| Previous changeset 12:89e05f831259 (2024-03-18) Next changeset 14:bf866bedd4b4 (2024-04-20) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115 |
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modified:
RepEnrich.py RepEnrich_setup.py edgeR_repenrich.R edger-repenrich.xml macros.xml repenrich.xml test-data/Normalized_counts_file.tab test-data/edgeR_plots.pdf test-data/edgeR_result_file.tab |
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added:
test-data/chrY-1-500k.fa test-data/chrY-1-500k.fa.out test-data/chrY-500k.R1.fastqsanger.gz test-data/chrY-500k.R2.fastqsanger.gz test-data/chrY_paired_class_fraction_counts.tab test-data/chrY_paired_family_fraction_counts.tab test-data/chrY_paired_fraction_counts.tab test-data/chrY_single_class_fraction_counts.tab test-data/chrY_single_family_fraction_counts.tab test-data/chrY_single_fraction_counts.tab |
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removed:
test-data/Samp-paired_class_fraction_counts.tab test-data/Samp-paired_family_fraction_counts.tab test-data/Samp-paired_fraction_counts.tab test-data/Samp.fastq test-data/Samp_L.fastq test-data/Samp_R.fastq test-data/Samp_class_fraction_counts.tabular test-data/Samp_family_fraction_counts.tabular test-data/Samp_fraction_counts.tabular test-data/aligned_353.tab test-data/aligned_354.tab test-data/aligned_355.tab test-data/aligned_356.tab test-data/aligned_reads.tab |
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| diff -r 89e05f831259 -r 530626b0757c RepEnrich.py --- a/RepEnrich.py Mon Mar 18 09:39:44 2024 +0000 +++ b/RepEnrich.py Tue Apr 02 21:16:37 2024 +0000 |
| [ |
| b'@@ -4,8 +4,8 @@\n import shlex\n import subprocess\n import sys\n-\n-import numpy\n+from collections import defaultdict\n+from concurrent.futures import ProcessPoolExecutor\n \n \n parser = argparse.ArgumentParser(description=\'\'\'\n@@ -17,26 +17,13 @@\n help=\'RepeatMasker.org annotation file for your\\\n organism. The file may be downloaded from\\\n RepeatMasker.org. E.g. hg19_repeatmasker.txt\')\n-parser.add_argument(\'--outputfolder\', action=\'store\', metavar=\'outputfolder\',\n- help=\'Folder that will contain results. Should be the\\\n- same as the one used for RepEnrich_setup.\\\n- Example: ./outputfolder\')\n-parser.add_argument(\'--outputprefix\', action=\'store\', metavar=\'outputprefix\',\n- help=\'Prefix name for Repenrich output files.\')\n-parser.add_argument(\'--setup_folder\', action=\'store\', metavar=\'setup_folder\',\n- help=\'Folder produced by RepEnrich_setup which contains\\\n- repeat element pseudogenomes.\')\n+parser.add_argument(\'--alignment_bam\', action=\'store\', metavar=\'alignment_bam\',\n+ help=\'Bam alignments of unique mapper reads.\')\n parser.add_argument(\'--fastqfile\', action=\'store\', metavar=\'fastqfile\',\n help=\'File of fastq reads mapping to multiple\\\n locations. Example: /data/multimap.fastq\')\n-parser.add_argument(\'--alignment_bam\', action=\'store\', metavar=\'alignment_bam\',\n- help=\'Bam alignments of unique mapper reads.\')\n-parser.add_argument(\'--pairedend\', action=\'store\', dest=\'pairedend\',\n- default=\'FALSE\',\n- help=\'Change to TRUE for paired-end fastq files.\\\n- Default FALSE\')\n parser.add_argument(\'--fastqfile2\', action=\'store\', dest=\'fastqfile2\',\n- metavar=\'fastqfile2\', default=\'none\',\n+ metavar=\'fastqfile2\', default=\'\',\n help=\'fastqfile #2 when using paired-end option.\\\n Default none\')\n parser.add_argument(\'--cpus\', action=\'store\', dest=\'cpus\', metavar=\'cpus\',\n@@ -48,18 +35,16 @@\n \n # parameters\n annotation_file = args.annotation_file\n-outputfolder = args.outputfolder\n-outputfile_prefix = args.outputprefix\n-setup_folder = args.setup_folder\n-repeat_bed = os.path.join(setup_folder, \'repnames.bed\')\n unique_mapper_bam = args.alignment_bam\n fastqfile_1 = args.fastqfile\n fastqfile_2 = args.fastqfile2\n cpus = args.cpus\n-b_opt = "-k1 -p 1 --quiet"\n # Change if simple repeats are differently annotated in your organism\n simple_repeat = "Simple_repeat"\n-paired_end = args.pairedend\n+if args.fastqfile2:\n+ paired_end = True\n+else:\n+ paired_end = False\n \n # check that the programs we need are available\n try:\n@@ -73,260 +58,147 @@\n print("Error: Bowtie or bedtools not loaded")\n raise\n \n-# define a csv reader that reads space deliminated files\n-print(\'Preparing for analysis using RepEnrich...\')\n-csv.field_size_limit(sys.maxsize)\n \n-\n-def import_text(filename, separator):\n- for line in csv.reader(open(filename), delimiter=separator,\n- skipinitialspace=True):\n- if line:\n- yield line\n+def starts_with_numerical(list):\n+ try:\n+ if len(list) == 0:\n+ return False\n+ int(list[0])\n+ return True\n+ except ValueError:\n+ return False\n \n \n-# build dictionaries to convert repclass and rep families\n-repeatclass, repeatfamily = {}, {}\n-repeats = import_text(annotation_file, \' \')\n-# skip three first lines of the iterator\n-for line in range(3):\n- next(repeats)\n-for repeat in repeats:\n- classfamily = []\n- classfamily = repeat[10].split(\'/\')\n- matching_repeat = repeat[9].translate(str.maketrans(\'()/\', \'___\'))\n- repeatclass[matching_repeat] = classfamily[0]\n- if len(classfamily) == 2:\n- repeatfamily[matching_repeat] = classfamily[1]\n- e'..b' mutimapper repeat reads\')\n \n-# building the total counts for repeat element enrichment...\n-for x in counts.keys():\n- count = counts[x]\n- x = x.strip(\',\').split(\',\')\n- for i in x:\n- reptotalcounts[rev_repeat_key[int(i)]] += int(count)\n-# building the fractional counts for repeat element enrichment...\n-for x in counts.keys():\n- count = counts[x]\n- x = x.strip(\',\') .split(\',\')\n- splits = len(x)\n- for i in x:\n- fractionalcounts[rev_repeat_key[int(i)]] += float(\n- numpy.divide(float(count), float(splits)))\n-# building categorized table of repeat element enrichment...\n-repcounts = {}\n-repcounts[\'other\'] = 0\n-for key in counts.keys():\n- key_list = key.strip(\',\').split(\',\')\n- repname = \'\'\n+# Populate fractionalcounts\n+for key, count in counts.items():\n+ key_list = key.split(\',\')\n for i in key_list:\n- repname = os.path.join(repname, rev_repeat_key[int(i)])\n- repcounts[repname] = counts[key]\n-# building the total counts for class enrichment...\n-for key in reptotalcounts.keys():\n- classtotalcounts[repeatclass[key]] += reptotalcounts[key]\n-# building total counts for family enrichment...\n-for key in reptotalcounts.keys():\n- familytotalcounts[repeatfamily[key]] += reptotalcounts[key]\n-# building unique counts table\n-repcounts2 = {}\n-for rep in repeat_list:\n- if "/" + rep in repcounts:\n- repcounts2[rep] = repcounts["/" + rep]\n- else:\n- repcounts2[rep] = 0\n-# building the fractionalcounts counts for class enrichment...