
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891 sequence_dict['sequence'] += line
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892
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893 return sequence_dict
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894
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895
3
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896 def compute_consensus_sequence(reference_file, sequence_to_analyse, compressed_vcf_file, outdir):
0
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897 sequence_dict = None
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898
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899 gene_fasta = os.path.join(outdir, str(sequence_to_analyse + '.fasta'))
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900
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901 run_successfully, stdout = index_fasta_samtools(reference_file, sequence_to_analyse, gene_fasta, False)
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902 if run_successfully:
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903 command = ['bcftools', 'norm', '-c', 's', '-f', gene_fasta, '-Ov', compressed_vcf_file]
3
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904 run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, False)
0
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905 if run_successfully:
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906 command = ['bcftools', 'consensus', '-f', gene_fasta, compressed_vcf_file, '-H', '1']
3
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907 run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, False)
0
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908 if run_successfully:
3
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909 sequence_dict = parse_fasta_in_memory(stdout)
0
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910
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911 return run_successfully, sequence_dict
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912
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913
3
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914 def create_sample_consensus_sequence(outdir, sequence_to_analyse, reference_file, variants, minimum_depth_presence,
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915 minimum_depth_call, minimum_depth_frequency_dominant_allele, sequence,
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916 length_extra_seq):
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917 variants_correct, variants_noMatter, variants_alignment, multiple_alleles_found = \
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918 get_true_variants(variants, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele,
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919 sequence)
0
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920
3
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921 variants_correct, variants_noMatter, variants_alignment, number_multi_alleles, number_diferences = \
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922 cleanning_variants_extra_seq(variants_correct, variants_noMatter, variants_alignment, multiple_alleles_found,
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923 length_extra_seq, len(sequence))
0
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924
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925 run_successfully = False
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926 consensus = {'correct': {}, 'noMatter': {}, 'alignment': {}}
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927 for variant_type in ['variants_correct', 'variants_noMatter', 'variants_alignment']:
3
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928 run_successfully, compressed_vcf_file = \
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diff changeset
929 write_variants_vcf(eval(variant_type), outdir, sequence_to_analyse, variant_type.split('_', 1)[1])
0
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930 if run_successfully:
3
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931 run_successfully, sequence_dict = \
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932 compute_consensus_sequence(reference_file, sequence_to_analyse, compressed_vcf_file, outdir)
0
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933 if run_successfully:
3
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934 consensus[variant_type.split('_', 1)[1]] = \
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935 {'header': sequence_dict['header'],
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936 'sequence': sequence_dict['sequence'][length_extra_seq:len(sequence_dict['sequence']) -
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937 length_extra_seq]}
0
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diff changeset
938
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939 return run_successfully, number_multi_alleles, consensus, number_diferences
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diff changeset
940
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diff changeset
941
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942 @utils.trace_unhandled_exceptions
3
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diff changeset
943 def analyse_sequence_data(bam_file, sequence_information, outdir, counter, reference_file, length_extra_seq,
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944 minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele):
0
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945 count_absent = None
3
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diff changeset
946 percentage_low_coverage = None
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947 mean_coverage = None
0
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diff changeset
948 number_diferences = 0
3
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diff changeset
949 number_multi_alleles = 0
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950 consensus_sequence = {'correct': {}, 'noMatter': {}, 'alignment': {}}
0
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diff changeset
951
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952 # Create vcf file (for multiple alleles check)
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953 run_successfully, gene_vcf = create_vcf(bam_file, sequence_information['header'], outdir, counter, reference_file)
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954 if run_successfully:
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parents:
diff changeset
955 # Create coverage tab file
3
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parents: 0
diff changeset
956 run_successfully, gene_coverage = \
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diff changeset
957 compute_genome_coverage_data(bam_file, sequence_information['header'], outdir, counter)
0
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diff changeset
958
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959 if run_successfully:
3
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parents: 0
diff changeset
960 try:
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961 variants = get_variants(gene_vcf=gene_vcf, seq_name=sequence_information['header'],
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diff changeset
962 encoding=sys.getdefaultencoding())
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parents: 0
diff changeset
963 except UnicodeDecodeError:
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parents: 0
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964 try:
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965 print('It was found an enconding error while parsing the following VCF, but lets try forcing it to'
