repenrich: RepEnrich.py annotate

annotate RepEnrich.py @ 9:db32bb7bda01 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ccf4b178d13aeedf7214f2400e7411bcfa3e73b4-dirty

author	artbio
date	Tue, 11 Dec 2018 12:50:46 -0500
parents	d1f7ab78f7b5
children	6f4143893463

rev	line source
0 f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	1 import argparse
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	2 import csv
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	3 import os
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	4 import shlex
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	5 import shutil
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	6 import subprocess
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	7 import sys
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	8
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	9 import numpy
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	10
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	11
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	12 parser = argparse.ArgumentParser(description='''
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	21 master_output.py\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	24 HeLa_InputChIPseq_Rep1 HeLa_InputChIPseq_Rep1\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	26 HeLa_InputChIPseq_Rep1_multimap.fastq\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	27 HeLa_InputChIPseq_Rep1.bam''')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	30 metavar='annotation_file',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	33 RepeatMasker.org website. Example:\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	34 /data/annotation/hg19/hg19_repeatmasker.txt')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	36 help='List folder to contain results.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	37 Example: /outputfolder')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	39 help='Enter prefix name for data.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	40 Example: HeLa_InputChIPseq_Rep1')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	43 pseudogenomes.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	44 Example: /data/annotation/hg19/setup_folder')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	46 help='Enter file for the fastq reads that map to multiple\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	47 locations. Example: /data/multimap.fastq')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	48 parser.add_argument('alignment_bam', action='store', metavar='alignment_bam',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	49 help='Enter bamfile output for reads that map uniquely.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	50 Example /bamfiles/old.bam')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	51 parser.add_argument('--pairedend', action='store', dest='pairedend',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	52 default='FALSE',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	53 help='Designate this option for paired-end sequencing.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	54 Default FALSE change to TRUE')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	55 parser.add_argument('--collapserepeat', action='store', dest='collapserepeat',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	56 metavar='collapserepeat', default='Simple_repeat',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	57 help='Designate this option to generate a collapsed repeat\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	59 collapsed repeat type. Simple_repeat is default to\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	64 Default Simple_repeat')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	66 metavar='fastqfile2', default='none',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	67 help='Enter fastqfile2 when using paired-end option.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	68 Default none')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	69 parser.add_argument('--cpus', action='store', dest='cpus', metavar='cpus',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	70 default="1", type=int,
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	71 help='Enter available cpus per node. The more cpus the\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	73 only work on one node. Default: "1"')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	74 parser.add_argument('--allcountmethod', action='store', dest='allcountmethod',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	75 metavar='allcountmethod', default="FALSE",
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	76 help='By default the pipeline only outputs the fraction\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	77 count method. Consdidered to be the best way to\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	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 artbio parents: diff changeset	81 counting strategy. Our evaluation of simulated data\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	82 indicated fraction counting is best.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	83 Default = FALSE, change to TRUE')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	84 parser.add_argument('--is_bed', action='store', dest='is_bed',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	85 metavar='is_bed', default='FALSE',
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	86 help='Is the annotation file a bed file.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	87 This is also a compatible format. The file needs to\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	88 be a tab seperated bed with optional fields.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	89 Ex. format: chr\tstart\tend\tName_element\tclass\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	90 \tfamily. The class and family should identical to\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	91 name_element if not applicable.\
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	92 Default FALSE change to TRUE')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	93 args = parser.parse_args()
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	94
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	95 # parameters
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	96 annotation_file = args.annotation_file
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	97 outputfolder = args.outputfolder
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	98 outputfile_prefix = args.outputprefix
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	99 setup_folder = args.setup_folder
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	100 repeat_bed = 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	101 unique_mapper_bam = args.alignment_bam
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	102 fastqfile_1 = args.fastqfile
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	103 fastqfile_2 = args.fastqfile2
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	104 cpus = args.cpus
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	105 b_opt = "-k1 -p " + str(1) + " --quiet"
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	106 simple_repeat = args.collapserepeat
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	107 paired_end = args.pairedend
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	108 allcountmethod = args.allcountmethod
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	109 is_bed = args.is_bed
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	110
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	111 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	112 # check that the programs we need are available
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	113 try:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: 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'),
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	116 stderr=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	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 parents: 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'))
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	120 except OSError:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	121 print("Error: Bowtie or BEDTools not loaded")
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 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 parents: diff changeset	124 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	125 # define a csv reader that reads space deliminated files
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	126 print('Preparing for analysis using RepEnrich...')
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	127 csv.field_size_limit(sys.maxsize)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	128
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	129
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: 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,
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	132 skipinitialspace=True):
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	133 if line:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 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
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 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 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	138 # build dictionaries to convert repclass and rep families'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	139 if is_bed == "FALSE":
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 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:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	145 if x > 2:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	146 classfamily = []
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	147 classfamily = line[10].split(os.path.sep)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 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("/", "_")
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	150 repeatclass[line9] = classfamily[0]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	151 if len(classfamily) == 2:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	152 repeatfamily[line9] = classfamily[1]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: 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]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 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":
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: 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]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	164 thefamily = line[5]
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 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
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	170 ##############################################################################
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	171 # build list of repeats initializing dictionaries for downstream analysis'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: 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 parents: 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 = {}
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: 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 parents: 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():
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	403 convert(key)
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310 artbio parents: diff changeset	404 repcounts[repname] = counts[key]
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")

Mercurial > repos > artbio > repenrich

annotate RepEnrich.py @ 9:db32bb7bda01 draft