\n-for key in fractionalcounts.keys():\n- classfractionalcounts[repeatclass[key]] += fractionalcounts[key]\n-# building fractional counts for family enrichment...\n-for key in fractionalcounts.keys():\n- familyfractionalcounts[repeatfamily[key]] += fractionalcounts[key]\n+ fractionalcounts[i] += count / len(key_list)\n \n-# print output to file of the categorized counts and total overlapping counts:\n-print(\'Writing final output...\')\n-with open(f"{os.path.join(outputfolder, outputfile_prefix)}_"\n- f"class_fraction_counts.txt", \'w\') as fout:\n- for key in sorted(classfractionalcounts.keys()):\n+# build repeat_ref for easy access to rep class and rep families\n+repeat_ref = defaultdict(dict)\n+repeats = import_text(annotation_file, \' \')\n+for repeat in repeats:\n+ repeat_name = repeat[9].translate(str.maketrans(\'()/\', \'___\'))\n+ try:\n+ repclass = repeat[10].split(\'/\')[0]\n+ repfamily = repeat[10].split(\'/\')[1]\n+ except IndexError:\n+ repclass, repfamily = repeat[10], repeat[10]\n+ repeat_ref[repeat_name][\'class\'] = repclass\n+ repeat_ref[repeat_name][\'family\'] = repfamily\n+\n+# Populate classfractionalcounts and familyfractionalcounts\n+for key, value in fractionalcounts.items():\n+ classfractionalcounts[repeat_ref[key][\'class\']] += value\n+ familyfractionalcounts[repeat_ref[key][\'family\']] += value\n+\n+# print class-, family- and fraction-repeats counts to files\n+with open("class_fraction_counts.tsv", \'w\') as fout:\n+ for key in sorted(classfractionalcounts):\n fout.write(f"{key}\\t{classfractionalcounts[key]}\\n")\n \n-with open(f"{os.path.join(outputfolder, outputfile_prefix)}_"\n- f"family_fraction_counts.txt", \'w\') as fout:\n- for key in sorted(familyfractionalcounts.keys()):\n+with open("family_fraction_counts.tsv", \'w\') as fout:\n+ for key in sorted(familyfractionalcounts):\n fout.write(f"{key}\\t{familyfractionalcounts[key]}\\n")\n \n-with open(f"{os.path.join(outputfolder, outputfile_prefix)}_"\n- f"fraction_counts.txt", \'w\') as fout:\n- for key in sorted(fractionalcounts.keys()):\n- fout.write(f"{key}\\t{repeatclass[key]}\\t{repeatfamily[key]}\\t"\n- f"{int(fractionalcounts[key])}\\n")\n+with open("fraction_counts.tsv", \'w\') as fout:\n+ for key in sorted(fractionalcounts):\n+ fout.write(f"{key}\\t{repeat_ref[key][\'class\']}\\t"\n+ f"{repeat_ref[key][\'family\']}\\t"\n+ f"{fractionalcounts[key]}\\n")\n' |
| b |
| diff -r 89e05f831259 -r 530626b0757c RepEnrich_setup.py --- a/RepEnrich_setup.py Mon Mar 18 09:39:44 2024 +0000 +++ b/RepEnrich_setup.py Tue Apr 02 21:16:37 2024 +0000 |
| [ |
| @@ -5,6 +5,9 @@ import shlex import subprocess import sys +from collections import defaultdict +from concurrent.futures import ProcessPoolExecutor + from Bio import SeqIO from Bio.Seq import Seq @@ -22,10 +25,6 @@ parser.add_argument('--genomefasta', action='store', metavar='genomefasta', help='''Genome of interest in fasta format.\ Example: mm9.fa''') -parser.add_argument('--setup_folder', action='store', metavar='setup_folder', - help='''Folder that contains bowtie indexes of repeats and\ - repeat element psuedogenomes.\ - Example working/setup''') parser.add_argument('--gaplength', action='store', dest='gaplength', metavar='gaplength', default='200', type=int, help='''Length of the N-spacer in the\ @@ -36,6 +35,10 @@ repeat pseudogenomes. Flanking length should be set\ according to the length of your reads.\ Default 25, for 50 nt reads''') +parser.add_argument('--cpus', action='store', dest='cpus', metavar='cpus', + default="1", type=int, + help='Number of CPUs. The more cpus the\ + faster RepEnrich performs. Default: "1"') args = parser.parse_args() # parameters from argsparse @@ -43,7 +46,7 @@ flankingl = args.flankinglength annotation_file = args.annotation_file genomefasta = args.genomefasta -setup_folder = args.setup_folder +cpus = args.cpus # check that the programs we need are available try: @@ -54,56 +57,51 @@ print("Error: Bowtie not available in the path") raise -# Define a text importer -csv.field_size_limit(sys.maxsize) - -def import_text(filename, separator): - for line in csv.reader(open(os.path.realpath(filename)), - delimiter=separator, skipinitialspace=True): - if line: - yield line +def starts_with_numerical(list): + try: + if len(list) == 0: + return False + int(list[0]) + return True + except ValueError: + return False -# Make a setup folder -if not os.path.exists(setup_folder): - os.makedirs(setup_folder) +# define a text importer for .out/.txt format of repbase +def import_text(filename, separator): + csv.field_size_limit(sys.maxsize) + file = csv.reader(open(filename), delimiter=separator, + skipinitialspace=True) + return [line for line in file if starts_with_numerical(line)] + + # load genome into dictionary and compute length g = SeqIO.to_dict(SeqIO.parse(genomefasta, "fasta")) -idxgenome, lgenome, genome = {}, {}, {} +genome = defaultdict(dict) -for k, chr in enumerate(g.keys()): - genome[chr] = g[chr].seq - lgenome[chr] = len(genome[chr]) - idxgenome[chr] = k +for chr in g.keys(): + genome[chr]['sequence'] = g[chr].seq + genome[chr]['length'] = len(g[chr].seq) # Build a bedfile of repeatcoordinates to use by RepEnrich region_sorter -repeat_elements = [] -# these dictionaries will contain lists -rep_chr, rep_start, rep_end = {}, {}, {} -fin = import_text(annotation_file, ' ') -with open(os.path.join(setup_folder, 'repnames.bed'), 'w') as fout: - for i in range(3): - next(fin) - for line in fin: +repeat_elements = set() +rep_coords = defaultdict(list) # Merged dictionary for coordinates + +with open('repnames.bed', 'w') as fout: + f_in = import_text(annotation_file, ' ') + for line in f_in: repname = line[9].translate(str.maketrans('()/', '___')) - if repname not in repeat_elements: - repeat_elements.append(repname) - repchr = line[4] - repstart = line[5] - repend = line[6] - fout.write('\t'.join([repchr, repstart, repend, repname]) + '\n') - if repname in rep_chr: - rep_chr[repname].append(repchr) - rep_start[repname].append(repstart) - rep_end[repname].append(repend) - else: - rep_chr[repname] = [repchr] - rep_start[repname] = [repstart] - rep_end[repname] = [repend] + repeat_elements.add(repname) + repchr, repstart, repend = line[4], line[5], line[6] + fout.write(f"{repchr}\t{repstart}\t{repend}\t{repname}\n") + rep_coords[repname].extend([repchr, repstart, repend]) +# repeat_elements now contains the unique repeat names +# rep_coords is a dictionary where keys are repeat names and values are lists +# containing chromosome, start, and end coordinates for each repeat instance -# sort repeat_elements and print them in repgenomes_key.txt -with open(os.path.join(setup_folder, 'repgenomes_key.txt'), 'w') as fout: +# sort repeat_elements and print them in repeatIDs.txt +with open('repeatIDs.txt', 'w') as fout: for i, repeat in enumerate(sorted(repeat_elements)): fout.write('\t'.join([repeat, str(i)]) + '\n') @@ -111,24 +109,41 @@ spacer = ''.join(['N' for i in range(gapl)]) # generate metagenomes and save them to FASTA files for bowtie build -for repname in rep_chr: +for repname in rep_coords: metagenome = '' - for i, repeat in enumerate(rep_chr[repname]): - try: - chromosome = rep_chr[repname][i] - start = max(int(rep_start[repname][i]) - flankingl, 0) - end = min(int(rep_end[repname][i]) + flankingl, - int(lgenome[chr])-1) + 1 - metagenome = f"{metagenome}{spacer}{genome[chromosome][start:end]}" - except KeyError: - print("Unrecognised Chromosome: " + rep_chr[repname][i]) + # iterating coordinate list by block of 3 (chr, start, end) + block = 3 + for i in range(0, len(rep_coords[repname]) - block + 1, block): + batch = rep_coords[repname][i:i+block] + print(batch) + chromosome = batch[0] + start = max(int(batch[1]) - flankingl, 0) + end = min(int(batch[2]) + flankingl, + int(genome[chromosome]['length'])-1) + 1 + metagenome = ( + f"{metagenome}{spacer}" + f"{genome[chromosome]['sequence'][start:end]}" + ) # Create Fasta of repeat pseudogenome - fastafilename = f"{os.path.join(setup_folder, repname)}.fa" + fastafilename = f"{repname}.fa" record = SeqRecord(Seq(metagenome), id=repname, name='', description='') SeqIO.write(record, fastafilename, "fasta") - # Generate repeat pseudogenome bowtie index - bowtie_build_cmd = ["bowtie-build", "-f", fastafilename, - os.path.join(setup_folder, repname)] - subprocess.run(bowtie_build_cmd, check=True) + +def bowtie_build(args): + """ + Function to be executed in parallel by ProcessPoolExecutor. + """ + try: + bowtie_base, fasta = args + command = shlex.split(f"bowtie-build -f {fasta} {bowtie_base}") + squash = subprocess.run(command, capture_output=True, text=True) + return squash.stdout + except Exception as e: + return str(e) + + +args_list = [(name, f"{name}.fa") for name in rep_coords] +with ProcessPoolExecutor(max_workers=cpus) as executor: + executor.map(bowtie_build, args_list) |
| b |
| diff -r 89e05f831259 -r 530626b0757c edgeR_repenrich.R --- a/edgeR_repenrich.R Mon Mar 18 09:39:44 2024 +0000 +++ b/edgeR_repenrich.R Tue Apr 02 21:16:37 2024 +0000 |
| [ |
| @@ -19,7 +19,6 @@ options(stringAsFactors = FALSE, useFancyQuotes = FALSE) # get options, using the spec as defined by the enclosed list. -# we read the options from the default: commandArgs(TRUE). spec <- matrix( c( "quiet", "q", 0, "logical", @@ -30,8 +29,6 @@ "levelNameB", "B", 1, "character", "levelAfiles", "a", 1, "character", "levelBfiles", "b", 1, "character", - "alignmentA", "i", 1, "character", - "alignmentB", "j", 1, "character", "plots", "p", 1, "character" ), byrow = TRUE, ncol = 4 @@ -65,17 +62,7 @@ counts <- cbind(counts, listB[[element]][, 4]) } colnames(counts) <- c(names(listA[-1]), names(listB[-1])) - -# build aligned counts vector -filesi <- fromJSON(opt$alignmentA, method = "C", unexpected.escape = "error") -filesj <- fromJSON(opt$alignmentB, method = "C", unexpected.escape = "error") -sizes <- c() -for (file in filesi) { - sizes <- c(sizes, read.delim(file, header = TRUE)[1, 1]) -} -for (file in filesj) { - sizes <- c(sizes, read.delim(file, header = TRUE)[1, 1]) -} +sizes <- colSums(counts) # build a meta data object meta <- data.frame( @@ -187,6 +174,3 @@ results$log2FC <- format(results$log2FC, digits = 5) results$FDR <- format(results$FDR, digits = 5) write.table(results, opt$outfile, quote = FALSE, sep = "\t", col.names = TRUE, row.names = FALSE) - -cat("Session information:\n\n") -sessionInfo() |
| b |
| diff -r 89e05f831259 -r 530626b0757c edger-repenrich.xml --- a/edger-repenrich.xml Mon Mar 18 09:39:44 2024 +0000 +++ b/edger-repenrich.xml Tue Apr 02 21:16:37 2024 +0000 |
| b |
| @@ -3,7 +3,7 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"/> + <expand macro="edgeR_requirements"/> <stdio> <regex match="Execution halted" source="both" @@ -46,20 +46,6 @@ $factorlevelsB.reverse() --levelBfiles '#echo json.dumps(factorlevelsB)#' - #set $alignedA = list() - #for file in $alignmentFiles_A: - $alignedA.append(str($file)) - #end for - $alignedA.reverse() - --alignmentA '#echo json.dumps(alignedA)#' - - #set $alignedB = list() - #for file in $alignmentFiles_B: - $alignedB.append(str($file)) - #end for - $alignedB.reverse() - --alignmentB '#echo json.dumps(alignedB)#' - -o 'edger_out' -p '$plots' @@ -83,7 +69,6 @@ </sanitizer> </param> <param name="countsFiles_A" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich" /> - <param name="alignmentFiles_A" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/> <param name="factorLevel_B" type="text" value="FactorLevel2" label="Specify a factor level, typical values could be 'wildtype' or 'control'" help="Only letters, numbers and underscores will be retained in this field"> <sanitizer> @@ -91,7 +76,6 @@ </sanitizer> </param> <param name="countsFiles_B" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich tool" /> - <param name="alignmentFiles_B" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/> <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Output normalized counts table" /> </inputs> @@ -111,10 +95,8 @@ <param name="factorName" value="Genotype"/> <param name="factorLevel_A" value="Mutant"/> <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/> - <param name="alignmentFiles_A" value="aligned_355.tab,aligned_356.tab"/> <param name="factorLevel_B" value="Wildtype"/> <param name="countsFiles_B" value="353_fraction_counts.tab,354_fraction_counts.tab"/> - <param name="alignmentFiles_B" value="aligned_353.tab,aligned_354.tab"/> <param name="normCounts" value="True"/> <output name="counts_out" file="Normalized_counts_file.tab"/> <output name="plots" file="edgeR_plots.pdf"/> @@ -164,11 +146,10 @@ Gypsy6_I-int LTR Gypsy 7489 ============== ========== ========== ========== -Count tables must be -generated for each sample individually. Here, edgeR_ is handling a single factor -(genotype, age, treatment, etc) that effect your experiment. This factor has two -levels/states (for instance, "wild-type" and "mutant". -You need to select appropriate count table from your history for each factor level. +Count tables must be generated for each sample individually. Here, edgeR_ is handling a +single factor (genotype, age, treatment, etc) that effect your experiment. This factor has +two levels/states (for instance, "wild-type" and "mutant". You need to select appropriate +count table from your history for each factor level. The following table gives some examples of factors and their levels: @@ -189,14 +170,10 @@ in above table, edgeR computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples. -*Number of aligned reads*: - -A file containing the number of reads aligned to transposons by repenrich must me provided -to edger-repenrich. This file is a single-column tabular file containing a single value. - **Output** -edgeR_ generates a tabular file containing the different columns and results visualized in a PDF: +edgeR_ generates a tabular file containing the different columns and results visualized in +a PDF: ====== ============================================================================= Column Description @@ -212,7 +189,8 @@ .