repenrich: RepEnrich.py annotate

annotate RepEnrich.py @ 0:1435d142041b draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5

author	drosofff
date	Tue, 23 May 2017 18:37:22 -0400
parents
children

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

Mercurial > repos > drosofff > repenrich

annotate RepEnrich.py @ 0:1435d142041b draft