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annotate RepEnrich.py @ 10:6f4143893463 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit e3881f05134c6f50889d0376d27e1c232251f8b3
author artbio
date Tue, 05 Feb 2019 17:20:55 -0500
parents d1f7ab78f7b5
children 89e05f831259
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f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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1 import argparse
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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2 import csv
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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3 import os
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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4 import shlex
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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5 import shutil
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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6 import subprocess
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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7 import sys
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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8
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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9 import numpy
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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10
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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11
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12 parser = argparse.ArgumentParser(description='''
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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13 Part II: Conducting the alignments to the psuedogenomes. Before\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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14 doing this step you will require 1) a bamfile of the unique\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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15 alignments with index 2) a fastq file of the reads mapping to\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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16 more than one location. These files can be obtained using the\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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17 following bowtie options [EXAMPLE: bowtie -S -m 1\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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18 --max multimap.fastq mm9 mate1_reads.fastq] Once you have the\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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19 unique alignment bamfile and the reads mapping to more than one\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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20 location in a fastq file you can run this step. EXAMPLE: python\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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21 master_output.py\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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22 /users/nneretti/data/annotation/hg19/hg19_repeatmasker.txt\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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23 /users/nneretti/datasets/repeatmapping/POL3/Pol3_human/
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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24 HeLa_InputChIPseq_Rep1 HeLa_InputChIPseq_Rep1\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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25 /users/nneretti/data/annotation/hg19/setup_folder\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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26 HeLa_InputChIPseq_Rep1_multimap.fastq\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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27 HeLa_InputChIPseq_Rep1.bam''')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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28 parser.add_argument('--version', action='version', version='%(prog)s 0.1')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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29 parser.add_argument('annotation_file', action='store',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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30 metavar='annotation_file',
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31 help='List RepeatMasker.org annotation file for your\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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32 organism. The file may be downloaded from the\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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33 RepeatMasker.org website. Example:\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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34 /data/annotation/hg19/hg19_repeatmasker.txt')
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35 parser.add_argument('outputfolder', action='store', metavar='outputfolder',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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36 help='List folder to contain results.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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37 Example: /outputfolder')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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38 parser.add_argument('outputprefix', action='store', metavar='outputprefix',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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39 help='Enter prefix name for data.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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40 Example: HeLa_InputChIPseq_Rep1')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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41 parser.add_argument('setup_folder', action='store', metavar='setup_folder',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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42 help='List folder that contains the repeat element\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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43 pseudogenomes.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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44 Example: /data/annotation/hg19/setup_folder')
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45 parser.add_argument('fastqfile', action='store', metavar='fastqfile',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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46 help='Enter file for the fastq reads that map to multiple\
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47 locations. Example: /data/multimap.fastq')
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48 parser.add_argument('alignment_bam', action='store', metavar='alignment_bam',
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49 help='Enter bamfile output for reads that map uniquely.\
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50 Example /bamfiles/old.bam')
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51 parser.add_argument('--pairedend', action='store', dest='pairedend',
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52 default='FALSE',
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53 help='Designate this option for paired-end sequencing.\
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54 Default FALSE change to TRUE')
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55 parser.add_argument('--collapserepeat', action='store', dest='collapserepeat',
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56 metavar='collapserepeat', default='Simple_repeat',
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57 help='Designate this option to generate a collapsed repeat\
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58 type. Uncollapsed output is generated in addition to\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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59 collapsed repeat type. Simple_repeat is default to\
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60 simplify downstream analysis. You can change the\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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61 default to another repeat name to collapse a\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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62 seperate specific repeat instead or if the name of\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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63 Simple_repeat is different for your organism.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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64 Default Simple_repeat')
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65 parser.add_argument('--fastqfile2', action='store', dest='fastqfile2',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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66 metavar='fastqfile2', default='none',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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67 help='Enter fastqfile2 when using paired-end option.\