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html ]]> -**Note**: This edgeR_ wrapper was adapted from code available at https://github.com/nskvir/RepEnrich +**Note**: This edgeR_ wrapper was adapted from code available at +https://github.com/nskvir/RepEnrich </help> <citations> |
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| diff -r 89e05f831259 -r 530626b0757c macros.xml --- a/macros.xml Mon Mar 18 09:39:44 2024 +0000 +++ b/macros.xml Tue Apr 02 21:16:37 2024 +0000 |
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| @@ -1,18 +1,24 @@ <macros> - <token name="@TOOL_VERSION@">1.83</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.31.1</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">23.0</token> - <xml name="requirements"> + <xml name="repenrich_requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bedtools</requirement> + <requirement type="package" version="1.3.1">bowtie</requirement> + <requirement type="package" version="1.19.2">samtools</requirement> + <requirement type="package" version="1.83">biopython</requirement> + </requirements> + </xml> + + <xml name="edgeR_requirements"> <requirements> <requirement type="package" version="4.0.2">bioconductor-edger</requirement> <requirement type="package" version="3.58.1">bioconductor-limma</requirement> <requirement type="package" version="1.20.4">r-getopt</requirement> <requirement type="package" version="0.2.21">r-rjson</requirement> - <requirement type="package" version="1.0.0">bowtie</requirement> - <requirement type="package" version="1.19.2">samtools</requirement> - <requirement type="package" version="2.23.0">bedtools</requirement> - <requirement type="package" version="@TOOL_VERSION@">biopython</requirement> </requirements> </xml> + </macros> |
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| diff -r 89e05f831259 -r 530626b0757c repenrich.xml --- a/repenrich.xml Mon Mar 18 09:39:44 2024 +0000 +++ b/repenrich.xml Tue Apr 02 21:16:37 2024 +0000 |
| [ |
| b'@@ -3,84 +3,59 @@\n <macros>\n <import>macros.xml</import>\n </macros>\n- <expand macro="requirements"/>\n+ <expand macro="repenrich_requirements"/>\n <stdio>\n <exit_code range="1:" level="fatal" description="Tool exception" />\n </stdio>\n <command detect_errors="exit_code"><![CDATA[\n #import re\n- #set input_base = \'Sample\'\n- #set baseReference = \'Genome\'\n-\n ## uncompress fastq.gz or fastqsanger.gz if needed\n #if $seq_method.seq_method_list == "single-read":\n #if $seq_method.input_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):\n- gunzip < \'$seq_method.input_fastq\' > \'${input_base}.fastq\' &&\n+ gunzip < \'$seq_method.input_fastq\' > \'input.fastq\' &&\n #else:\n- ln -f -s \'$seq_method.input_fastq\' \'${input_base}.fastq\' &&\n+ ln -f -s \'$seq_method.input_fastq\' \'input.fastq\' &&\n #end if\n #elif $seq_method.seq_method_list == \'paired_collection\':\n #if $seq_method.input_fastq.forward.is_of_type("fastq.gz", "fastqsanger.gz"):\n- gunzip < \'$seq_method.input_fastq.forward\' > \'${input_base}.fastq\' &&\n- gunzip < \'$seq_method.input_fastq.reverse\' > \'${input_base}_2.fastq\' &&\n+ gunzip < \'$seq_method.input_fastq.forward\' > \'input.fastq\' &&\n+ gunzip < \'$seq_method.input_fastq.reverse\' > \'input_2.fastq\' &&\n #else:\n- ln -f -s \'$seq_method.input_fastq.forward\' \'${input_base}.fastq\' &&\n- ln -f -s \'$seq_method.input_fastq.reverse\' \'${input_base}_2.fastq\' &&\n+ ln -f -s \'$seq_method.input_fastq.forward\' \'input.fastq\' &&\n+ ln -f -s \'$seq_method.input_fastq.reverse\' \'input_2.fastq\' &&\n #end if\n #else:\n #if $seq_method.input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):\n- gunzip < \'$seq_method.input_fastq\' > \'${input_base}.fastq\' &&\n- gunzip < \'$seq_method.input2_fastq\' > \'${input_base}_2.fastq\' &&\n+ gunzip < \'$seq_method.input_fastq\' > \'input.fastq\' &&\n+ gunzip < \'$seq_method.input2_fastq\' > \'input_2.fastq\' &&\n #else:\n- ln -f -s \'$seq_method.input_fastq\' \'${input_base}.fastq\' &&\n- ln -f -s \'$seq_method.input2_fastq\' \'${input_base}_2.fastq\' &&\n+ ln -f -s \'$seq_method.input_fastq\' \'input.fastq\' &&\n+ ln -f -s \'$seq_method.input2_fastq\' \'input_2.fastq\' &&\n #end if\n #end if\n- ln -f -s \'$genome\' \'${baseReference}.fa\' &&\n- bowtie-build \'$genome\' ${baseReference} &&\n+ ln -f -s \'$genome\' \'genome.fa\' &&\n+ bowtie-build \'$genome\' genome &&\n python $__tool_directory__/RepEnrich_setup.py\n- --annotation_file $repeatmasker\n- --genomefasta ${baseReference}.fa\n- --setup_folder setup_folder_${baseReference} &&\n- #if $seq_method.seq_method_list == "single-read":\n- bowtie $baseReference -p \\${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&\n- TOTAL=\\$(grep \'reads processed:\' bowtie_alignments.txt | cut -d \' \' -f 4) &&\n- NONALIGNED=\\$(grep \'reads that failed to align:\' bowtie_alignments.txt | cut -d \' \' -f 7) &&\n- echo -e "# Total reads aligned to repeated sequences\\n" > bowtie_aligned.numb &&\n- echo \\$((\\$TOTAL-\\$NONALIGNED)) >> bowtie_aligned.numb &&\n- #else:\n- bowtie $baseReference -p \\${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq -1 ${input_base}.fastq -2 ${input_base}_2.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&\n- TOTAL=\\$(grep \'reads processed:\' bowtie_alignments.txt | cut -d \' \' -f 4) &&\n- NONALIGNED=\\$(grep \'reads that failed to align:\' bowtie_alignments.txt | cut -d \' \' -f 7) &&\n- '..b'overlap to RepeatMasker annotated genomic instances of each repetitive element subfamily. Reads mapping to multiple locations are separately mapped to repetitive element assemblies \xe2\x80\x93 referred to as repetitive element psuedogenomes \xe2\x80\x93 built from RepeatMasker annotated genomic instances of repetitive element subfamilies. RepEnrich then return tables of counts merged from both strategies, that can be further processed in statistical analysis for differential expression. For detailed information see the `original publication`_.