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parents: 0
diff changeset
966 ' "utf_8" encoding: {}'.format(gene_vcf))
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parents: 0
diff changeset
967 variants = get_variants(gene_vcf=gene_vcf, seq_name=sequence_information['header'],
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parents: 0
diff changeset
968 encoding='utf_8')
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parents: 0
diff changeset
969 except UnicodeDecodeError:
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diff changeset
970 print('It was found an enconding error while parsing the following VCF, but lets try forcing it to'
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cstrittmatter
parents: 0
diff changeset
971 ' "latin_1" encoding: {}'.format(gene_vcf))
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parents: 0
diff changeset
972 variants = get_variants(gene_vcf=gene_vcf, seq_name=sequence_information['header'],
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parents: 0
diff changeset
973 encoding='latin_1')
0
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parents:
diff changeset
974
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parents:
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975 coverage = get_coverage(gene_coverage)
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parents:
diff changeset
976
3
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parents: 0
diff changeset
977 run_successfully, number_multi_alleles, consensus_sequence, number_diferences = \
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diff changeset
978 create_sample_consensus_sequence(outdir, sequence_information['header'], reference_file, variants,
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parents: 0
diff changeset
979 minimum_depth_presence, minimum_depth_call,
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parents: 0
diff changeset
980 minimum_depth_frequency_dominant_allele,
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parents: 0
diff changeset
981 sequence_information['sequence'], length_extra_seq)
0
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parents:
diff changeset
982
3
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parents: 0
diff changeset
983 try:
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parents: 0
diff changeset
984 count_absent, percentage_low_coverage, mean_coverage = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
985 get_coverage_report(coverage, sequence_information['length'], minimum_depth_presence,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
986 minimum_depth_call, length_extra_seq)
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parents: 0
diff changeset
987 except KeyError:
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parents: 0
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988 print('ERROR: KeyError')
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parents: 0
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989 print(sequence_information)
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990 raise KeyError
0
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991
3
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992 utils.save_variable_to_pickle([run_successfully, counter, number_multi_alleles, count_absent,
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993 percentage_low_coverage, mean_coverage, consensus_sequence, number_diferences],
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994 outdir, str('coverage_info.' + str(counter)))
0
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995
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996
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997 def clean_header(header):
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998 problematic_characters = ["|", " ", ",", ".", "(", ")", "'", "/", ":"]
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999 new_header = str(header)
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1000 if any(x in header for x in problematic_characters):
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1001 for x in problematic_characters:
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1002 new_header = new_header.replace(x, '_')
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1003 return header, new_header
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1004
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1005
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1006 def get_sequence_information(fasta_file, length_extra_seq):
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1007 sequence_dict = {}
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1008 headers = {}
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1009 headers_changed = False
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1010
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1011 with open(fasta_file, 'rtU') as reader:
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1012 blank_line_found = False
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1013 sequence_counter = 0
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1014 temp_sequence_dict = {}
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1015 for line in reader:
3
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1016 line = line.rstrip('\r\n')
0
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1017 if len(line) > 0:
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1018 if not blank_line_found:
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1019 if line.startswith('>'):
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1020 if len(temp_sequence_dict) > 0:
3
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1021 if list(temp_sequence_dict.values())[0]['length'] - 2 * length_extra_seq > 0:
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1022 sequence_dict[list(temp_sequence_dict.keys())[0]] = list(temp_sequence_dict.values())[0]
0
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1023 else:
3
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1024 print('{header} sequence ignored due to'
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1025 ' length = 0'.format(header=list(temp_sequence_dict.values())[0]['header']))
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1026 del headers[list(temp_sequence_dict.values())[0]['header']]
0
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1027 temp_sequence_dict = {}
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1028
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1029 original_header, new_header = clean_header(line[1:])
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1030 if new_header in headers:
3
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1031 sys.exit('Found duplicated sequence'
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1032 ' headers: {original_header}'.format(original_header=original_header))
0
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1033
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1034 sequence_counter += 1
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1035 temp_sequence_dict[sequence_counter] = {'header': new_header, 'sequence': '', 'length': 0}
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1036 headers[new_header] = str(original_header)
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1037 if new_header != original_header:
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1038 headers_changed = True
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1039 else:
3
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1040 temp_sequence_dict[sequence_counter]['sequence'] += line.replace(' ', '')
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1041 temp_sequence_dict[sequence_counter]['length'] += len(line.replace(' ', ''))