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68 Default none')
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69 parser.add_argument('--cpus', action='store', dest='cpus', metavar='cpus',
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70 default="1", type=int,
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71 help='Enter available cpus per node. The more cpus the\
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72 faster RepEnrich performs. RepEnrich is designed to\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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73 only work on one node. Default: "1"')
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74 parser.add_argument('--allcountmethod', action='store', dest='allcountmethod',
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75 metavar='allcountmethod', default="FALSE",
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76 help='By default the pipeline only outputs the fraction\
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77 count method. Consdidered to be the best way to\
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78 count multimapped reads. Changing this option will\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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79 include the unique count method, a conservative\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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80 count, and the total count method, a liberal\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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81 counting strategy. Our evaluation of simulated data\
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82 indicated fraction counting is best.\
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83 Default = FALSE, change to TRUE')
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84 parser.add_argument('--is_bed', action='store', dest='is_bed',
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85 metavar='is_bed', default='FALSE',
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86 help='Is the annotation file a bed file.\
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artbio
parents:
diff changeset
87 This is also a compatible format. The file needs to\
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artbio
parents:
diff changeset
88 be a tab seperated bed with optional fields.\
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artbio
parents:
diff changeset
89 Ex. format: chr\tstart\tend\tName_element\tclass\
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artbio
parents:
diff changeset
90 \tfamily. The class and family should identical to\
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artbio
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diff changeset
91 name_element if not applicable.\
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artbio
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diff changeset
92 Default FALSE change to TRUE')
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artbio
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diff changeset
93 args = parser.parse_args()
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artbio
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diff changeset
94
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artbio
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95 # parameters
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artbio
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diff changeset
96 annotation_file = args.annotation_file
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artbio
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diff changeset
97 outputfolder = args.outputfolder
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artbio
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diff changeset
98 outputfile_prefix = args.outputprefix
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artbio
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diff changeset
99 setup_folder = args.setup_folder
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artbio
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diff changeset
100 repeat_bed = setup_folder + os.path.sep + 'repnames.bed'
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artbio
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diff changeset
101 unique_mapper_bam = args.alignment_bam
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artbio
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diff changeset
102 fastqfile_1 = args.fastqfile
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artbio
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diff changeset
103 fastqfile_2 = args.fastqfile2
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artbio
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diff changeset
104 cpus = args.cpus
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artbio
parents:
diff changeset
105 b_opt = "-k1 -p " + str(1) + " --quiet"
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artbio
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diff changeset
106 simple_repeat = args.collapserepeat
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artbio
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diff changeset
107 paired_end = args.pairedend
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artbio
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diff changeset
108 allcountmethod = args.allcountmethod
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artbio
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diff changeset
109 is_bed = args.is_bed
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artbio
parents:
diff changeset
110
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artbio
parents:
diff changeset
111 ##############################################################################
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artbio
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diff changeset
112 # check that the programs we need are available
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artbio
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diff changeset
113 try:
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artbio
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diff changeset
114 subprocess.call(shlex.split("coverageBed -h"),
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
115 stdout=open(os.devnull, 'wb'),
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artbio
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diff changeset
116 stderr=open(os.devnull, 'wb'))
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artbio
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diff changeset
117 subprocess.call(shlex.split("bowtie --version"),
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff changeset
118 stdout=open(os.devnull, 'wb'),
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
119 stderr=open(os.devnull, 'wb'))
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artbio
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diff changeset
120 except OSError:
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artbio
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diff changeset
121 print("Error: Bowtie or BEDTools not loaded")
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artbio
parents:
diff changeset
122 raise
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
123
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff changeset
124 ##############################################################################
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artbio
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diff changeset
125 # define a csv reader that reads space deliminated files
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artbio
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diff changeset
126 print('Preparing for analysis using RepEnrich...')
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artbio
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diff changeset
127 csv.field_size_limit(sys.maxsize)
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artbio
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diff changeset
128
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artbio
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diff changeset
129
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artbio
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diff changeset
130 def import_text(filename, separator):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
131 for line in csv.reader(open(filename), delimiter=separator,
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artbio
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diff changeset
132 skipinitialspace=True):
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artbio
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diff changeset
133 if line:
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artbio
parents:
diff changeset
134 yield line
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
135
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artbio
parents:
diff changeset
136
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
137 ##############################################################################
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artbio
parents:
diff changeset