\n+Reads are mapped to the genome using the Bowtie1 aligner. Reads mapping uniquely to the\n+genome are assigned to subfamilies of repetitive elements based on their degree of overlap\n+to RepeatMasker annotated genomic instances of each repetitive element subfamily.\n+\n+Reads mapping to multiple locations are separately mapped to repetitive element assemblies\n+\xe2\x80\x93 referred to as repetitive element psuedogenomes \xe2\x80\x93 built from RepeatMasker annotated\n+genomic instances of repetitive element subfamilies.\n+\n+RepEnrich then return tables of counts merged from both strategies, that can be further\n+processed in statistical analysis for differential expression. For detailed information\n+see the `original publication`_.\n \n .. _original publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-583\n \n@@ -171,7 +132,8 @@\n \n *Sequencing dataset*: Single-reads or Paired-end sequencing datasets in fastq format.\n \n-*RepeatMasker description file*: a txt repeatmasker file which can be downloaded from http://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html\n+*RepeatMasker description file*: a txt repeatmasker file which can be downloaded from\n+https://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html\n \n This file looks like:\n \n@@ -221,27 +183,29 @@\n \n **Outputs**\n \n-(1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned in tabular format,\n-for further statistical tests differential expression analysis or graphics.\n-\n-The "aligned_reads.tab" output file contains a single value corresponding to the number of reads that were aligned to\n-transposons. This value is used in downstream analysis by the edger-repenrich tool.\n+(1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned\n+in tabular format for further statistical tests, differential expression analysis or graphics.\n \n **RepEnrich**\n \n-This Galaxy tool is a wrapper of the RepEnrich tool by steven_criscione@brown.edu et al. whose code and manual are available in `GitHub`_.\n+.. class:: warningmark\n \n-.. _GitHub: https://github.com/nskvir/RepEnrich\n+Earlier versions of the RepEnrich.py and RepEnrich_setpup.py scripts of this galaxy wrapper\n+were directly derived from the `nskvir/RepEnrich GitHub repository`_ which is not maintained\n+anymore.\n \n-Python scripts RepEnrich.py and RepEnrich_setup.py have been adapted to python 3. Note that sorting of Fraction counts, Family fraction counts and Class fraction counts is different with this Galaxy wrapper or with RepEnrich as found in the `RepEnrich code repository`_. However, this different sorting does not affect subsequent statistical analyses\n+Starting from 2024, python codes were extensively rewritten for clarity, maintenance and\n+optimization and we now refer exclusively to our `GitHub repository`_ for code review.\n \n-.. _RepEnrich code repository: https://github.com/nskvir/RepEnrich\n+.. _nskvir/RepEnrich GitHub repository: https://github.com/nskvir/RepEnrich\n+.. _GitHub repository: https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich\n \n **Execution time**\n \n .. class:: warningmark\n \n-This tool includes steps to index the reference genome, index repeat sequences and align reads to these indexes. Therefore the run time may be **long to very long**. \n+This tool includes time-consuming steps to index the reference genome, index repeat\n+sequences and to align reads to these indexes.\n \n .. class:: infomark\n \n' |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/Normalized_counts_file.tab --- a/test-data/Normalized_counts_file.tab Mon Mar 18 09:39:44 2024 +0000 +++ b/test-data/Normalized_counts_file.tab Tue Apr 02 21:16:37 2024 +0000 |
| b |
| b'@@ -1,211 +1,211 @@\n Tag\tMutant_1\tMutant_2\tWildtype_1\tWildtype_2\n-5S_DM\t247.942840217287\t356.138990129468\t271.810660587451\t503.611727197063\n-ACCORD_I-int\t160.687012069425\t174.461719477315\t117.166444321613\t104.919109832721\n-ACCORD_LTR\t30.9390054922851\t29.5494000493336\t12.6933900385148\t10.6615261723782\n-ACCORD2_I-int\t89.5272994371693\t103.079302497675\t126.245445332212\t119.118324235025\n-ACCORD2_LTR\t8.34178249348953\t6.52835582485276\t10.1116835900033\t9.30460465953003\n-ALA_DM\t0.352469682823501\t0\t0.215142204042624\t0.290768895610313\n-ARS406_DM\t29.5682900590826\t19.7568663120544\t24.2250121751994\t34.8438059906359\n-Baggins1\t215.398139503251\t157.367735146451\t220.994071992583\t188.660551768492\n-BARI_DM\t43.7454039682056\t44.8394965864887\t42.5981564004395\t43.7122573067505\n-BARI1\t14.490420293855\t10.7374273435078\t16.9962341193673\t15.6045973977535\n-BATUMI_I-int\t184.968256886155\t158.226729333931\t275.166878970516\t232.082040179632\n-BATUMI_LTR\t13.628827735842\t14.5170017684226\t23.8377562079227\t19.5299774884927\n-BEL_I-int\t1148.97283940843\t1304.98396962057\t1022.22666828812\t1059.36800967358\n-BEL_LTR\t36.3043773308206\t51.9691483425779\t37.6498857074591\t41.5799520722748\n-Bica_I-int\t61.1339083208317\t53.0858407863027\t79.6886723773878\t67.3614608163893\n-Bica_LTR\t4.81708566525452\t5.7552610561202\t6.02398171319346\t6.05768532521486\n-BLASTOPIA_I-int\t539.670247700872\t1034.65849882041\t443.580196295081\t462.322544020398\n-BLASTOPIA_LTR\t40.6515034189771\t78.9415658294696\t23.6656424446886\t23.1645886836216\n-BLOOD_I-int\t1071.58616237963\t1140.74428097427\t960.825083254357\t834.603653366803\n-BLOOD_LTR\t49.6982252781137\t46.55748496145\t32.1852737247765\t36.1522660208823\n-BS\t203.649150075801\t355.194096523239\t313.935504138996\t242.355874491196\n-BS2\t204.197436249082\t179.186187508459\t240.744126323696\t241.871259665179\n-BS3_DM\t33.3279666758666\t38.9124366928724\t53.871607892273\t42.5007202417075\n-BS4_DM\t0.313306384732001\t1.97568663120544\t1.46296698748984\t1.0176911346361\n-BURDOCK_I-int\t203.257517094886\t191.727502645676\t134.205706881789\t161.473660028927\n-BURDOCK_LTR\t21.2656708636846\t16.5785878183761\t12.3491625120466\t17.930748562636\n-Chimpo_I-int\t53.4970651929892\t31.7827849367832\t55.4206317613799\t51.369171557822\n-Chimpo_LTR\t4.19047289579051\t2.83468081868607\t4.04467343600132\t5.81537791220627\n-Chouto_I-int\t48.2100199506366\t44.4958989114965\t72.7180649664068\t63.1937733126415\n-Chouto_LTR\t6.34445429082302\t13.658007580942\t12.8655038017489\t13.617676611083\n-CIRCE\t143.964283784354\t134.862087434458\t162.088136525713\t161.037506685