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annotate RepEnrich_setup.py @ 3:89968ee4bf95 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
author drosofff
date Mon, 29 May 2017 13:12:29 -0400
parents 041de602103e
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041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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1 #!/usr/bin/env python
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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2 import argparse
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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3 import csv
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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4 import os
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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5 import shlex
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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6 import subprocess
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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7 import sys
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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8 from Bio import SeqIO
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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9 from Bio.Seq import Seq
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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10 from Bio.SeqRecord import SeqRecord
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11 from Bio.Alphabet import IUPAC
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12
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13 parser = argparse.ArgumentParser(description='Part I: Prepartion of repetive element psuedogenomes and repetive element bamfiles. This script prepares the annotation used by downstream applications to analyze for repetitive element enrichment. For this script to run properly bowtie must be loaded. The repeat element psuedogenomes are prepared in order to analyze reads that map to multiple locations of the genome. The repeat element bamfiles are prepared in order to use a region sorter to analyze reads that map to a single location of the genome.You will 1) annotation_file: The repetitive element annotation file downloaded from RepeatMasker.org database for your organism of interest. 2) genomefasta: Your genome of interest in fasta format, 3)setup_folder: a folder to contain repeat element setup files command-line usage EXAMPLE: python master_setup.py /users/nneretti/data/annotation/mm9/mm9_repeatmasker.txt /users/nneretti/data/annotation/mm9/mm9.fa /users/nneretti/data/annotation/mm9/setup_folder', prog='getargs_genome_maker.py')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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14 parser.add_argument('--version', action='version', version='%(prog)s 0.1')
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15 parser.add_argument('annotation_file', action= 'store', metavar='annotation_file', help='List annotation file. The annotation file contains the repeat masker annotation for the genome of interest and may be downloaded at RepeatMasker.org Example /data/annotation/mm9/mm9.fa.out')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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16 parser.add_argument('genomefasta', action= 'store', metavar='genomefasta', help='File name and path for genome of interest in fasta format. Example /data/annotation/mm9/mm9.fa')
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17 parser.add_argument('setup_folder', action= 'store', metavar='setup_folder', help='List folder to contain bamfiles for repeats and repeat element psuedogenomes. Example /data/annotation/mm9/setup')
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18 parser.add_argument('--nfragmentsfile1', action= 'store', dest='nfragmentsfile1', metavar='nfragmentsfile1', default='./repnames_nfragments.txt', help='Output location of a description file that saves the number of fragments processed per repname. Default ./repnames_nfragments.txt')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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19 parser.add_argument('--gaplength', action= 'store', dest='gaplength', metavar='gaplength', default= '200', type=int, help='Length of the spacer used to build repeat psuedogeneomes. Default 200')
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20 parser.add_argument('--flankinglength', action= 'store', dest='flankinglength', metavar='flankinglength', default= '25', type=int, help='Length of the flanking region adjacent to the repeat element that is used to build repeat psuedogeneomes. The flanking length should be set according to the length of your reads. Default 25')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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21 parser.add_argument('--is_bed', action= 'store', dest='is_bed', metavar='is_bed', default= 'FALSE', help='Is the annotation file a bed file. This is also a compatible format. The file needs to be a tab seperated bed with optional fields. Ex. format chr\tstart\tend\tName_element\tclass\tfamily. The class and family should identical to name_element if not applicable. Default FALSE change to TRUE')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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22 args = parser.parse_args()
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23
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24 # parameters and paths specified in args_parse
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25 gapl = args.gaplength
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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26 flankingl = args.flankinglength
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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27 annotation_file = args.annotation_file
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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28 genomefasta = args.genomefasta
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29 setup_folder = args.setup_folder
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30 nfragmentsfile1 = args.nfragmentsfile1
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31 is_bed = args.is_bed
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32
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33 ################################################################################
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34 # check that the programs we need are available
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35 try:
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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36 subprocess.call(shlex.split("bowtie --version"), stdout=open(os.devnull, 'wb'), stderr=open(os.devnull, 'wb'))
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37 except OSError:
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38 print ("Error: Bowtie or BEDTools not loaded")
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39 raise
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40
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41 ################################################################################
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42 # Define a text importer
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43 csv.field_size_limit(sys.maxsize)
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44 def import_text(filename, separator):
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45 for line in csv.reader(open(os.path.realpath(filename)), delimiter=separator,
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46 skipinitialspace=True):
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47 if line:
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48 yield line
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49 # Make a setup folder
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50 if not os.path.exists(setup_folder):
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51 os.makedirs(setup_folder)
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52
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53 ################################################################################
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54 # load genome into dictionary
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55 print ("loading genome...")
