annotate RepEnrich.py @ 6:77807fc5d609 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit e9282183531bacbb4bbe2d6e53258f6e0ad0bc34
author drosofff
date Wed, 31 May 2017 13:09:15 -0400
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1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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1 #!/usr/bin/env python
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2 import argparse
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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3 import csv
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4 import numpy
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5 import os
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6 import shlex
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7 import shutil
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8 import subprocess
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9 import sys
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10
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11 parser = argparse.ArgumentParser(description='Part II: Conducting the alignments to the psuedogenomes. Before doing this step you will require 1) a bamfile of the unique alignments with index 2) a fastq file of the reads mapping to more than one location. These files can be obtained using the following bowtie options [EXAMPLE: bowtie -S -m 1 --max multimap.fastq mm9 mate1_reads.fastq] Once you have the unique alignment bamfile and the reads mapping to more than one location in a fastq file you can run this step. EXAMPLE: python master_output.py /users/nneretti/data/annotation/hg19/hg19_repeatmasker.txt /users/nneretti/datasets/repeatmapping/POL3/Pol3_human/HeLa_InputChIPseq_Rep1 HeLa_InputChIPseq_Rep1 /users/nneretti/data/annotation/hg19/setup_folder HeLa_InputChIPseq_Rep1_multimap.fastq HeLa_InputChIPseq_Rep1.bam')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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12 parser.add_argument('--version', action='version', version='%(prog)s 0.1')
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13 parser.add_argument('annotation_file', action= 'store', metavar='annotation_file', help='List RepeatMasker.org annotation file for your organism. The file may be downloaded from the RepeatMasker.org website. Example: /data/annotation/hg19/hg19_repeatmasker.txt')
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14 parser.add_argument('outputfolder', action= 'store', metavar='outputfolder', help='List folder to contain results. Example: /outputfolder')
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15 parser.add_argument('outputprefix', action= 'store', metavar='outputprefix', help='Enter prefix name for data. Example: HeLa_InputChIPseq_Rep1')
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16 parser.add_argument('setup_folder', action= 'store', metavar='setup_folder', help='List folder that contains the repeat element psuedogenomes. Example /data/annotation/hg19/setup_folder')
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17 parser.add_argument('fastqfile', action= 'store', metavar='fastqfile', help='Enter file for the fastq reads that map to multiple locations. Example /data/multimap.fastq')
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18 parser.add_argument('alignment_bam', action= 'store', metavar='alignment_bam', help='Enter bamfile output for reads that map uniquely. Example /bamfiles/old.bam')
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19 parser.add_argument('--pairedend', action= 'store', dest='pairedend', default= 'FALSE', help='Designate this option for paired-end sequencing. Default FALSE change to TRUE')
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20 parser.add_argument('--collapserepeat', action= 'store', dest='collapserepeat', metavar='collapserepeat', default= 'Simple_repeat', help='Designate this option to generate a collapsed repeat type. Uncollapsed output is generated in addition to collapsed repeat type. Simple_repeat is default to simplify downstream analysis. You can change the default to another repeat name to collapse a seperate specific repeat instead or if the name of Simple_repeat is different for your organism. Default Simple_repeat')
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21 parser.add_argument('--fastqfile2', action= 'store', dest='fastqfile2', metavar='fastqfile2', default= 'none', help='Enter fastqfile2 when using paired-end option. Default none')
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22 parser.add_argument('--cpus', action= 'store', dest='cpus', metavar='cpus', default= "1", type=int, help='Enter available cpus per node. The more cpus the faster RepEnrich performs. RepEnrich is designed to only work on one node. Default: "1"')
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23 parser.add_argument('--allcountmethod', action= 'store', dest='allcountmethod', metavar='allcountmethod', default= "FALSE", help='By default the pipeline only outputs the fraction count method. Consdidered to be the best way to count multimapped reads. Changing this option will include the unique count method, a conservative count, and the total count method, a liberal counting strategy. Our evaluation of simulated data indicated fraction counting is best. Default = FALSE, change to TRUE')
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24 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')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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25 args = parser.parse_args()
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26
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27 # parameters
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28 annotation_file = args.annotation_file
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29 outputfolder = args.outputfolder
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30 outputfile_prefix = args.outputprefix
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31 setup_folder = args.setup_folder
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32 repeat_bed = setup_folder + os.path.sep + 'repnames.bed'
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33 unique_mapper_bam = args.alignment_bam
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34 fastqfile_1 = args.fastqfile
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35 fastqfile_2 = args.fastqfile2
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36 cpus = args.cpus
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37 b_opt = "-k1 -p " +str(1) +" --quiet"
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38 simple_repeat = args.collapserepeat
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39 paired_end = args.pairedend
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40 allcountmethod = args.allcountmethod
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41 is_bed = args.is_bed
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42
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43 ################################################################################
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44 # check that the programs we need are available
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45 try:
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46 subprocess.call(shlex.split("coverageBed -h"), stdout=open(os.devnull, 'wb'), stderr=open(os.devnull, 'wb'))
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47 subprocess.call(shlex.split("bowtie --version"), stdout=open(os.devnull, 'wb'), stderr=open(os.devnull, 'wb'))
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48 except OSError:
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49 print ("Error: Bowtie or BEDTools not loaded")
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50 raise
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51
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52 ################################################################################