512\n-Copia_I-int\t1992.94191328026\t7492.14730320603\t1188.10130760498\t1295.52081439175\n-Copia_LTR\t102.294534614998\t264.140712650293\t60.5840446584028\t54.7130138573406\n-Copia1-I_DM\t160.56952217515\t167.16026888373\t154.386045620987\t170.487495792847\n-Copia1-LTR_DM\t23.4979788549001\t33.4148738929964\t33.1749278633726\t27.4291991525729\n-Copia2_I-int\t141.536159302681\t162.521700271335\t181.493963330357\t167.434422388939\n-Copia2_LTR_DM\t29.2549836743506\t39.5137326241088\t38.3383407603955\t23.5522805444354\n-DIVER_I-int\t968.978321379896\t1009.40406970848\t567.028792974739\t757.307588617061\n-DIVER_LTR\t21.4223240560506\t28.1750093493646\t20.1803387391981\t20.7899760361374\n-DIVER2_I-int\t252.44661949781\t229.179649219831\t287.386956160137\t272.692762599872\n-DIVER2_LTR\t25.3778171632921\t20.615860499535\t34.1215535611601\t25.9268931919196\n-DM1731_I-int\t737.405739764856\t590.386705055435\t222.887323388158\t236.54049657899\n-DM1731_LTR\t49.8940417685711\t27.5737134181281\t24.8274103465188\t21.3230523447563\n-DM176_I-int\t185.08574678043\t197.396864283048\t156.064154812519\t136.322150558635\n-DM176_LTR\t21.9314469312401\t28.3468081868607\t38.6825682868637\t42.2584128286989\n-DM297_I-int\t3226.54663986442\t3668.33467763602\t509.327653850507\t558.760894397819\n-DM297_LTR\t239.992690704713\t216.122937570126\t64.0693483638933\t71.6260712853405\n-DM412\t1711.00533031955\t2019.32353592946\t1036.38302531413\t1142.04329899211\n-DM412B_LTR\t219.588612399041\t257.784155662936\t132.441540808639\t141.022914371002\n-DMCR1A\t684.926920322246\t693.380108134362\t876.919623677734\t870.2'..b'789344043\t303.554556241254\t361.924932338747\t415.117944475564\n+POGON1\t85.9627029802447\t75.30035503659\t49.3601782464464\t67.1318345199247\n+PROTOP\t640.361788971401\t605.638402423199\t736.972812368393\t725.123760955911\n+PROTOP_A\t598.788562881111\t584.75431958102\t526.856524908444\t563.707513685918\n+PROTOP_B\t1256.71839255518\t1264.81065100522\t1295.89108447619\t1380.11724317016\n+QUASIMODO_I-int\t2401.85961057127\t2353.13609489344\t2222.84838955145\t2168.54149325156\n+QUASIMODO_LTR\t217.924169021681\t155.306982262967\t198.633708230413\t195.565195350847\n+QUASIMODO2-I_DM\t533.344258584139\t532.691183481502\t405.17100995648\t370.641021853182\n+QUASIMODO2-LTR_DM\t39.9639399190529\t30.8849112454764\t46.6759389460354\t33.3160469081512\n+R1_DM\t2068.46915876333\t1770.44076939545\t1095.0205101621\t900.699328161867\n+R1-2_DM\t24.6757212923011\t20.0016568065942\t39.8162162894296\t29.4847015137138\n+R2_DM\t7247.42027216596\t4449.78035544349\t2285.62976429995\t1400.44003178414\n+ROO_I-int\t4562.72861699979\t6747.9118941188\t4741.11222655369\t4669.91029511555\n+ROO_LTR\t297.583834497914\t427.388343235021\t244.414900742978\t308.340014134939\n+ROOA_I-int\t550.241763382128\t758.592248591272\t743.385161808263\t764.436696307529\n+ROOA_LTR\t58.3366237073423\t81.1831952738236\t59.6497622313551\t80.4582532831851\n+ROVER-I_DM\t931.642585965304\t902.721834403496\t971.24725353204\t931.016930848285\n+ROVER-LTR_DM\t55.6544800886139\t49.4158579927622\t84.1061647462108\t69.1307973344137\n+S_DM\t667.049117977749\t600.343846209689\t538.637352949137\t579.032895263668\n+S2_DM\t96.0207415504761\t60.2991124316444\t114.080170267467\t122.103311918374\n+SSU-rRNA_Cel\t516.983182509896\t534.456035552672\t516.417816517957\t363.64465200247\n+SSU-rRNA_Dme\t1335.43930776486\t1124.21076933534\t1060.72189687907\t691.80771404776\n+SSU-rRNA_Hsa\t75592.5969999742\t88775.8830260092\t47428.2715721784\t28668.4583644641\n+Stalker2_I-int\t1470.61934614877\t1415.99964510213\t1827.07221714641\t2077.92184566139\n+Stalker2_LTR\t105.944672939771\t104.714556222758\t108.26431844991\t111.941917611388\n+Stalker3_LTR\t72.8201992484756\t69.1233727874948\t88.430772507984\t73.1287229633919\n+STALKER4_I-int\t977.239027483686\t921.252781150781\t925.615185425053\t956.33712649848\n+STALKER4_LTR\t273.578649110295\t236.196035524929\t192.668732007277\t201.562083794315\n+TABOR_I-int\t738.125923874051\t1085.67816578146\t588.594028817897\t513.233702620069\n+TABOR_LTR\t59.4094811548337\t25.8844970438278\t57.2637717421009\t45.4764040296264\n+TAHRE\t510.411930644011\t416.799230808\t680.007289437449\t651.995037992519\n+TART_B1\t1794.62229529116\t1496.88869836409\t3765.09299204314\t3583.64058567528\n+TART-A\t682.873765328246\t536.809171647566\t551.3129274233\t567.705439314896\n+TC1_DM\t351.092599691545\t436.800887614595\t274.388906264234\t326.497259699882\n+TC1-2_DM\t595.167668995828\t672.702781127662\t567.716612036923\t657.658765966905\n+TIRANT_I-int\t3106.59284639215\t3743.83952697546\t1627.99113569926\t1425.76022743433\n+TIRANT_LTR\t432.495658519952\t469.450650931241\t204.44956004797\t213.056119977627\n+TLD2\t4.42553697090183\t0.29414201186168\t9.69308636259521\t2.83186398719285\n+TOM_I-int\t929.228656708448\t997.141420211095\t382.205851497408\t384.966922023687\n+Transib-N1_DM\t49.0832282227294\t38.2384615420184\t45.9303169181435\t61.8012670146205\n+TRANSIB1\t164.817725370859\t85.0070414280255\t310.477012414204\t352.48377628824\n+TRANSIB2\t450.197806403559\t436.506745602733\t476.750724634106\t512.400801447365\n+TRANSIB3\t241.661140047427\t217.959230789505\t176.563296204811\t188.568825500136\n+TRANSIB4\t48.8150138608566\t45.003727814837\t94.6939975422763\t95.1173139227717\n+Transib5\t130.486287051136\t96.478579890631\t167.46670746453\t160.749926331829\n+TRANSPAC_I-int\t3818.5678699836\t4929.82011880175\t1442.62949956532\t2495.70507388961\n+TRANSPAC_LTR\t195.394162624363\t287.965029612585\t80.2289302011727\t92.4520301701196\n+XDMR\t237.503817438398\t265.610236711097\t186.256382567406\t239.875537738689\n+XDMR_DM\t542.999975611561\t466.803372824486\t494.645653303513\t720.959255092392\n+ZAM_I-int\t924.803119737546\t850.658698303978\t764.859076211551\t737.284118077386\n+ZAM_LTR\t50.55840721303\t34.7087573996782\t38.6232210448025\t37.4805527716701\n' |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/Samp-paired_class_fraction_counts.tab --- a/test-data/Samp-paired_class_fraction_counts.tab Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -Low_complexity 2.0 -Simple_repeat 121.0 -rRNA 111.0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/Samp-paired_family_fraction_counts.tab --- a/test-data/Samp-paired_family_fraction_counts.tab Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -Low_complexity 2.0 -Simple_repeat 121.0 -rRNA 111.0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/Samp-paired_fraction_counts.tab --- a/test-data/Samp-paired_fraction_counts.tab Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -A-rich Low_complexity Low_complexity 2 -LSU-rRNA_Cel rRNA rRNA 111 -_ATA_n Simple_repeat Simple_repeat 0 -_ATTTAT_n Simple_repeat Simple_repeat 1 -_ATT_n Simple_repeat Simple_repeat 11 -_AT_n Simple_repeat Simple_repeat 0 -_CTAATT_n Simple_repeat Simple_repeat 29 -_TAT_n Simple_repeat Simple_repeat 0 -_TA_n Simple_repeat Simple_repeat 0 -_TTA_n Simple_repeat Simple_repeat 80 -_T_n Simple_repeat Simple_repeat 0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/Samp.fastq --- a/test-data/Samp.fastq Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,10040 +0,0 @@\n-@HISEQ:262:CA81LANXX:2:1101:1338:1996\n-GCGGGTGATAAACTTCTGTGAAAAAAAGCTCAAAAAAATCTCACAAAAAATAAAACTTCTGATAAAATAAATAAAATTATTCCTCATCGTAAACCAATAGTTACTGCATAAGTATGTAATCCTTG\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFF\n-@HISEQ:262:CA81LANXX:2:1101:7367:1984\n-GGGTCTTCTCGTCTTTTAAATAAATTTTAGCTTTTTGACTAAAAAATAAAATTCTATAAAAATTTTAAATGAAACAGTTAATATTTCGTCCAACCATTCATTCCAGCCTTCAATTAAAAGACTAA\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFF<FBF/FFFFFFFFFFFFFFB/FFFFBFFFFFFFFFFB<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFF<FFFFFBF\n-@HISEQ:262:CA81LANXX:2:1101:19502:1983\n-GTCCAACCATTCATTCCAGCCTTCAATTAAAAGACTAATGATTATGCTACCTTTGCACAGTCAAAATACTGCGGCCATTTAAAATTTTCAGTGGGCGGGAGATCGGAAGAGCACACGTCTGACCT\n-+\n-B<BBBFFFFFFF///FBF///</<<<B/BBF<BFFFFB<//<FBFFFFFBFFF//</</<<B/FB</<B///<<BF//</<FFBF</BF//<FB###############################\n-@HISEQ:262:CA81LANXX:2:1101:1225:2201\n-TCGTCTTTTAAATAAATTTTAGCTTTTTGACTAAAAAATAAAATTCTATAAAAATTTTAAATGAAACAGTTAATATTTCGTCCAACCATTCATTCCAGCCTTCAATTAAAAGACTAATGATTATG\n-+\n-<<BBBBFFFFFFFB<BFFFFFFFFFFFFF/B/FFFFFF/B<BFBFFFFFFFFFFFFFFFB/</FFB/FFFFFFFFFFFFBFFFBFFFF/BFFFBF//B<FFFBBFFF<<BFFFBFFFF/BBFFFB\n-@HISEQ:262:CA81LANXX:2:1101:3596:2043\n-AGGGTCTTCTCGTCTTTTAAATAAATTTTAGCTTTTTGACTAAAAAATAAAATTCTATAAAAATTTTAAATGAAACAGTTAATATTTCGTCCAACCATTCATTCCAGCCTTCAATTAAAAGACTA\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFBFFF/F/FFFBFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFB<FFFFFFFFFBFB/FFFF\n-@HISEQ:262:CA81LANXX:2:1101:4635:2158\n-TCGTCTTTTAAATAAATTTTAGCTTTTTGACTAAAAAATAAAATTCTATAAAAATTTTAAATGAAACAGTTAATATTTCGTCCAACCATTCATTCCAGCCTTCAATTAAAAGACTAATGATTATG\n-+\n-BBBBBFFFFFFFFF<FFFFFFFFFFFFFFBFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB/BFFFFFFFFFFFFF<FF/BFF\n-@HISEQ:262:CA81LANXX:2:1101:4872:2211\n-GCCGATTCTTTTTAAAGTTACAGATGGTTCATTAATTTCATCTAATAAATAAAGTAAACGTAAAGAAGGAAGAGCAATAAATAGTAAAATAATTGCTGGTAAAATAGTTCAAATTATTTCAATAA\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFF\n-@HISEQ:262:CA81LANXX:2:1101:5610:2019\n-GTCCTTTCGTACTAAAATATCATAATTTTTTAAAGATAGAAACCAACCTGGCTTACACCGGTTTGAACTCAGATCATGTAAGAATTTAAAAGTCGAACAGACTTAAAATTTGAACGGCTACACCC\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n-@HISEQ:262:CA81LANXX:2:1101:6566:2127\n-CTAACCAAGAAGTTCTTAAGATAATATTAAATCGAATTAATAAATATACACCAGCTGTAACTAATGTAGAAGAATGAACTAAAGCAGAAACAGGTGTAGGAGCAGCTATAGCTGCAGGTAACCAA\n-+\n-BBBBBFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFBFFFFFFFFFFFFFFFBFFFFFFFFF\n-@HISEQ:262:CA81LANXX:2:1101:6892:2032\n-ACCGTCAACTTTTACTCCTAAAGCAGGTACTGTTCAAGAATGAATAACATCAGCAGCTGTTACTAAAATTCGAATTTGTGAGTTTATGGGTAAAACTACTCGGTTATCAACATCTAATAATCGAA\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFF\n-@HISEQ:262:CA81LANXX:2:1101:7493:2161\n-GTCCAACCATTCATTCCAGCCTTCAATTAAAAGACTAATGATTATGCTACCTTTGCACAGTCAAAATACTGCGGCCATTTAAAATTTTCAGTGGGCAGGTTAGACTTTATATATAATTCAAAAAG\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF\n-@HISEQ:262:CA81LANXX:2:1101:7572:2014\n-CTAAAATTGAAGAAATTCCTGCTAAATGTAGAGAAAAAATAGCTAAATCAACTGAAGCTCCACCATGAGCAATTCCAGCGGATAGAGGTGGATAAACAGTTCATCCTGTCCCAGCTCCATTTTCA\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFBBBF<F/<BFFFFFFFFFFFB\n-@HISEQ:262:CA81LANXX:2:1101:9943:2018\n-GCTGCTTCAAAACCAAAATGATGATTTTTTGAGAAGTGATTATTTAAATGTCGTAGTAAACATACTAATAAAAAAGTTGTTCCGATTAATACATGAATTCCGTGAAATCCTGTTGCTATAAAAAA\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFF\n-@HISEQ:262:CA81LANXX:2:1101:9821:2111\n-GTCCTTTCGTACTAAAATATCATAATTTTTTAAAGATAGAAACCAACCTGGCTTACACCGGTTTGAACTCAGATCATGTAAGAATTTAAA'..b'\n-@HISEQ:262:CA81LANXX:2:1101:13847:33438\n-GTCCAACCATTCATTCCAGCCTTCAATTAAAAGACTAATGATTATGCTACCTTTGCACAGTCAAAATACTGCGGCCATTTAAAATTTTCAGTGGGCAGGTTAGACTTTATATATAATTCAAAAAG\n-+\n-BBBBBBFB<FFFFBFFFBFBFFFFF<BFFFFBFFF/<F<F<FFF/FFF<FBFFFBFFF<FFFFF/</<FB/<B/<///<F/BFFFFFFFFFFF<B</BFFF/7BF<FFFFFF<BFFFBF/7/7B7\n-@HISEQ:262:CA81LANXX:2:1101:15264:33251\n-TAAGAATTTAAAAGTCGAACAGACTTAAAATTTGAACGGCTACACCCAAAATTATATCTTAATCCAACATCGAGGTCGCAATCTTTTTTATCGATATGAACTCTCCAAAAAAATTACGCTGTTAT\n-+\n-BBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n-@HISEQ:262:CA81LANXX:2:1101:16362:33356\n-GTCTTTTAAATAAATTTTAGCTTTTTGACTAAAAAATAAAATTCTATAAAAATTTTAAATGAAACAGTTAATATTTCGTCCAACCATTCATTCCAGCCTTCAATTAAAAGACTAATGATTATGCT\n-+\n-BBBBBFFFFFFFFFBFFFFFFFFFFFBFFBF/FBFFFBFFF/FFFFFFFFFFFFFFFFFBBFBFFFFFFFFFFFFFFB<<FFFFFFFFFBFF/BFFBBFFFFFFFF//F/FBFB/F7F<FFF/BF\n-@HISEQ:262:CA81LANXX:2:1115:5809:65592 1:N:0:CGTACG\n-CCCTATTCATAAATTTATTATATAATTAAATCTTAAAAAGTATTTTTTTTTTAAAAAAAAATTATTTATTAAATTATACTTAATAAACTATTTTTATAATAAATTATTTTATGAATAAAATTATT\n-+\n-BBBBBFFFFFFFFFFFFFFBFFFF/F<FFFFFFFFFB/FFFFFFFFFFFFFFFFFFFFFF<B<<BFFFFFFFFFF<FFFFFFF/<F<F///BFFF//FBFFF7BF<FFFF//<</<FFFB77/BF\n-@HISEQ:262:CA81LANXX:2:1215:17203:64615 1:N:0:CGTACG\n-CCCTATTCATAAATTTATTATATAATTAAATCTTAAAAAGTATTTTTTTTTTAAAAAAAAATTATTTATTAAATTATACTTAATAAACTATTTTTATAATAAATTATTTTATGAATAAAATTATT\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBF/FFBFFFFFFFBF\n-@HISEQ:262:CA81LANXX:2:1215:14166:68404 1:N:0:CGTACG\n-CCCCCTATTCATAAATTTATTATATAATTAAATCTTAAAAAGTATTTTTTTTTAAAAAAAAATTATTTATTTAATTTTTATTAATAAAATATTTTTTTAATTAATTATTTTATGAATAAAATTTT\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFBBBFFFBFFFFBBFFFFFFFFFFBBF/BFFFFFFF/B#############################################################\n-@HISEQ:262:CA81LANXX:2:1301:20643:41959 1:N:0:CGTACG\n-CATATATATAGATATATATATATATATATCAGGGATCGTGGCGGAGCGAGGTGGAAGGGGTGGGGGGGGAGAGGATAACCAGGGGGCGGGGGGGGAGGTTTGGGAGTCATAGAAAATTTGGGATA\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFF##################################################################################################\n-@HISEQ:262:CA81LANXX:2:1310:4460:5881 1:N:0:CGTACG\n-CCCTATTCATAAATTTATTATATAATTAAATCTTAAAAAGTATTTTTTTTTTAAAAAAAAATTATTTATTAAATTATACTTAATAAACTATTTTTATAATAAATTATTTTATGAATAAAATTATT\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFBF7<77<FFFFFFFBFFFFFFFFBBFBFFFFFFFFFFFBF<F<FFFFFFB7BF\n-@HISEQ:262:CA81LANXX:2:1314:2827:42596 1:N:0:CGTACG\n-CCCCCTATTCATAAATTTATTATATAATTAAATCTTAAAAAGTATTTTTTTTTTAAAAAAAAATTATTTATTAAATTATACTTAATAAACTATTTTTATAATAAATTATTTTATGAATAAAATTA\n-+\n-BBBBBFFFFFBFFFFFFFFF<FFFFBFFFFFBBFF/BB/FFFF/FFFBFFBBFFFFFFFFF<</<BB//</B7FF/<//<<<BBBFFBFF/BBFFFBFFFFFB/BFBFFB<F/7BB/FF/7FFFB\n-@HISEQ:262:CA81LANXX:2:2103:4469:38754 