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56 g = SeqIO.to_dict(SeqIO.parse(genomefasta, "fasta"))
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57
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58 print ("Precomputing length of all chromosomes...")
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59 idxgenome = {}
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60 lgenome = {}
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61 genome = {}
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62 allchrs = g.keys()
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63 k = 0
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64 for chr in allchrs:
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65 genome[chr] = str(g[chr].seq)
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66 # del g[chr]
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67 lgenome[chr] = len(genome[chr])
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68 idxgenome[chr] = k
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69 k = k + 1
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70 del g
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71
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72 ################################################################################
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73 # Build a bedfile of repeatcoordinates to use by RepEnrich region_sorter
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74 if is_bed == "FALSE":
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75 repeat_elements= []
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76 fout = open(os.path.realpath(setup_folder + os.path.sep + 'repnames.bed'), 'w')
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77 fin = import_text(annotation_file, ' ')
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78 x = 0
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79 rep_chr = {}
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80 rep_start = {}
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81 rep_end = {}
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82 x = 0
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83 for line in fin:
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84 if x>2:
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85 line9 = line[9].replace("(","_").replace(")","_").replace("/","_")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
86 repname = line9
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
87 if not repname in repeat_elements:
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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parents:
diff changeset
88 repeat_elements.append(repname)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
89 repchr = line[4]
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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parents:
diff changeset
90 repstart = int(line[5])
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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parents:
diff changeset
91 repend = int(line[6])
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
92 # print >> fout, str(repchr) + '\t'+str(repstart)+ '\t'+str(repend)+ '\t'+str(repname)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
93 fout.write(str(repchr) + '\t'+str(repstart)+ '\t'+str(repend)+ '\t'+str(repname)+ '\n')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
94 # if rep_chr.has_key(repname):
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
95 if repname in rep_chr:
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
96 rep_chr[repname].append(repchr)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
97 rep_start[repname].append(int(repstart))
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
98 rep_end[repname].append(int(repend))
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
99 else:
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
100 rep_chr[repname] = [repchr]
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
101 rep_start[repname] = [int(repstart)]
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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parents:
diff changeset
102 rep_end[repname] = [int(repend)]
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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parents:
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103 x +=1
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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104 if is_bed == "TRUE":
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
105 repeat_elements= []
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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106 fout = open(os.path.realpath(setup_folder + os.path.sep + 'repnames.bed'), 'w')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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107 fin = open(os.path.realpath(annotation_file), 'r')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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108 x =0
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
109 rep_chr = {}
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
110 rep_start = {}
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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111 rep_end = {}
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112 x =0
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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113 for line in fin:
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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114 line=line.strip('\n')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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115 line=line.split('\t')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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116 line3 = line[3].replace("(","_").replace(")","_").replace("/","_")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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117 repname = line3
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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118 if not repname in repeat_elements:
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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119 repeat_elements.append(repname)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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120 repchr = line[0]
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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121 repstart = int(line[1])
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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122 repend = int(line[2])
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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123 # print >> fout, str(repchr) + '\t'+str(repstart)+ '\t'+str(repend)+ '\t'+str(repname)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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124 fout.write(str(repchr) + '\t'+str(repstart)+ '\t'+str(repend)+ '\t'+str(repname) + '\n')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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125 # if rep_chr.has_key(repname):
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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126 if repname in rep_chr:
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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127 rep_chr[repname].append(repchr)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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128 rep_start[repname].append(int(repstart))
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129 rep_end[repname].append(int(repend))
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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130 else:
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131 rep_chr[repname] = [repchr]