138 # build dictionaries to convert repclass and rep families'
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artbio
parents:
diff changeset
139 if is_bed == "FALSE":
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artbio
parents:
diff changeset
140 repeatclass = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
141 repeatfamily = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
142 fin = import_text(annotation_file, ' ')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
143 x = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
144 for line in fin:
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artbio
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diff changeset
145 if x > 2:
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artbio
parents:
diff changeset
146 classfamily = []
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artbio
parents:
diff changeset
147 classfamily = line[10].split(os.path.sep)
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artbio
parents:
diff changeset
148 line9 = line[9].replace("(", "_").replace(
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
149 ")", "_").replace("/", "_")
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artbio
parents:
diff changeset
150 repeatclass[line9] = classfamily[0]
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artbio
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diff changeset
151 if len(classfamily) == 2:
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artbio
parents:
diff changeset
152 repeatfamily[line9] = classfamily[1]
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artbio
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diff changeset
153 else:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
154 repeatfamily[line9] = classfamily[0]
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artbio
parents:
diff changeset
155 x += 1
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
156 if is_bed == "TRUE":
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artbio
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diff changeset
157 repeatclass = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
158 repeatfamily = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
159 fin = open(annotation_file, 'r')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
160 for line in fin:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
161 line = line.strip('\n')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
162 line = line.split('\t')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
163 theclass = line[4]
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artbio
parents:
diff changeset
164 thefamily = line[5]
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artbio
parents:
diff changeset
165 line3 = line[3].replace("(", "_").replace(")", "_").replace("/", "_")
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
166 repeatclass[line3] = theclass
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
167 repeatfamily[line3] = thefamily
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
168 fin.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
169
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artbio
parents:
diff changeset
170 ##############################################################################
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artbio
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diff changeset
171 # build list of repeats initializing dictionaries for downstream analysis'
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artbio
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diff changeset
172 fin = import_text(setup_folder + os.path.sep + 'repgenomes_key.txt', '\t')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff changeset
173 repeat_key = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
174 rev_repeat_key = {}
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artbio
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diff changeset
175 repeat_list = []
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
176 reptotalcounts = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff changeset
177 classfractionalcounts = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
178 familyfractionalcounts = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
179 classtotalcounts = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
180 familytotalcounts = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
181 reptotalcounts_simple = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
182 fractionalcounts = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
183 i = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
184 for line in fin:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
185 reptotalcounts[line[0]] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
186 fractionalcounts[line[0]] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
187 if line[0] in repeatclass:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
188 classtotalcounts[repeatclass[line[0]]] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
189 classfractionalcounts[repeatclass[line[0]]] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
190 if line[0] in repeatfamily:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
191 familytotalcounts[repeatfamily[line[0]]] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
192 familyfractionalcounts[repeatfamily[line[0]]] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
193 if line[0] in repeatfamily:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
194 if repeatfamily[line[0]] == simple_repeat:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
195 reptotalcounts_simple[simple_repeat] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
196 else:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
197 reptotalcounts_simple[line[0]] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
198 repeat_list.append(line[0])
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
199 repeat_key[line[0]] = int(line[1])
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
200 rev_repeat_key[int(line[1])] = line[0]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
201 fin.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
202 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
203 # map the repeats to the psuedogenomes:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
204 if not os.path.exists(outputfolder):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
205 os.mkdir(outputfolder)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
206 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
207 # Conduct the regions sorting
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
208 print('Conducting region sorting on unique mapping reads....')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
209 fileout = outputfolder + os.path.sep + outputfile_prefix + '_regionsorter.txt'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
210 with open(fileout, 'w') as stdout:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
211 command = shlex.split("coverageBed -abam " + unique_mapper_bam + " -b " +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
212 setup_folder + os.path.sep + 'repnames.bed')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
213 p = subprocess.Popen(command, stdout=stdout)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
214 p.communicate()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
215 stdout.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
216 filein = open(outputfolder + os.path.sep + outputfile_prefix
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
217 + '_regionsorter.txt', 'r')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
218 counts = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
219 sumofrepeatreads = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
220 for line in filein:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
221 line = line.split('\t')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
222 if not str(repeat_key[line[3]]) in counts:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
223 counts[str(repeat_key[line[3]])] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
224 counts[str(repeat_key[line[3]])] += int(line[4])
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
225 sumofrepeatreads += int(line[4])
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
226 print('Identified ' + str(sumofrepeatreads) +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
227 'unique reads that mapped to repeats.')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
228 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
229 if paired_end == 'TRUE':
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
230 if not os.path.exists(outputfolder + os.path.sep + 'pair1_bowtie'):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
231 os.mkdir(outputfolder + os.path.sep + 'pair1_bowtie')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
232 if not os.path.exists(outputfolder + os.path.sep + 'pair2_bowtie'):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
233 os.mkdir(outputfolder + os.path.sep + 'pair2_bowtie')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
234 folder_pair1 = outputfolder + os.path.sep + 'pair1_bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
235 folder_pair2 = outputfolder + os.path.sep + 'pair2_bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
236 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
237 print("Processing repeat psuedogenomes...")