0
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1042 else:
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1043 sys.exit('It was found a blank line between the fasta file above line ' + line)
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1044 else:
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1045 blank_line_found = True
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1046
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1047 if len(temp_sequence_dict) > 0:
3
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1048 if list(temp_sequence_dict.values())[0]['length'] - 2 * length_extra_seq > 0:
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1049 sequence_dict[list(temp_sequence_dict.keys())[0]] = list(temp_sequence_dict.values())[0]
0
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1050 else:
3
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1051 print('{header} sequence ignored due to'
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1052 ' length <= 0'.format(header=list(temp_sequence_dict.values())[0]['header']))
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1053 del headers[list(temp_sequence_dict.values())[0]['header']]
0
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1054
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1055 return sequence_dict, headers, headers_changed
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1056
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1057
3
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1058 def sequence_data(sample, reference_file, bam_file, outdir, threads, length_extra_seq, minimum_depth_presence,
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1059 minimum_depth_call, minimum_depth_frequency_dominant_allele, debug_mode_true, not_write_consensus):
0
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1060 sequence_data_outdir = os.path.join(outdir, 'sequence_data', '')
3
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1061 utils.remove_directory(sequence_data_outdir)
0
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1062 os.mkdir(sequence_data_outdir)
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1063
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1064 sequences, headers, headers_changed = get_sequence_information(reference_file, length_extra_seq)
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1065
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1066 pool = multiprocessing.Pool(processes=threads)
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1067 for sequence_counter in sequences:
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1068 sequence_dir = os.path.join(sequence_data_outdir, str(sequence_counter), '')
3
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1069 utils.remove_directory(sequence_dir)
0
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1070 os.makedirs(sequence_dir)
3
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1071 pool.apply_async(analyse_sequence_data, args=(bam_file, sequences[sequence_counter], sequence_dir,
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1072 sequence_counter, reference_file, length_extra_seq,
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1073 minimum_depth_presence, minimum_depth_call,
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1074 minimum_depth_frequency_dominant_allele,))
0
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1075 pool.close()
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1076 pool.join()
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1077
3
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1078 run_successfully, sample_data, consensus_files, consensus_sequences = \
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1079 gather_data_together(sample, sequence_data_outdir, sequences, outdir.rsplit('/', 2)[0], debug_mode_true,
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1080 length_extra_seq, not_write_consensus)
0
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1081
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1082 return run_successfully, sample_data, consensus_files, consensus_sequences
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1083
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1084
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1085 def chunkstring(string, length):
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1086 return (string[0 + i:length + i] for i in range(0, len(string), length))
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1087
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1088
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1089 def write_consensus(outdir, sample, consensus_sequence):
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1090 consensus_files = {}
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1091 for consensus_type in ['correct', 'noMatter', 'alignment']:
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1092 consensus_files[consensus_type] = os.path.join(outdir, str(sample + '.' + consensus_type + '.fasta'))
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1093 with open(consensus_files[consensus_type], 'at') as writer:
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1094 writer.write('>' + consensus_sequence[consensus_type]['header'] + '\n')
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1095 fasta_sequence_lines = chunkstring(consensus_sequence[consensus_type]['sequence'], 80)
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1096 for line in fasta_sequence_lines:
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1097 writer.write(line + '\n')
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1098 return consensus_files
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1099
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1100
3
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1101 def gather_data_together(sample, data_directory, sequences_information, outdir, debug_mode_true, length_extra_seq,
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1102 not_write_consensus):
0
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1103 run_successfully = True
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1104 counter = 0
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1105 sample_data = {}
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1106
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1107 consensus_files = None
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1108 consensus_sequences_together = {'correct': {}, 'noMatter': {}, 'alignment': {}}
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1109
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1110 write_consensus_first_time = True
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1111
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1112 genes_directories = [d for d in os.listdir(data_directory) if
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diff changeset
1113 not d.startswith('.') and
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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1114 os.path.isdir(os.path.join(data_directory, d, ''))]
0
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diff changeset
1115 for gene_dir in genes_directories:
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1116 gene_dir_path = os.path.join(data_directory, gene_dir, '')
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diff changeset
1117
3
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1118 files = [f for f in os.listdir(gene_dir_path) if
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diff changeset
1119 not f.startswith('.') and
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diff changeset
1120 os.path.isfile(os.path.join(gene_dir_path, f))]