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132 rep_start[repname] = [int(repstart)]
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133 rep_end[repname] = [int(repend)]
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134
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135 fin.close()
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136 fout.close()
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
137 repeat_elements = sorted(repeat_elements)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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138 print ("Writing a key for all repeats...")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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139 #print to fout the binary key that contains each repeat type with the associated binary number; sort the binary key:
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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140 fout = open(os.path.realpath(setup_folder + os.path.sep + 'repgenomes_key.txt'), 'w')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
141 x = 0
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
142 for repeat in repeat_elements:
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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143 # print >> fout, str(repeat) + '\t' + str(x)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
144 fout.write(str(repeat) + '\t' + str(x) + '\n')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
145 x +=1
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
146 fout.close()
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
147 ################################################################################
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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148 # generate spacer for psuedogenomes
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
149 spacer = ""
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
150 for i in range(gapl):
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
151 spacer = spacer + "N"
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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152
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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153 # save file with number of fragments processed per repname
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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154 print ("Saving number of fragments processed per repname to " + nfragmentsfile1)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
155 fout1 = open(os.path.realpath(nfragmentsfile1),"w")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
156 for repname in rep_chr.keys():
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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157 rep_chr_current = rep_chr[repname]
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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158 # print >>fout1, str(len(rep_chr[repname])) + "\t" + repname
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
159 fout1.write(str(len(rep_chr[repname])) + "\t" + repname + '\n')
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
160 fout1.close()
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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161
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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162 # generate metagenomes and save them to FASTA files
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diff changeset
163 k = 1
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
164 nrepgenomes = len(rep_chr.keys())
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
165 for repname in rep_chr.keys():
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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166 metagenome = ""
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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167 newname = repname.replace("(","_").replace(")","_").replace("/","_")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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168 print ("processing repgenome " + newname + ".fa" + " (" + str(k) + " of " + str(nrepgenomes) + ")")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
169 rep_chr_current = rep_chr[repname]
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
170 rep_start_current = rep_start[repname]
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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171 rep_end_current = rep_end[repname]
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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172 print ("-------> " + str(len(rep_chr[repname])) + " fragments")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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173 for i in range(len(rep_chr[repname])):
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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diff changeset
174 try:
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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175 chr = rep_chr_current[i]
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176 rstart = max(rep_start_current[i] - flankingl, 0)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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177 rend = min(rep_end_current[i] + flankingl, lgenome[chr]-1)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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178 metagenome = metagenome + spacer + genome[chr][rstart:(rend+1)]
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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179 except KeyError:
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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180 print ("Unrecognised Chromosome: "+chr)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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181 pass
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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182
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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183 # Convert metagenome to SeqRecord object (required by SeqIO.write)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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184 record = SeqRecord(Seq(metagenome, IUPAC.unambiguous_dna), id = "repname", name = "", description = "")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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185 print ("saving repgenome " + newname + ".fa" + " (" + str(k) + " of " + str(nrepgenomes) + ")")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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186 fastafilename = os.path.realpath(setup_folder + os.path.sep + newname + ".fa")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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187 SeqIO.write(record, fastafilename, "fasta")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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188 print ("indexing repgenome " + newname + ".fa" + " (" + str(k) + " of " + str(nrepgenomes) + ")")
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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189 command = shlex.split('bowtie-build -f ' + fastafilename + ' ' + setup_folder + os.path.sep + newname)
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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190 p = subprocess.Popen(command).communicate()
041de602103e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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191 k += 1
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192
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193 print ("... Done")
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194