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
238 ps = []
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
239 psb = []
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
240 ticker = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
241 for metagenome in repeat_list:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
242 metagenomepath = setup_folder + os.path.sep + metagenome
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
243 file1 = folder_pair1 + os.path.sep + metagenome + '.bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
244 file2 = folder_pair2 + os.path.sep + metagenome + '.bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
245 with open(file1, 'w') as stdout:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
246 command = shlex.split("bowtie " + b_opt + " " +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
247 metagenomepath + " " + fastqfile_1)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
248 p = subprocess.Popen(command, stdout=stdout)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
249 with open(file2, 'w') as stdout:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
250 command = shlex.split("bowtie " + b_opt + " " +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
251 metagenomepath + " " + fastqfile_2)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
252 pp = subprocess.Popen(command, stdout=stdout)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
253 ps.append(p)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
254 ticker += 1
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
255 psb.append(pp)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
256 ticker += 1
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
257 if ticker == cpus:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
258 for p in ps:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
259 p.communicate()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
260 for p in psb:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
261 p.communicate()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
262 ticker = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
263 psb = []
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
264 ps = []
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
265 if len(ps) > 0:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
266 for p in ps:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
267 p.communicate()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
268 stdout.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
269
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
270 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
271 # combine the output from both read pairs:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
272 print('sorting and combining the output for both read pairs...')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
273 if not os.path.exists(outputfolder + os.path.sep + 'sorted_bowtie'):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
274 os.mkdir(outputfolder + os.path.sep + 'sorted_bowtie')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
275 sorted_bowtie = outputfolder + os.path.sep + 'sorted_bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
276 for metagenome in repeat_list:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
277 file1 = folder_pair1 + os.path.sep + metagenome + '.bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
278 file2 = folder_pair2 + os.path.sep + metagenome + '.bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
279 fileout = sorted_bowtie + os.path.sep + metagenome + '.bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
280 with open(fileout, 'w') as stdout:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
281 p1 = subprocess.Popen(['cat', file1, file2],
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
282 stdout=subprocess.PIPE)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
283 p2 = subprocess.Popen(['cut', '-f1', "-d "], stdin=p1.stdout,
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
284 stdout=subprocess.PIPE)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
285 p3 = subprocess.Popen(['cut', '-f1', "-d/"], stdin=p2.stdout,
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
286 stdout=subprocess.PIPE)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
287 p4 = subprocess.Popen(['sort'], stdin=p3.stdout,
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
288 stdout=subprocess.PIPE)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
289 p5 = subprocess.Popen(['uniq'], stdin=p4.stdout, stdout=stdout)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
290 p5.communicate()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
291 stdout.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
292 print('completed ...')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
293 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
294 if paired_end == 'FALSE':
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
295 if not os.path.exists(outputfolder + os.path.sep + 'pair1_bowtie'):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
296 os.mkdir(outputfolder + os.path.sep + 'pair1_bowtie')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
297 folder_pair1 = outputfolder + os.path.sep + 'pair1_bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
298 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
299 ps = []
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
300 ticker = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
301 print("Processing repeat psuedogenomes...")
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
302 for metagenome in repeat_list:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
303 metagenomepath = setup_folder + os.path.sep + metagenome
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
304 file1 = folder_pair1 + os.path.sep + metagenome + '.bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
305 with open(file1, 'w') as stdout:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
306 command = shlex.split("bowtie " + b_opt + " " +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
307 metagenomepath + " " + fastqfile_1)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
308 p = subprocess.Popen(command, stdout=stdout)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
309 ps.append(p)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
310 ticker += 1
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
311 if ticker == cpus:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
312 for p in ps:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
313 p.communicate()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
314 ticker = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
315 ps = []
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
316 if len(ps) > 0:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
317 for p in ps:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
318 p.communicate()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
319 stdout.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
320
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
321 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
322 # combine the output from both read pairs:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
323 print('Sorting and combining the output for both read pairs....')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
324 if not os.path.exists(outputfolder + os.path.sep + 'sorted_bowtie'):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
325 os.mkdir(outputfolder + os.path.sep + 'sorted_bowtie')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
326 sorted_bowtie = outputfolder + os.path.sep + 'sorted_bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
327 for metagenome in repeat_list:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
328 file1 = folder_pair1 + os.path.sep + metagenome + '.bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
329 fileout = sorted_bowtie + os.path.sep + metagenome + '.bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
