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annotate RepEnrich.py @ 14:bf866bedd4b4 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 205141a3f695f202d5c3e01e6ab3b2b869fe62b5
author artbio
date Sat, 20 Apr 2024 12:13:52 +0000
parents 530626b0757c
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f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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1 import argparse
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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2 import csv
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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3 import shlex
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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4 import subprocess
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5 import sys
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6 from collections import defaultdict
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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7 from concurrent.futures import ProcessPoolExecutor
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10 parser = argparse.ArgumentParser(description='''
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11 Repenrich aligns reads to Repeat Elements pseudogenomes\
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12 and counts aligned reads. RepEnrich_setup must be run\
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13 before its use''')
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14 parser.add_argument('--annotation_file', action='store',
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15 metavar='annotation_file',
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16 help='RepeatMasker.org annotation file for your\
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17 organism. The file may be downloaded from\
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18 RepeatMasker.org. E.g. hg19_repeatmasker.txt')
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19 parser.add_argument('--alignment_bam', action='store', metavar='alignment_bam',
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20 help='Bam alignments of unique mapper reads.')
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21 parser.add_argument('--fastqfile', action='store', metavar='fastqfile',
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22 help='File of fastq reads mapping to multiple\
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23 locations. Example: /data/multimap.fastq')
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24 parser.add_argument('--fastqfile2', action='store', dest='fastqfile2',
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25 metavar='fastqfile2', default='',
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26 help='fastqfile #2 when using paired-end option.\
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27 Default none')
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28 parser.add_argument('--cpus', action='store', dest='cpus', metavar='cpus',
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29 default="1", type=int,
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30 help='Number of CPUs. The more cpus the\
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31 faster RepEnrich performs. Default: "1"')
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33 args = parser.parse_args()
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35 # parameters
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36 annotation_file = args.annotation_file
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37 unique_mapper_bam = args.alignment_bam
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38 fastqfile_1 = args.fastqfile
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39 fastqfile_2 = args.fastqfile2
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40 cpus = args.cpus
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41 # Change if simple repeats are differently annotated in your organism
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42 simple_repeat = "Simple_repeat"
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43 if args.fastqfile2:
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44 paired_end = True
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45 else:
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46 paired_end = False
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48
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49 def starts_with_numerical(list):
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50 try:
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51 if len(list) == 0:
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52 return False
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53 int(list[0])
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54 return True
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55 except ValueError:
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56 return False
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59 # define a text importer for .out/.txt format of repbase
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60 def import_text(filename, separator):
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61 csv.field_size_limit(sys.maxsize)
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62 file = csv.reader(open(filename), delimiter=separator,
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63 skipinitialspace=True)
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64 return [line for line in file if starts_with_numerical(line)]
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65
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66
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67 def run_bowtie(args):
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68 metagenome, fastqfile = args
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69 b_opt = "-k 1 -p 1 --quiet"
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70 command = shlex.split(f"bowtie {b_opt} -x {metagenome} {fastqfile}")
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71 bowtie_align = subprocess.run(command, check=True,
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72 capture_output=True, text=True).stdout
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73 bowtie_align = bowtie_align.rstrip('\r\n').split('\n')
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74 readlist = [metagenome]
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75 if paired_end:
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76 for line in bowtie_align:
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77 readlist.append(line.split("/")[0])
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78 else:
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79 for line in bowtie_align:
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80 readlist.append(line.split("\t")[0])
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81 return readlist
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83
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84 # set a reference repeat list for the script
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85 repeat_list = [listline[9].translate(
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86 str.maketrans(
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87 '()/', '___')) for listline in import_text(annotation_file, ' ')]
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88 repeat_list = sorted(list(set(repeat_list)))
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89
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90 # unique mapper counting
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91 cmd = f"bedtools bamtobed -i {unique_mapper_bam} | \
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92 bedtools coverage -b stdin -a repnames.bed"
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93 p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
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94 bedtools_counts = p.communicate()[0].decode().rstrip('\r\n').split('\n')
12
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95
13
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96 # parse bedtools output
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97 counts = defaultdict(int) # key: repeat names, value: unique mapper counts
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98 sumofrepeatreads = 0
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99 for line in bedtools_counts:
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100 line = line.split('\t')
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101 counts[line[3]] += int(line[4])
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102 sumofrepeatreads += int(line[4])
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103 print(f"Identified {sumofrepeatreads} unique reads that mapped to repeats.")
