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annotate RepEnrich2.py @ 9:2b61c6407efb draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 961a14cd73dd8e40b2f30d5e4df136b98cd8f07a
author artbio
date Thu, 25 Apr 2024 16:22:34 +0000
parents 567549a49eb2
children
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4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
artbio
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diff changeset
1 import argparse
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
artbio
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2 import csv
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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3 import os
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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4 import shlex
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
artbio
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5 import subprocess
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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6 import sys
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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7 from collections import defaultdict
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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8 from concurrent.futures import ProcessPoolExecutor
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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9
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10
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11 parser = argparse.ArgumentParser(description='''
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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12 Repenrich aligns reads to Repeat Elements pseudogenomes\
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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13 and counts aligned reads. RepEnrich_setup must be run\
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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14 before its use''')
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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15 parser.add_argument('--annotation_file', action='store',
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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16 metavar='annotation_file',
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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17 help='RepeatMasker.org annotation file for your\
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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18 organism. The file may be downloaded from\
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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19 RepeatMasker.org. E.g. hg19_repeatmasker.txt')
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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20 parser.add_argument('--alignment_bam', action='store', metavar='alignment_bam',
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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21 help='Bam alignments of unique mapper reads.')
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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22 parser.add_argument('--fastqfile', action='store', metavar='fastqfile',
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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23 help='File of fastq reads mapping to multiple\
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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24 locations. Example: /data/multimap.fastq')
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25 parser.add_argument('--fastqfile2', action='store', dest='fastqfile2',
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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26 metavar='fastqfile2', default='',
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27 help='fastqfile #2 when using paired-end option.\
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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28 Default none')
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29 parser.add_argument('--cpus', action='store', dest='cpus', metavar='cpus',
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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30 default="1", type=int,
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31 help='Number of CPUs. The more cpus the\
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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32 faster RepEnrich performs. Default: "1"')
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33
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34 args = parser.parse_args()
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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35
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36 # parameters
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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37 annotation_file = args.annotation_file
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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38 unique_mapper_bam = args.alignment_bam
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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39 fastqfile_1 = args.fastqfile
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40 fastqfile_2 = args.fastqfile2
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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41 cpus = args.cpus
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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42 # Change if simple repeats are differently annotated in your organism
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43 simple_repeat = "Simple_repeat"
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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44 if args.fastqfile2:
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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45 paired_end = True
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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46 else:
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47 paired_end = False
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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48
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49 # check that the programs we need are available
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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50 try:
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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51 subprocess.call(shlex.split("coverageBed -h"),
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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52 stdout=open(os.devnull, 'wb'),
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53 stderr=open(os.devnull, 'wb'))
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54 subprocess.call(shlex.split("bowtie2 --version"),
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55 stdout=open(os.devnull, 'wb'),
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56 stderr=open(os.devnull, 'wb'))
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57 except OSError:
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58 print("Error: Bowtie2 or bedtools not loaded")
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59 raise
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60
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61
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62 def starts_with_numerical(list):
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63 try:
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64 if len(list) == 0:
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65 return False
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66 int(list[0])
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67 return True
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68 except ValueError:
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69 return False
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70
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71
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72 # define a text importer for .out/.txt format of repbase
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73 def import_text(filename, separator):
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74 csv.field_size_limit(sys.maxsize)
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75 file = csv.reader(open(filename), delimiter=separator,
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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76 skipinitialspace=True)
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77 return [line for line in file if starts_with_numerical(line)]
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78
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79
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80 # set a reference repeat list for the script
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81 repeat_list = [listline[9].translate(
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82 str.maketrans(
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83 '()/', '___')) for listline in import_text(annotation_file, ' ')]
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84 repeat_list = sorted(list(set(repeat_list)))
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85
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86 # unique mapper counting
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87 cmd = f"bedtools bamtobed -i {unique_mapper_bam} | \
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88 bedtools coverage -b stdin -a repnames.bed"
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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89 p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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90 bedtools_counts = p.communicate()[0].decode().rstrip('\r\n').split('\n')
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91
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92 # parse bedtools output
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93 counts = defaultdict(int) # key: repeat names, value: unique mapper counts
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94 sumofrepeatreads = 0
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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95 for line in bedtools_counts:
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96 line = line.split('\t')
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97 counts[line[3]] += int(line[4])
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98 sumofrepeatreads += int(line[4])
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99 print(f"Identified {sumofrepeatreads} unique reads that mapped to repeats.")