330 with open(fileout, 'w') as stdout:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
331 p1 = subprocess.Popen(['cat', file1], stdout=subprocess.PIPE)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
332 p2 = subprocess.Popen(['cut', '-f1'], stdin=p1.stdout,
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
333 stdout=subprocess.PIPE)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
334 p3 = subprocess.Popen(['cut', '-f1', "-d/"], stdin=p2.stdout,
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
335 stdout=subprocess.PIPE)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
336 p4 = subprocess.Popen(['sort'], stdin=p3.stdout,
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
337 stdout=subprocess.PIPE)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
338 p5 = subprocess.Popen(['uniq'], stdin=p4.stdout, stdout=stdout)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
339 p5.communicate()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
340 stdout.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
341 print('completed ...')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
342
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
343 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
344 # build a file of repeat keys for all reads
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
345 print('Writing and processing intermediate files...')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
346 sorted_bowtie = outputfolder + os.path.sep + 'sorted_bowtie'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
347 readid = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
348 sumofrepeatreads = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
349 for rep in repeat_list:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
350 for data in import_text(sorted_bowtie + os.path.sep +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
351 rep + '.bowtie', '\t'):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
352 readid[data[0]] = ''
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
353 for rep in repeat_list:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
354 for data in import_text(sorted_bowtie + os.path.sep
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
355 + rep + '.bowtie', '\t'):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
356 readid[data[0]] += str(repeat_key[rep]) + str(',')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
357 for subfamilies in readid.values():
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
358 if subfamilies not in counts:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
359 counts[subfamilies] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
360 counts[subfamilies] += 1
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
361 sumofrepeatreads += 1
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
362 del readid
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
363 print('Identified ' + str(sumofrepeatreads) +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
364 ' reads that mapped to repeats for unique and multimappers.')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
365
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
366 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
367 print("Conducting final calculations...")
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
368
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
369
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
370 def convert(x):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
371 '''
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
372 build a converter to numeric label for repeat and yield a combined list
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
373 of repnames seperated by backslash
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
374 '''
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
375 x = x.strip(',')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
376 x = x.split(',')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
377 global repname
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
378 repname = ""
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
379 for i in x:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
380 repname = repname + os.path.sep + rev_repeat_key[int(i)]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
381
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
382
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
383 # building the total counts for repeat element enrichment...
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
384 for x in counts.keys():
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
385 count = counts[x]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
386 x = x.strip(',')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
387 x = x.split(',')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
388 for i in x:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
389 reptotalcounts[rev_repeat_key[int(i)]] += int(count)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
390 # building the fractional counts for repeat element enrichment...
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
391 for x in counts.keys():
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
392 count = counts[x]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
393 x = x.strip(',')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
394 x = x.split(',')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
395 splits = len(x)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
396 for i in x:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
397 fractionalcounts[rev_repeat_key[int(i)]] += float(
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
398 numpy.divide(float(count), float(splits)))
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
399 # building categorized table of repeat element enrichment...
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
400 repcounts = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
401 repcounts['other'] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
402 for key in counts.keys():
10
6f4143893463 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit e3881f05134c6f50889d0376d27e1c232251f8b3
artbio
parents: 4
diff changeset
403 convert(key)
6f4143893463 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit e3881f05134c6f50889d0376d27e1c232251f8b3
artbio
parents: 4
diff changeset
404 repcounts[repname] = counts[key]
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
405 # building the total counts for class enrichment...
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
406 for key in reptotalcounts.keys():
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
407 classtotalcounts[repeatclass[key]] += reptotalcounts[key]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
408 # building total counts for family enrichment...
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
409 for key in reptotalcounts.keys():
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
410 familytotalcounts[repeatfamily[key]] += reptotalcounts[key]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
411 # building unique counts table'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
412 repcounts2 = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
413 for rep in repeat_list:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
414 if "/" + rep in repcounts:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
415 repcounts2[rep] = repcounts["/" + rep]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
416 else:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
417 repcounts2[rep] = 0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
418 # building the fractionalcounts counts for class enrichment...
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
419 for key in fractionalcounts.keys():
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
420 classfractionalcounts[repeatclass[key]] += fractionalcounts[key]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
421 # building fractional counts for family enrichment...