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53 # define a csv reader that reads space deliminated files
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54 print ('Preparing for analysis using RepEnrich...')
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55 csv.field_size_limit(sys.maxsize)
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56 def import_text(filename, separator):
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57 for line in csv.reader(open(filename), delimiter=separator,
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58 skipinitialspace=True):
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59 if line:
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60 yield line
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61
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62 ################################################################################
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63 # build dictionaries to convert repclass and rep families'
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64 if is_bed == "FALSE":
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65 repeatclass = {}
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66 repeatfamily = {}
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67 fin = import_text(annotation_file, ' ')
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68 x = 0
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69 for line in fin:
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70 if x>2:
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71 classfamily =[]
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72 classfamily = line[10].split(os.path.sep)
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73 line9 = line[9].replace("(","_").replace(")","_").replace("/","_")
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74 repeatclass[line9] = classfamily[0]
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75 if len(classfamily) == 2:
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76 repeatfamily[line9] = classfamily[1]
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77 else:
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78 repeatfamily[line9] = classfamily[0]
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79 x +=1
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80 if is_bed == "TRUE":
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81 repeatclass = {}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
82 repeatfamily = {}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
83 fin = open(annotation_file, 'r')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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parents:
diff changeset
84 for line in fin:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
85 line=line.strip('\n')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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parents:
diff changeset
86 line=line.split('\t')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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parents:
diff changeset
87 theclass =line[4]
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
88 thefamily = line[5]
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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parents:
diff changeset
89 line3 = line[3].replace("(","_").replace(")","_").replace("/","_")
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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parents:
diff changeset
90 repeatclass[line3] = theclass
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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parents:
diff changeset
91 repeatfamily[line3] = thefamily
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
92 fin.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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parents:
diff changeset
93
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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parents:
diff changeset
94 ################################################################################
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
95 # build list of repeats initializing dictionaries for downstream analysis'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
96 fin = import_text(setup_folder + os.path.sep + 'repgenomes_key.txt', '\t')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
97 repeat_key ={}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
98 rev_repeat_key ={}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
99 repeat_list = []
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
100 reptotalcounts = {}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
101 classfractionalcounts = {}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
102 familyfractionalcounts = {}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
103 classtotalcounts = {}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
104 familytotalcounts = {}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
105 reptotalcounts_simple = {}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
106 fractionalcounts = {}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
107 i = 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
108 for line in fin:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
109 reptotalcounts[line[0]] = 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
110 fractionalcounts[line[0]] = 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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111 if line[0] in repeatclass:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
112 classtotalcounts[repeatclass[line[0]]] = 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
113 classfractionalcounts[repeatclass[line[0]]] = 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
114 if line[0] in repeatfamily:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
115 familytotalcounts[repeatfamily[line[0]]] = 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
116 familyfractionalcounts[repeatfamily[line[0]]] = 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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117 if line[0] in repeatfamily:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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118 if repeatfamily[line[0]] == simple_repeat:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
119 reptotalcounts_simple[simple_repeat] = 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
120 else:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
121 reptotalcounts_simple[line[0]] = 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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122 repeat_list.append(line[0])
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
123 repeat_key[line[0]] = int(line[1])
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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124 rev_repeat_key[int(line[1])] = line[0]
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125 fin.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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126 ################################################################################
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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127 # map the repeats to the psuedogenomes:
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128 if not os.path.exists(outputfolder):
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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129 os.mkdir(outputfolder)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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130 ################################################################################
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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131 # Conduct the regions sorting
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132 print ('Conducting region sorting on unique mapping reads....')