0
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diff changeset
1121 for file_found in files:
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diff changeset
1122 if file_found.startswith('coverage_info.') and file_found.endswith('.pkl'):
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1123 file_path = os.path.join(gene_dir_path, file_found)
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diff changeset
1124
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1125 if run_successfully:
3
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diff changeset
1126 run_successfully, sequence_counter, multiple_alleles_found, count_absent, percentage_low_coverage, \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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diff changeset
1127 mean_coverage, consensus_sequence, \
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diff changeset
1128 number_diferences = utils.extract_variable_from_pickle(file_path)
0
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diff changeset
1129
3
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diff changeset
1130 if not not_write_consensus:
0
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1131 for consensus_type in consensus_sequence:
3
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diff changeset
1132 consensus_sequences_together[consensus_type][sequence_counter] = \
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diff changeset
1133 {'header': consensus_sequence[consensus_type]['header'],
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diff changeset
1134 'sequence': consensus_sequence[consensus_type]['sequence']}
0
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diff changeset
1135
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1136 if write_consensus_first_time:
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1137 for consensus_type in ['correct', 'noMatter', 'alignment']:
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1138 file_to_remove = os.path.join(outdir, str(sample + '.' + consensus_type + '.fasta'))
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parents:
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1139 if os.path.isfile(file_to_remove):
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parents:
diff changeset
1140 os.remove(file_to_remove)
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1141 write_consensus_first_time = False
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1142 consensus_files = write_consensus(outdir, sample, consensus_sequence)
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1143
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1144 gene_identity = 0
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1145 if sequences_information[sequence_counter]['length'] - 2 * length_extra_seq - count_absent > 0:
3
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diff changeset
1146 gene_identity = 100 - \
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parents: 0
diff changeset
1147 (float(number_diferences) /
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
1148 (sequences_information[sequence_counter]['length'] - 2 * length_extra_seq -
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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diff changeset
1149 count_absent)) * 100
0
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1150
3
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diff changeset
1151 sample_data[sequence_counter] = \
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diff changeset
1152 {'header': sequences_information[sequence_counter]['header'],
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diff changeset
1153 'gene_coverage': 100 - (float(count_absent) /
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parents: 0
diff changeset
1154 (sequences_information[sequence_counter]['length'] - 2 *
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
1155 length_extra_seq)) * 100,
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parents: 0
diff changeset
1156 'gene_low_coverage': percentage_low_coverage,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
1157 'gene_number_positions_multiple_alleles': multiple_alleles_found,
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parents: 0
diff changeset
1158 'gene_mean_read_coverage': mean_coverage,
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parents: 0
diff changeset
1159 'gene_identity': gene_identity}
0
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parents:
diff changeset
1160 counter += 1
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diff changeset
1161
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1162 if not debug_mode_true:
3
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diff changeset
1163 utils.remove_directory(gene_dir_path)
0
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diff changeset
1164
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1165 if counter != len(sequences_information):
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diff changeset
1166 run_successfully = False
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1167
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1168 return run_successfully, sample_data, consensus_files, consensus_sequences_together
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diff changeset
1169
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diff changeset
1170
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1171 rematch_timer = functools.partial(utils.timer, name='ReMatCh module')
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diff changeset
1172
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1173
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diff changeset
1174 @rematch_timer
3
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diff changeset
1175 def run_rematch_module(sample, fastq_files, reference_file, threads, outdir, length_extra_seq, minimum_depth_presence,
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diff changeset
1176 minimum_depth_call, minimum_depth_frequency_dominant_allele, minimum_gene_coverage,
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diff changeset
1177 debug_mode_true, num_map_loc, minimum_gene_identity, rematch_run,
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diff changeset
1178 soft_clip_base_quality, soft_clip_recode_run, reference_dict, soft_clip_cigar_flag_recode,
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parents: 0
diff changeset
1179 bowtie_algorithm, bowtie_opt, gene_list_reference, not_write_consensus, clean_run=True):
0
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diff changeset
1180 rematch_folder = os.path.join(outdir, 'rematch_module', '')
3
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diff changeset
1181
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diff changeset
1182 utils.remove_directory(rematch_folder)
0
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diff changeset
1183 os.mkdir(rematch_folder)
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diff changeset
1184
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diff changeset
1185 # Map reads
3
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diff changeset
1186 run_successfully, bam_file, reference_file = mapping_reads(fastq_files=fastq_files, reference_file=reference_file,
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diff changeset
1187 threads=threads, outdir=rematch_folder,
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diff changeset
1188 num_map_loc=num_map_loc, rematch_run=rematch_run,
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parents: 0
diff changeset
1189 soft_clip_base_quality=soft_clip_base_quality,
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parents: 0