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
422 for key in fractionalcounts.keys():
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
423 familyfractionalcounts[repeatfamily[key]] += fractionalcounts[key]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
424
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
425 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
426 print('Writing final output and removing intermediate files...')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
427 # print output to file of the categorized counts and total overlapping counts:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
428 if allcountmethod == "TRUE":
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
429 fout1 = open(outputfolder + os.path.sep + outputfile_prefix
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
430 + '_total_counts.txt', 'w')
2
15e3e29f310e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents: 0
diff changeset
431 for key in sorted(reptotalcounts.keys()):
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
432 fout1.write(str(key) + '\t' + repeatclass[key] + '\t' +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
433 repeatfamily[key] + '\t' + str(reptotalcounts[key])
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
434 + '\n')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
435 fout2 = open(outputfolder + os.path.sep + outputfile_prefix
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
436 + '_class_total_counts.txt', 'w')
2
15e3e29f310e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents: 0
diff changeset
437 for key in sorted(classtotalcounts.keys()):
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
438 fout2.write(str(key) + '\t' + str(classtotalcounts[key]) + '\n')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
439 fout3 = open(outputfolder + os.path.sep + outputfile_prefix
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
440 + '_family_total_counts.txt', 'w')
2
15e3e29f310e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents: 0
diff changeset
441 for key in sorted(familytotalcounts.keys()):
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
442 fout3.write(str(key) + '\t' + str(familytotalcounts[key]) + '\n')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
443 fout4 = open(outputfolder + os.path.sep + outputfile_prefix +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
444 '_unique_counts.txt', 'w')
2
15e3e29f310e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents: 0
diff changeset
445 for key in sorted(repcounts2.keys()):
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
446 fout4.write(str(key) + '\t' + repeatclass[key] + '\t' +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
447 repeatfamily[key] + '\t' + str(repcounts2[key]) + '\n')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
448 fout5 = open(outputfolder + os.path.sep + outputfile_prefix
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
449 + '_class_fraction_counts.txt', 'w')
2
15e3e29f310e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents: 0
diff changeset
450 for key in sorted(classfractionalcounts.keys()):
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
451 fout5.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
452 fout6 = open(outputfolder + os.path.sep + outputfile_prefix +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
453 '_family_fraction_counts.txt', 'w')
2
15e3e29f310e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents: 0
diff changeset
454 for key in sorted(familyfractionalcounts.keys()):
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
455 fout6.write(str(key) + '\t' + str(familyfractionalcounts[key]) + '\n')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
456 fout7 = open(outputfolder + os.path.sep + outputfile_prefix
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
457 + '_fraction_counts.txt', 'w')
2
15e3e29f310e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents: 0
diff changeset
458 for key in sorted(fractionalcounts.keys()):
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
459 fout7.write(str(key) + '\t' + repeatclass[key] + '\t' +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
460 repeatfamily[key] + '\t' + str(int(fractionalcounts[key]))
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
461 + '\n')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
462 fout1.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
463 fout2.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
464 fout3.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
465 fout4.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
466 fout5.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
467 fout6.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
468 fout7.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
469 else:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
470 fout1 = open(outputfolder + os.path.sep + outputfile_prefix +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
471 '_class_fraction_counts.txt', 'w')
2
15e3e29f310e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents: 0
diff changeset
472 for key in sorted(classfractionalcounts.keys()):
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
473 fout1.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
474 fout2 = open(outputfolder + os.path.sep + outputfile_prefix +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
475 '_family_fraction_counts.txt', 'w')
2
15e3e29f310e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents: 0
diff changeset
476 for key in sorted(familyfractionalcounts.keys()):
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
477 fout2.write(str(key) + '\t' + str(familyfractionalcounts[key]) + '\n')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
478 fout3 = open(outputfolder + os.path.sep + outputfile_prefix +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
479 '_fraction_counts.txt', 'w')
2
15e3e29f310e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents: 0
diff changeset
480 for key in sorted(fractionalcounts.keys()):
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
481 fout3.write(str(key) + '\t' + repeatclass[key] + '\t' +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
482 repeatfamily[key] + '\t' + str(int(fractionalcounts[key]))
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
483 + '\n')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
484 fout1.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
485 fout2.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
486 fout3.close()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
487 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
488 # Remove Large intermediate files
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
489 if os.path.exists(outputfolder + os.path.sep + outputfile_prefix +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
490 '_regionsorter.txt'):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
491 os.remove(outputfolder + os.path.sep + outputfile_prefix +
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
492 '_regionsorter.txt')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
493 if os.path.exists(outputfolder + os.path.sep + 'pair1_bowtie'):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
494 shutil.rmtree(outputfolder + os.path.sep + 'pair1_bowtie')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
495 if os.path.exists(outputfolder + os.path.sep + 'pair2_bowtie'):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
496 shutil.rmtree(outputfolder + os.path.sep + 'pair2_bowtie')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
497 if os.path.exists(outputfolder + os.path.sep + 'sorted_bowtie'):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
498 shutil.rmtree(outputfolder + os.path.sep + 'sorted_bowtie')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff changeset
499 print("... Done")