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133 fileout= outputfolder + os.path.sep + outputfile_prefix + '_regionsorter.txt'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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134 with open(fileout, 'w') as stdout:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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135 command = shlex.split("coverageBed -abam " +unique_mapper_bam+" -b " +setup_folder + os.path.sep + 'repnames.bed')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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136 p = subprocess.Popen(command, stdout=stdout)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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137 p.communicate()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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138 stdout.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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139 filein = open(outputfolder + os.path.sep + outputfile_prefix + '_regionsorter.txt','r')
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diff changeset
140 counts = {}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
141 sumofrepeatreads=0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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142 for line in filein:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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143 line= line.split('\t')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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144 if not str(repeat_key[line[3]]) in counts:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
145 counts[str(repeat_key[line[3]])]=0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
146 counts[str(repeat_key[line[3]])]+=int(line[4])
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
147 sumofrepeatreads+=int(line[4])
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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148 print ('Identified ' + str(sumofrepeatreads) + 'unique reads that mapped to repeats.')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
149 ################################################################################
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diff changeset
150 if paired_end == 'TRUE':
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
151 if not os.path.exists(outputfolder + os.path.sep + 'pair1_bowtie'):
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
152 os.mkdir(outputfolder + os.path.sep + 'pair1_bowtie')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
153 if not os.path.exists(outputfolder + os.path.sep + 'pair2_bowtie'):
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
154 os.mkdir(outputfolder + os.path.sep + 'pair2_bowtie')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
155 folder_pair1 = outputfolder + os.path.sep + 'pair1_bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
156 folder_pair2 = outputfolder + os.path.sep + 'pair2_bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
157 ################################################################################
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
158 print ("Processing repeat psuedogenomes...")
