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annotate RepEnrich_setup.py @ 13:530626b0757c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
author artbio
date Tue, 02 Apr 2024 21:16:37 +0000
parents 89e05f831259
children bf866bedd4b4
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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 #!/usr/bin/env python
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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2 import argparse
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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3 import csv
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4 import os
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5 import shlex
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6 import subprocess
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7 import sys
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8 from collections import defaultdict
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9 from concurrent.futures import ProcessPoolExecutor
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10
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12 from Bio import SeqIO
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13 from Bio.Seq import Seq
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14 from Bio.SeqRecord import SeqRecord
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16 parser = argparse.ArgumentParser(description='''
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17 Prepartion of repetive element pseudogenomes bowtie\
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18 indexes and annotation files used by RepEnrich.py enrichment.''',
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19 prog='getargs_genome_maker.py')
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20 parser.add_argument('--annotation_file', action='store',
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21 metavar='annotation_file',
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22 help='''Repeat masker annotation of the genome of\
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23 interest. Download from RepeatMasker.org\
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24 Example: mm9.fa.out''')
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25 parser.add_argument('--genomefasta', action='store', metavar='genomefasta',
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26 help='''Genome of interest in fasta format.\
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27 Example: mm9.fa''')
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28 parser.add_argument('--gaplength', action='store', dest='gaplength',
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29 metavar='gaplength', default='200', type=int,
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30 help='''Length of the N-spacer in the\
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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31 repeat pseudogenomes. Default 200''')
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32 parser.add_argument('--flankinglength', action='store', dest='flankinglength',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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33 metavar='flankinglength', default='25', type=int,
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34 help='''Length of the flanking regions used to build\
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35 repeat pseudogenomes. Flanking length should be set\
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36 according to the length of your reads.\
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37 Default 25, for 50 nt reads''')
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38 parser.add_argument('--cpus', action='store', dest='cpus', metavar='cpus',
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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39 default="1", type=int,
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40 help='Number of CPUs. The more cpus the\
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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41 faster RepEnrich performs. Default: "1"')
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42 args = parser.parse_args()
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43
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44 # parameters from argsparse
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45 gapl = args.gaplength
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46 flankingl = args.flankinglength
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47 annotation_file = args.annotation_file
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48 genomefasta = args.genomefasta
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49 cpus = args.cpus
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51 # check that the programs we need are available
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52 try:
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53 subprocess.call(shlex.split("bowtie --version"),
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54 stdout=open(os.devnull, 'wb'),
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55 stderr=open(os.devnull, 'wb'))
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56 except OSError:
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57 print("Error: Bowtie not available in the path")
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58 raise
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60
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61 def starts_with_numerical(list):
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62 try:
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63 if len(list) == 0:
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64 return False
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65 int(list[0])
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66 return True
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67 except ValueError:
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68 return False
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71 # define a text importer for .out/.txt format of repbase
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72 def import_text(filename, separator):
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73 csv.field_size_limit(sys.maxsize)
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74 file = csv.reader(open(filename), delimiter=separator,
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75 skipinitialspace=True)
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76 return [line for line in file if starts_with_numerical(line)]
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78
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79 # load genome into dictionary and compute length
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80 g = SeqIO.to_dict(SeqIO.parse(genomefasta, "fasta"))
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81 genome = defaultdict(dict)
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82
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83 for chr in g.keys():
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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84 genome[chr]['sequence'] = g[chr].seq
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85 genome[chr]['length'] = len(g[chr].seq)
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87 # Build a bedfile of repeatcoordinates to use by RepEnrich region_sorter
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88 repeat_elements = set()
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89 rep_coords = defaultdict(list) # Merged dictionary for coordinates
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90
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91 with open('repnames.bed', 'w') as fout:
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92 f_in = import_text(annotation_file, ' ')
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93 for line in f_in:
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94 repname = line[9].translate(str.maketrans('()/', '___'))
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95 repeat_elements.add(repname)
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96 repchr, repstart, repend = line[4], line[5], line[6]
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97 fout.write(f"{repchr}\t{repstart}\t{repend}\t{repname}\n")
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98 rep_coords[repname].extend([repchr, repstart, repend])
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99 # repeat_elements now contains the unique repeat names
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100 # rep_coords is a dictionary where keys are repeat names and values are lists
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101 # containing chromosome, start, and end coordinates for each repeat instance
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102
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103 # sort repeat_elements and print them in repeatIDs.txt
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104 with open('repeatIDs.txt', 'w') as fout:
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105 for i, repeat in enumerate(sorted(repeat_elements)):
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106 fout.write('\t'.join([repeat, str(i)]) + '\n')
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107
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108 # generate spacer for pseudogenomes
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109 spacer = ''.join(['N' for i in range(gapl)])
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110
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111 # generate metagenomes and save them to FASTA files for bowtie build
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112 for repname in rep_coords:
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113 metagenome = ''
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114 # iterating coordinate list by block of 3 (chr, start, end)
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115 block = 3
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116 for i in range(0, len(rep_coords[repname]) - block + 1, block):
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117 batch = rep_coords[repname][i:i+block]
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118 print(batch)
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119 chromosome = batch[0]
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120 start = max(int(batch[1]) - flankingl, 0)
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121 end = min(int(batch[2]) + flankingl,
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122 int(genome[chromosome]['length'])-1) + 1
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123 metagenome = (
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124 f"{metagenome}{spacer}"
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125 f"{genome[chromosome]['sequence'][start:end]}"
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126 )
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127
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128 # Create Fasta of repeat pseudogenome
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129 fastafilename = f"{repname}.fa"
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130 record = SeqRecord(Seq(metagenome), id=repname, name='', description='')
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131 SeqIO.write(record, fastafilename, "fasta")
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132
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133
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134 def bowtie_build(args):
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135 """
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136 Function to be executed in parallel by ProcessPoolExecutor.
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137 """
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138 try:
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139 bowtie_base, fasta = args
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140 command = shlex.split(f"bowtie-build -f {fasta} {bowtie_base}")
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141 squash = subprocess.run(command, capture_output=True, text=True)
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142 return squash.stdout
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143 except Exception as e:
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144 return str(e)
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145
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146
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147 args_list = [(name, f"{name}.fa") for name in rep_coords]
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148 with ProcessPoolExecutor(max_workers=cpus) as executor:
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149 executor.map(bowtie_build, args_list)