12
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104
13
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105 # multimapper parsing
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106 if not paired_end:
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107 args_list = [(metagenome, fastqfile_1) for
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108 metagenome in repeat_list]
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109 with ProcessPoolExecutor(max_workers=cpus) as executor:
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110 results = executor.map(run_bowtie, args_list)
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111 else:
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112 args_list = [(metagenome, fastqfile_1) for
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113 metagenome in repeat_list]
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114 args_list.extend([(metagenome, fastqfile_2) for
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115 metagenome in repeat_list])
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116 with ProcessPoolExecutor(max_workers=cpus) as executor:
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117 results = executor.map(run_bowtie, args_list)
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118
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119 # Aggregate results (avoiding race conditions)
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120 metagenome_reads = defaultdict(list) # repeat_name: list of multimap reads
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121 for result in results:
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122 metagenome_reads[result[0]] += result[1:]
0
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123
13
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124 for name in metagenome_reads:
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125 # read are only once in list
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126 metagenome_reads[name] = list(set(metagenome_reads[name]))
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127 # remove "no read" instances
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128 metagenome_reads[name] = [read for read in metagenome_reads[name]
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129 if read != ""]
0
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130
13
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131 # implement repeats_by_reads from the inverse dictionnary metagenome_reads
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132 repeats_by_reads = defaultdict(list) # readids: list of repeats names
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133 for repname in metagenome_reads:
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134 for read in metagenome_reads[repname]:
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135 repeats_by_reads[read].append(repname)
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136 for repname in repeats_by_reads:
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137 repeats_by_reads[repname] = list(set(repeats_by_reads[repname]))
12
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138
13
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139 # 3 dictionnaries and 1 pointer variable to be populated
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140 fractionalcounts = defaultdict(float)
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141 familyfractionalcounts = defaultdict(float)
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142 classfractionalcounts = defaultdict(float)
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143 sumofrepeatreads = 0
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144
13
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145 # Update counts dictionnary with sets of repeats (was "subfamilies")
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146 # matched by multimappers
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147 for repeat_set in repeats_by_reads.values():
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148 repeat_set_string = ','.join(repeat_set)
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149 counts[repeat_set_string] += 1
0
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150 sumofrepeatreads += 1
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151
13
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152 print(f'Identified more {sumofrepeatreads} mutimapper repeat reads')
0
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153
13
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154 # Populate fractionalcounts
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155 for key, count in counts.items():
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156 key_list = key.split(',')
12
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157 for i in key_list:
13
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158 fractionalcounts[i] += count / len(key_list)
0
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159
13
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160 # build repeat_ref for easy access to rep class and rep families
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161 repeat_ref = defaultdict(dict)
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162 repeats = import_text(annotation_file, ' ')
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163 for repeat in repeats:
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164 repeat_name = repeat[9].translate(str.maketrans('()/', '___'))
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165 try:
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166 repclass = repeat[10].split('/')[0]
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167 repfamily = repeat[10].split('/')[1]
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168 except IndexError:
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169 repclass, repfamily = repeat[10], repeat[10]
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170 repeat_ref[repeat_name]['class'] = repclass
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171 repeat_ref[repeat_name]['family'] = repfamily
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172
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173 # Populate classfractionalcounts and familyfractionalcounts
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174 for key, value in fractionalcounts.items():
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175 classfractionalcounts[repeat_ref[key]['class']] += value
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176 familyfractionalcounts[repeat_ref[key]['family']] += value
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177
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178 # print class-, family- and fraction-repeats counts to files
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179 with open("class_fraction_counts.tsv", 'w') as fout:
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180 for key in sorted(classfractionalcounts):
12
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
parents: 10
diff changeset
181 fout.write(f"{key}\t{classfractionalcounts[key]}\n")
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
parents: 10
diff changeset
182
13
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
artbio
parents: 12
diff changeset
183 with open("family_fraction_counts.tsv", 'w') as fout:
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
artbio
parents: 12
diff changeset
184 for key in sorted(familyfractionalcounts):
12
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
parents: 10
diff changeset
185 fout.write(f"{key}\t{familyfractionalcounts[key]}\n")
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
parents: 10
diff changeset
186
13
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
artbio
parents: 12
diff changeset
187 with open("fraction_counts.tsv", 'w') as fout:
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
artbio
parents: 12
diff changeset
188 for key in sorted(fractionalcounts):
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
artbio
parents: 12
diff changeset
189 fout.write(f"{key}\t{repeat_ref[key]['class']}\t"
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
artbio
parents: 12
diff changeset
190 f"{repeat_ref[key]['family']}\t"
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
artbio
parents: 12
diff changeset
191 f"{fractionalcounts[key]}\n")