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
159 ps = []
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
160 psb= []
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
161 ticker= 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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162 for metagenome in repeat_list:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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163 metagenomepath = setup_folder + os.path.sep + metagenome
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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164 file1=folder_pair1 + os.path.sep + metagenome + '.bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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165 file2 =folder_pair2 + os.path.sep + metagenome + '.bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
166 with open(file1, 'w') as stdout:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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167 command = shlex.split("bowtie " + b_opt + " " + metagenomepath + " " + fastqfile_1)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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168 p = subprocess.Popen(command,stdout=stdout)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
169 with open(file2, 'w') as stdout:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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170 command = shlex.split("bowtie " + b_opt + " " + metagenomepath + " " + fastqfile_2)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
171 pp = subprocess.Popen(command,stdout=stdout)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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172 ps.append(p)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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173 ticker +=1
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
174 psb.append(pp)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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175 ticker +=1
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
176 if ticker == cpus:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
177 for p in ps:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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178 p.communicate()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
179 for p in psb:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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180 p.communicate()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
181 ticker = 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
182 psb =[]
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
183 ps = []
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
184 if len(ps) > 0:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
185 for p in ps:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
186 p.communicate()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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187 stdout.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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188
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
189 ################################################################################
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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190 # combine the output from both read pairs:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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191 print ('sorting and combining the output for both read pairs...')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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192 if not os.path.exists(outputfolder + os.path.sep + 'sorted_bowtie'):
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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193 os.mkdir(outputfolder + os.path.sep + 'sorted_bowtie')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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194 sorted_bowtie = outputfolder + os.path.sep + 'sorted_bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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195 for metagenome in repeat_list:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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196 file1 = folder_pair1 + os.path.sep + metagenome + '.bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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197 file2 = folder_pair2 + os.path.sep + metagenome + '.bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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198 fileout= sorted_bowtie + os.path.sep + metagenome + '.bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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199 with open(fileout, 'w') as stdout:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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200 p1 = subprocess.Popen(['cat',file1,file2], stdout = subprocess.PIPE)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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201 p2 = subprocess.Popen(['cut', '-f1',"-d "], stdin = p1.stdout, stdout = subprocess.PIPE)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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202 p3 = subprocess.Popen(['cut', '-f1', "-d/"], stdin = p2.stdout, stdout = subprocess.PIPE)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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203 p4 = subprocess.Popen(['sort'], stdin=p3.stdout, stdout = subprocess.PIPE)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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204 p5 = subprocess.Popen(['uniq'], stdin=p4.stdout, stdout = stdout)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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205 p5.communicate()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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206 stdout.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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207 print ('completed ...')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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208 ################################################################################
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
209 if paired_end == 'FALSE':
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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210 if not os.path.exists(outputfolder + os.path.sep + 'pair1_bowtie'):
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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211 os.mkdir(outputfolder + os.path.sep + 'pair1_bowtie')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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212 folder_pair1 = outputfolder + os.path.sep + 'pair1_bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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213 ################################################################################
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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214 ps = []
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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215 ticker= 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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216 print ("Processing repeat psuedogenomes...")
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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217 for metagenome in repeat_list:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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218 metagenomepath = setup_folder + os.path.sep + metagenome
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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219 file1=folder_pair1 + os.path.sep + metagenome + '.bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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220 with open(file1, 'w') as stdout:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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221 command = shlex.split("bowtie " + b_opt + " " + metagenomepath + " " + fastqfile_1)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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222 p = subprocess.Popen(command,stdout=stdout)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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223 ps.append(p)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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224 ticker +=1
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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225 if ticker == cpus:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
226 for p in ps:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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227 p.communicate()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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228 ticker = 0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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229 ps = []
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
230 if len(ps) > 0:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
231 for p in ps:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
232 p.communicate()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
233 stdout.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
234
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
235 ################################################################################