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100
5
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101 # print unique mapper counts
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102 with open("unique_mapper_counts.tsv", 'w') as fout:
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103 fout.write("#element\tcount\n")
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104 for count in sorted(counts):
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105 fout.write(f"{count}\t{counts[count]}\n")
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106
7
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107
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108 def run_bowtie(args):
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109 '''
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110 write to files to save memory
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111 '''
9
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112 metagenome = args
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113 b_opt = "-k 1 -p 2 --quiet --no-hd --no-unal"
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114 if paired_end is True:
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115 command = shlex.split(f"bowtie2 {b_opt} -x {metagenome}"
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116 f" -1 {fastqfile_1} -2 {fastqfile_1}")
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117 else:
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118 command = shlex.split(f"bowtie2 {b_opt} -x {metagenome} {fastqfile_1}")
7
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119 bowtie_align = subprocess.run(command, check=True,
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120 capture_output=True, text=True).stdout
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121 bowtie_align = bowtie_align.rstrip('\r\n').split('\n')
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122 with open(f"{metagenome}.reads", "a+") as readfile:
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123 for line in bowtie_align:
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124 read = line.split()[0].split("/")[0]
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125 if read:
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126 readfile.write(f"{read}\n")
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127
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128
0
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129 # multimapper parsing
9
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130 args_list = [metagenome for metagenome in repeat_list]
7
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131 with ProcessPoolExecutor(max_workers=cpus) as executor:
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132 results = executor.map(run_bowtie, args_list)
0
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133
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134 # Aggregate results (avoiding race conditions)
7
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135 metagenome_reads = defaultdict(list) # metagenome: list of multimap reads
0
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136
9
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137 # Now we read .reads files to populate metagnomes_reads
7
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138 for metagenome in repeat_list:
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139 with open(f"{metagenome}.reads") as readfile:
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140 for read in readfile:
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141 metagenome_reads[metagenome].append(read)
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142 # read are only once in list
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143 metagenome_reads[metagenome] = list(set(metagenome_reads[metagenome]))
0
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144
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145 # implement repeats_by_reads from the inverse dictionnary metagenome_reads
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146 repeats_by_reads = defaultdict(list) # readids: list of repeats names
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147 for repname in metagenome_reads:
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148 for read in metagenome_reads[repname]:
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149 repeats_by_reads[read].append(repname)
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150 for repname in repeats_by_reads:
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151 repeats_by_reads[repname] = list(set(repeats_by_reads[repname]))
8
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diff changeset
152 # this repeats_by_reads dictionary is far too big
0
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153
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154 # 3 dictionnaries and 1 pointer variable to be populated
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155 fractionalcounts = defaultdict(float)
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156 familyfractionalcounts = defaultdict(float)
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157 classfractionalcounts = defaultdict(float)
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158 sumofrepeatreads = 0
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159
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160 # Update counts dictionnary with sets of repeats (was "subfamilies")
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161 # matched by multimappers
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162 for repeat_set in repeats_by_reads.values():
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163 repeat_set_string = ','.join(repeat_set)
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164 counts[repeat_set_string] += 1
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165 sumofrepeatreads += 1
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166
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167 print(f'Identified more {sumofrepeatreads} mutimapper repeat reads')
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168
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169 # Populate fractionalcounts
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170 for key, count in counts.items():
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171 key_list = key.split(',')
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172 for i in key_list:
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173 fractionalcounts[i] += count / len(key_list)
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174
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175 # build repeat_ref for easy access to rep class and rep families
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176 repeat_ref = defaultdict(dict)
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177 repeats = import_text(annotation_file, ' ')
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178 for repeat in repeats:
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179 repeat_name = repeat[9].translate(str.maketrans('()/', '___'))
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180 try:
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181 repclass = repeat[10].split('/')[0]
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182 repfamily = repeat[10].split('/')[1]
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183 except IndexError:
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184 repclass, repfamily = repeat[10], repeat[10]
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185 repeat_ref[repeat_name]['class'] = repclass
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186 repeat_ref[repeat_name]['family'] = repfamily
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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187
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188 # Populate classfractionalcounts and familyfractionalcounts
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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189 for key, value in fractionalcounts.items():
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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190 classfractionalcounts[repeat_ref[key]['class']] += value
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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191 familyfractionalcounts[repeat_ref[key]['family']] += value
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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192
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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193 # print class-, family- and fraction-repeats counts to files
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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194 with open("class_fraction_counts.tsv", 'w') as fout:
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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195 for key in sorted(classfractionalcounts):
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196 fout.write(f"{key}\t{round(classfractionalcounts[key], 2)}\n")
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4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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197
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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198 with open("family_fraction_counts.tsv", 'w') as fout:
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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199 for key in sorted(familyfractionalcounts):
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200 fout.write(f"{key}\t{round(familyfractionalcounts[key], 2)}\n")
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4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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201
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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202 with open("fraction_counts.tsv", 'w') as fout:
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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203 for key in sorted(fractionalcounts):
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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204 fout.write(f"{key}\t{repeat_ref[key]['class']}\t"
4905a332a094 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
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205 f"{repeat_ref[key]['family']}\t"
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206 f"{round(fractionalcounts[key], 2)}\n")