diff changeset
1190 soft_clip_recode_run=soft_clip_recode_run,
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diff changeset
1191 reference_dict=reference_dict,
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diff changeset
1192 soft_clip_cigar_flag_recode=soft_clip_cigar_flag_recode,
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diff changeset
1193 bowtie_algorithm=bowtie_algorithm, bowtie_opt=bowtie_opt,
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parents: 0
diff changeset
1194 clean_run=clean_run)
0
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diff changeset
1195 if run_successfully:
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parents:
diff changeset
1196 # Index reference file
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diff changeset
1197 run_successfully, stdout = index_fasta_samtools(reference_file, None, None, True)
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1198 if run_successfully:
3
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diff changeset
1199 print('Analysing alignment data')
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diff changeset
1200 run_successfully, sample_data, consensus_files, consensus_sequences = \
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parents: 0
diff changeset
1201 sequence_data(sample, reference_file, bam_file, rematch_folder, threads, length_extra_seq,
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diff changeset
1202 minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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diff changeset
1203 debug_mode_true, not_write_consensus)
0
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diff changeset
1204
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1205 if run_successfully:
3
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parents: 0
diff changeset
1206 print('Writing report file')
0
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parents:
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1207 number_absent_genes = 0
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parents:
diff changeset
1208 number_genes_multiple_alleles = 0
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parents:
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1209 mean_sample_coverage = 0
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parents:
diff changeset
1210 with open(os.path.join(outdir, 'rematchModule_report.txt'), 'wt') as writer:
3
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parents: 0
diff changeset
1211 print('\n'.join(outdir, 'rematchModule_report.txt'))
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parents: 0
diff changeset
1212 writer.write('\t'.join(['#gene', 'percentage_gene_coverage', 'gene_mean_read_coverage',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
1213 'percentage_gene_low_coverage', 'number_positions_multiple_alleles',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
1214 'percentage_gene_identity']) + '\n')
0
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parents:
diff changeset
1215 for i in range(1, len(sample_data) + 1):
3
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parents: 0
diff changeset
1216 writer.write('\t'.join([gene_list_reference[sample_data[i]['header']],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
1217 str(round(sample_data[i]['gene_coverage'], 2)),
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
1218 str(round(sample_data[i]['gene_mean_read_coverage'], 2)),
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
1219 str(round(sample_data[i]['gene_low_coverage'], 2)),
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parents: 0
diff changeset
1220 str(sample_data[i]['gene_number_positions_multiple_alleles']),
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
1221 str(round(sample_data[i]['gene_identity'], 2))]) + '\n')
0
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diff changeset
1222
3
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parents: 0
diff changeset
1223 if sample_data[i]['gene_coverage'] < minimum_gene_coverage or \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
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parents: 0
diff changeset
1224 sample_data[i]['gene_identity'] < minimum_gene_identity:
0
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parents:
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1225 number_absent_genes += 1
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parents:
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1226 else:
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1227 mean_sample_coverage += sample_data[i]['gene_mean_read_coverage']
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parents:
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1228 if sample_data[i]['gene_number_positions_multiple_alleles'] > 0:
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parents:
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1229 number_genes_multiple_alleles += 1
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diff changeset
1230
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parents:
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1231 if len(sample_data) - number_absent_genes > 0:
3
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1232 mean_sample_coverage = \
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1233 float(mean_sample_coverage) / float(len(sample_data) - number_absent_genes)
0
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1234 else:
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1235 mean_sample_coverage = 0
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1236
3
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1237 writer.write('\n'.join(['#general',
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1238 '>number_absent_genes', str(number_absent_genes),
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1239 '>number_genes_multiple_alleles', str(number_genes_multiple_alleles),
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1240 '>mean_sample_coverage', str(round(mean_sample_coverage, 2))]) + '\n')
0
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1241
3
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1242 print('\n'.join([str('number_absent_genes: ' + str(number_absent_genes)),
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1243 str('number_genes_multiple_alleles: ' + str(number_genes_multiple_alleles)),
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1244 str('mean_sample_coverage: ' + str(round(mean_sample_coverage, 2)))]))
0
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1245
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1246 if not debug_mode_true:
3
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1247 utils.remove_directory(rematch_folder)
0
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1248
3
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1249 return run_successfully, sample_data if 'sample_data' in locals() else None, \
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1250 {'number_absent_genes': number_absent_genes if 'number_absent_genes' in locals() else None,
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1251 'number_genes_multiple_alleles': number_genes_multiple_alleles if
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1252 'number_genes_multiple_alleles' in locals() else None,
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1253 'mean_sample_coverage': round(mean_sample_coverage, 2) if 'mean_sample_coverage' in locals() else None}, \
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1254 consensus_files if 'consensus_files' in locals() else None,\
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1255 consensus_sequences if 'consensus_sequences' in locals() else None