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
236 # combine the output from both read pairs:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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237 print ('Sorting and combining the output for both read pairs....')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
238 if not os.path.exists(outputfolder + os.path.sep + 'sorted_bowtie'):
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
239 os.mkdir(outputfolder + os.path.sep + 'sorted_bowtie')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
240 sorted_bowtie = outputfolder + os.path.sep + 'sorted_bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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parents:
diff changeset
241 for metagenome in repeat_list:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
242 file1 = folder_pair1 + os.path.sep + metagenome + '.bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
243 fileout= sorted_bowtie + os.path.sep + metagenome + '.bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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parents:
diff changeset
244 with open(fileout, 'w') as stdout:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
245 p1 = subprocess.Popen(['cat',file1], stdout = subprocess.PIPE)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
246 p2 = subprocess.Popen(['cut', '-f1'], stdin = p1.stdout, stdout = subprocess.PIPE)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
247 p3 = subprocess.Popen(['cut', '-f1', "-d/"], stdin = p2.stdout, stdout = subprocess.PIPE)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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248 p4 = subprocess.Popen(['sort'], stdin = p3.stdout,stdout = subprocess.PIPE)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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249 p5 = subprocess.Popen(['uniq'], stdin = p4.stdout,stdout = stdout)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
250 p5.communicate()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
251 stdout.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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252 print ('completed ...')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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253
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
254 ################################################################################
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
255 # build a file of repeat keys for all reads
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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256 print ('Writing and processing intermediate files...')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
257 sorted_bowtie = outputfolder + os.path.sep + 'sorted_bowtie'
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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parents:
diff changeset
258 readid = {}
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
259 sumofrepeatreads=0
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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diff changeset
260 for rep in repeat_list:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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261 for data in import_text(sorted_bowtie + os.path.sep + rep + '.bowtie', '\t'):
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262 readid[data[0]] = ''
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263 for rep in repeat_list:
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264 for data in import_text(sorted_bowtie + os.path.sep + rep + '.bowtie', '\t'):
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265 readid[data[0]]+=str(repeat_key[rep]) + str(',')
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266 for subfamilies in readid.values():
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267 if not subfamilies in counts:
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268 counts[subfamilies]=0
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269 counts[subfamilies] +=1
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270 sumofrepeatreads+=1
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271 del readid
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272 print ('Identified ' + str(sumofrepeatreads) + ' reads that mapped to repeats for unique and multimappers.')
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273
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274 ################################################################################
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275 print ("Conducting final calculations...")
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276 # build a converter to numeric label for repeat and yield a combined list of repnames seperated by backslash
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277 def convert(x):
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278 x = x.strip(',')
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279 x = x.split(',')
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280 global repname
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281 repname = ""
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282 for i in x:
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283 repname = repname + os.path.sep + rev_repeat_key[int(i)]
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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284 # building the total counts for repeat element enrichment...
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285 for x in counts.keys():
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286 count= counts[x]
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287 x = x.strip(',')
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288 x = x.split(',')
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289 for i in x:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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290 reptotalcounts[rev_repeat_key[int(i)]] += int(count)
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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291 # building the fractional counts for repeat element enrichment...
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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292 for x in counts.keys():
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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293 count= counts[x]
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294 x = x.strip(',')
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295 x = x.split(',')
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296 splits = len(x)
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297 for i in x:
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298 fractionalcounts[rev_repeat_key[int(i)]] += float(numpy.divide(float(count),float(splits)))
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299 # building categorized table of repeat element enrichment...
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300 repcounts = {}
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301 repcounts['other'] = 0
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302 for key in counts.keys():
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303 convert(key)
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304 repcounts[repname] = counts[key]
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305 # building the total counts for class enrichment...
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306 for key in reptotalcounts.keys():
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307 classtotalcounts[repeatclass[key]] += reptotalcounts[key]
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308 # building total counts for family enrichment...
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309 for key in reptotalcounts.keys():
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310 familytotalcounts[repeatfamily[key]] += reptotalcounts[key]
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311 # building unique counts table'
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312 repcounts2 = {}
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313 for rep in repeat_list:
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314 if "/" +rep in repcounts:
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315 repcounts2[rep] = repcounts["/" +rep]
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316 else:
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317 repcounts2[rep] = 0
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318 # building the fractionalcounts counts for class enrichment...
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319 for key in fractionalcounts.keys():
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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320 classfractionalcounts[repeatclass[key]] += fractionalcounts[key]
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321 # building fractional counts for family enrichment...
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322 for key in fractionalcounts.keys():
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323 familyfractionalcounts[repeatfamily[key]] += fractionalcounts[key]
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324
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325 ################################################################################
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326 print ('Writing final output and removing intermediate files...')
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327 # print output to file of the categorized counts and total overlapping counts:
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328 if allcountmethod == "TRUE":
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329 fout1 = open(outputfolder + os.path.sep + outputfile_prefix + '_total_counts.txt' , 'w')
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330 for key in reptotalcounts.keys():
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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331 fout1.write(str(key) + '\t' + repeatclass[key] + '\t' + repeatfamily[key] + '\t' + str(reptotalcounts[key]) + '\n')
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332 fout2 = open(outputfolder + os.path.sep + outputfile_prefix + '_class_total_counts.txt' , 'w')
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333 for key in classtotalcounts.keys():
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334 fout2.write(str(key) + '\t' + str(classtotalcounts[key]) + '\n')
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335 fout3 = open(outputfolder + os.path.sep + outputfile_prefix + '_family_total_counts.txt' , 'w')
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336 for key in familytotalcounts.keys():
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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337 fout3.write(str(key) + '\t' + str(familytotalcounts[key]) + '\n')
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338 fout4 = open(outputfolder + os.path.sep + outputfile_prefix + '_unique_counts.txt' , 'w')
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339 for key in repcounts2.keys():
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340 fout4.write(str(key) + '\t' + repeatclass[key] + '\t' + repeatfamily[key] + '\t' + str(repcounts2[key]) + '\n')
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341 fout5 = open(outputfolder + os.path.sep + outputfile_prefix + '_class_fraction_counts.txt' , 'w')
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342 for key in classfractionalcounts.keys():
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343 fout5.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n')
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344 fout6 = open(outputfolder + os.path.sep + outputfile_prefix + '_family_fraction_counts.txt' , 'w')
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345 for key in familyfractionalcounts.keys():
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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346 fout6.write(str(key) + '\t' + str(familyfractionalcounts[key]) + '\n')
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347 fout7 = open(outputfolder + os.path.sep + outputfile_prefix + '_fraction_counts.txt' , 'w')
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348 for key in fractionalcounts.keys():
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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349 fout7.write(str(key) + '\t' + repeatclass[key] + '\t' + repeatfamily[key] + '\t' + str(int(fractionalcounts[key])) + '\n')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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350 fout1.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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351 fout2.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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352 fout3.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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353 fout4.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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354 fout5.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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355 fout6.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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356 fout7.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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357 else:
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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358 fout1 = open(outputfolder + os.path.sep + outputfile_prefix + '_class_fraction_counts.txt' , 'w')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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359 for key in classfractionalcounts.keys():
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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360 fout1.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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361 fout2 = open(outputfolder + os.path.sep + outputfile_prefix + '_family_fraction_counts.txt' , 'w')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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362 for key in familyfractionalcounts.keys():
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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363 fout2.write(str(key) + '\t' + str(familyfractionalcounts[key])+ '\n')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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364 fout3 = open(outputfolder + os.path.sep + outputfile_prefix + '_fraction_counts.txt' , 'w')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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365 for key in fractionalcounts.keys():
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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366 fout3.write(str(key) + '\t' + repeatclass[key] + '\t' + repeatfamily[key] + '\t' + str(int(fractionalcounts[key])) + '\n')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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367 fout1.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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368 fout2.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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369 fout3.close()
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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370
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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371 ################################################################################
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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372 # Remove Large intermediate files
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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373 if os.path.exists(outputfolder + os.path.sep + outputfile_prefix + '_regionsorter.txt'):
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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374 os.remove(outputfolder + os.path.sep + outputfile_prefix + '_regionsorter.txt')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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375 if os.path.exists(outputfolder + os.path.sep + 'pair1_bowtie'):
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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376 shutil.rmtree(outputfolder + os.path.sep + 'pair1_bowtie')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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377 if os.path.exists(outputfolder + os.path.sep + 'pair2_bowtie'):
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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378 shutil.rmtree(outputfolder + os.path.sep + 'pair2_bowtie')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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379 if os.path.exists(outputfolder + os.path.sep + 'sorted_bowtie'):
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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380 shutil.rmtree(outputfolder + os.path.sep + 'sorted_bowtie')
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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381
1435d142041b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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382 print ("... Done")