1:N:0:CGTACG\n-ATTTTTTTTTTTTTTTTTTTTTTTTATTAAAATAATTTATTGTTTTGTGTTTTTTTTTTTTTTTTTTATTTTTAAATTTATATTAATTATTAATTTATATAAAATATAATATAAAAAAATTATAA\n-+\n-BBBBBFFFBFFFFFFFFBF<BB#######################################################################################################\n-@HISEQ:262:CA81LANXX:2:2108:19262:60414 1:N:0:CGTACG\n-CCCTATTCATAAATTTATTATATAATTAAATCTTAAAAAGTATTTTTTTTTTAAAAAAAAATTATTTATTAAGTTATACTTAATAAACTATTTTTATAATAAATTATTTTATGAATAAAATTATT\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<<<FFFFBFFFFFFFFFFFFFFFFFBFFFFBFFFFFFFFF<B<BBFFFBFFFF\n-@HISEQ:262:CA81LANXX:2:2110:11698:64422 1:N:0:CGTACG\n-ATTTTTTTTTTTTTTTTTTTTTTTAATTTTAAAAAATTTTTTTTGTTTTTTTTTTTTTTTTTTTTAATTTTAAATTTATATTTAAATTTTTTTTTTATAAAAATTAAAAAAAAAAAAATAAAAAG\n-+\n-BBBBBFFFFFFFFFFFFFFFFF#######################################################################################################\n-@HISEQ:262:CA81LANXX:2:2110:8000:79787 1:N:0:CGTACG\n-CCTATTCATAAATTTATTATATAATTAAATCTTAAAAAGTAGTTTTTTTTTAAAAAAAAATTATTTATTAAATTATACTTAATAAACTATTTTTATAATAAATTATTTTATGAATAAAATTATTT\n-+\n-BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFF/<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFBFFFFFFFFFFFFFFFFFFF/FBFFFBFFFFFFF\n' |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/Samp_L.fastq --- a/test-data/Samp_L.fastq Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,10000 +0,0 @@\n-@ERR1044075.680 HWI-ST790:248:H0G15ADXX:1:1101:10892:2723/1\n-GCTCCTAAAATTGAAGAAATTCCTGCTAAATGTAGAGAAAAAATAGCTAAA\n-+\n-CCCFFFFFHHDHHJIGGIIIGIIJJJGIJIGIAEFFHJIIIIGEEIICFHI\n-@ERR1044075.759 HWI-ST790:248:H0G15ADXX:1:1101:15792:2653/1\n-GAAAATAATCATTCACAGACTACCCAAGGATTATTTTTTACAGTTTTACTA\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJ\n-@ERR1044075.753 HWI-ST790:248:H0G15ADXX:1:1101:15644:2508/1\n-CTTATCTTACCTTAATAATAAAAGCGACGGGCGATGTGTACATATTTTAGA\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJIJIJJFHHIIJIJJJJJIHH\n-@ERR1044075.814 HWI-ST790:248:H0G15ADXX:1:1101:19529:2745/1\n-TGAGTCTGCAATAGTAAATGGAGCTTCAATATATTCATAAGCTTGAAGAAT\n-+\n-?@?DDDFFHHGHHJHHIGJIEDBGGIHIJGIFCHEHI>GAEGIIGIEDHEH\n-@ERR1044075.946 HWI-ST790:248:H0G15ADXX:1:1101:8484:2908/1\n-CATACACAACATATATTTGCTCATTTAGTTCCTCAAGGAACACCCGCTATT\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJJJJIIJJJJJJJJIJJJIJJJGIIJJJ\n-@ERR1044075.818 HWI-ST790:248:H0G15ADXX:1:1101:19811:2591/1\n-ATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGAGGTTTTTC\n-+\n-@@CFFDD?FHDDDC@FHEGGG9CGDEGGGFHEI)09*?B<*7?########\n-@ERR1044075.978 HWI-ST790:248:H0G15ADXX:1:1101:10873:2966/1\n-CTCATCAGTAAATTGTGATATATAAAAATAATCAAACTACATCGACAAAAT\n-+\n-CCCFFFFFHHHHHJJHIJJJJJJJJJJJJJJJJJJJJIJJJIJJJJJJJJJ\n-@ERR1044075.998 HWI-ST790:248:H0G15ADXX:1:1101:12703:2936/1\n-TTTTCATTTAGTGGATTATAGTCCATGACCATTAACAGGAGCTATCGGAGC\n-+\n-BCCFDFFFHHHDHIIIJJJIJGHJJJJFJIFIIJIJJJIGGHJIIGIIIJI\n-@ERR1044075.1137 HWI-ST790:248:H0G15ADXX:1:1101:1525:3138/1\n-TTGGAAGATTAGTAATATTAGCTGCTATAACTAAAAGAGCTCAGATTCCTT\n-+\n-BB@DDDEBFHHHDGIJJJJIJIJIJHHIJGGJJJJIGDFGGHEGCGHJGIJ\n-@ERR1044075.1446 HWI-ST790:248:H0G15ADXX:1:1101:1567:3357/1\n-TAATCCAGCTATAAATATTGTTAATCCAGATAATAATAATATTAATTGTCC\n-+\n-@@CFFDFFHHGHHIBFGHIFC>HHHIHCFGHC>FH@HG<DFHGHEGHC?CG\n-@ERR1044075.1652 HWI-ST790:248:H0G15ADXX:1:1101:16002:3269/1\n-CTTGAGCCCACCATAGACTTATAGAAAATAATCATTCACAGACTACTCAAG\n-+\n-BCCFFFFFHHHHHJIJIJJJJJJIJJJJGIJGIJHIIJIJHGGIIJEGIII\n-@ERR1044075.2019 HWI-ST790:248:H0G15ADXX:1:1101:20598:3595/1\n-CTAAAATTGAAGAAATTCCTGCTAAATGTAGAGAAAAAATAGCTAAATCAA\n-+\n-@@@DDDE>DHBHHJJJIIJJGIJGIGHGGHHGCHGGIIGFGHIEGHGHIEC\n-@ERR1044075.2025 HWI-ST790:248:H0G15ADXX:1:1101:1366:3788/1\n-CTACCTTTGCACAGTCAAAATACTGCGGCCATTTAAAATTTTCAGTGGGCA\n-+\n-@@CDDDFFHHBF<GG<FHGIJFIJJJIGJFIGHIJJJGIIIEDDBDHIIC?\n-@ERR1044075.2112 HWI-ST790:248:H0G15ADXX:1:1101:7863:3843/1\n-CCGTGGGAATGCTATATCAGGAGCACCTAATATTAAAGGCACTAATCAATT\n-+\n-CCCFFFFFHHHHHJJIJIIIHIIIIJIJJIJJJJJJJJJHIIIGHHIIHJJ\n-@ERR1044075.2117 HWI-ST790:248:H0G15ADXX:1:1101:8122:3811/1\n-TAAGATTTTGACTTCTACCTCCTGCTCTTTCTTTACTATTAGTAAGTAGAA\n-+\n-BBBFDFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJFIGIGIEFFGIBGEGG\n-@ERR1044075.2555 HWI-ST790:248:H0G15ADXX:1:1101:1876:4399/1\n-CTGTTACTAAAATTCGAATTTGTGAGTTTATGGGTAAAACTACTCGGTTAT\n-+\n-CCCFFFFFHHHHHJJJJJJJJJIJHIJIJHHJJICHIIIIHIGIGHGJIGI\n-@ERR1044075.3073 HWI-ST790:248:H0G15ADXX:1:1101:1378:4822/1\n-TTTATTTGTTTGATCAGTAGTTATTACTGCTTTATTATTATTATTATCACT\n-+\n-BB@ADDEFFHHHHIGIIJGIIIJJJIIIGGIJGHGIAHG@FI<EF?D?FGH\n-@ERR1044075.3103 HWI-ST790:248:H0G15ADXX:1:1101:3753:4970/1\n-TAGATACTCGAGCTTATTTTACCTCAGCTACTATAATTATTGCAGTTCCTA\n-+\n-@BCFFFFFHHFHHJJIJJJJJJIJIJJHIIIIGIJJJIGIIHIHGIJJDCA\n-@ERR1044075.3115 HWI-ST790:248:H0G15ADXX:1:1101:4946:4934/1\n-GCTGAGGTAAAATAAGCTCGAGTATCTACATCTATTCCAACGGTAAATATA\n-+\n-CCCFFFFDFHHHHJJJJIJJJJHFHIJJJJJIJIJJJIIIGHJFHIJIHGH\n-@ERR1044075.3167 HWI-ST790:248:H0G15ADXX:1:1101:8133:4808/1\n-CTGGGTCAAAAAATGATGTATTTAAATTTCGATCTGTTAATAATATAGTAA\n-+\n-CCCFFDFFHHHHHJJIJJIJJJJJJJJJJJJJJJJJJJJIJJJJIJIIFGI\n-@ERR1044075.3206 HWI-ST790:248:H0G15ADXX:1:1101:9789:4942/1\n-TCATCATATATTTACCGTTGGAATAGATGTAGATACTCGAGCTTATTTTAC\n-+\n-8?<:DDBD<D?A:A<A)CC7B9AFEFE<A2+22@9:CE7D?DDB*99?D##\n-@ERR1044075.3251 HWI-ST790:248:H0G15ADXX:1:1101:12710:4758/1\n-TTTAGCTAATTCATCAGTAGATATTATTTTACATGATACTTATTATGTAGT\n-+\n-BCCFFFFFHHHHHJJJJGHJIJJJJJJJJJIIGJJGIIIIJGHIIJJFHEH\n-@ERR1044075.3552 HWI-ST790:248:H0G15ADXX:1:1101:10536:5030/1\n-CTCTTTCTTTACTATTAGTAAGTAGAATAGTTGAAAATGGAGCTGGGACAG\n-+\n-CCCFFFFFHHHHHIJJJJHIJJIHJIJJJJJJJJJJJIIIIJIIJJIIJJJ\n-@ERR1044075.3658 HWI-ST790:248:H0G15ADXX:1:1101:18523:5017/1\n-TCT'..b'JIJGG\n-@ERR1044075.659985 HWI-ST790:248:H0G15ADXX:1:1106:11631:62123/1\n-AAAGAATCGGCCATCAATGATATTGAAGTTACGAATATTCAGATTTTAATA\n-+\n-<<@DDDDDBF1CDC:C?,C9AAC42?C@H@AGG1?DFGEFF@HGGGCEHE?\n-@ERR1044075.660170 HWI-ST790:248:H0G15ADXX:1:1106:7215:62363/1\n-TGGAAGTGATAATAATAATAATAAAGCAGTAATAACTACTGATCAAACAAA\n-+\n-BBCDDFDDHHHHHIJJJIIJJIIJJJIJJIJJJJJIIIJJIIJGIJJGJJJ\n-@ERR1044075.660255 HWI-ST790:248:H0G15ADXX:1:1106:12160:62309/1\n-CAGCTGTTACTAAAATTCGAATTTGTGAGTTTATGGGTAAAACTACTCGGT\n-+\n-CCCFFF=DFHFGHJIGHGIGEHIHFCEFGGHJHIJJJ:DGGIIGGEHGCHD\n-@ERR1044075.660247 HWI-ST790:248:H0G15ADXX:1:1106:11554:62387/1\n-CTTGAGCCCACCATAGACTTATAGAAAATAATCATTCACAGACTACTCAAG\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJJJJJIIJJJIIJIJJJJJJJJJIJJJJ\n-@ERR1044075.660686 HWI-ST790:248:H0G15ADXX:1:1106:8134:62985/1\n-TATCATTCAATTGATGAATTTAGTTGAATTGGGTAAATTACTTGTCGTTGT\n-+\n-CCBFFFFFHHHHHJJJJJJJJIIJJJJJJJIJJCFGHJJIIJJJHIGHIGG\n-@ERR1044075.661147 HWI-ST790:248:H0G15ADXX:1:1106:8314:63385/1\n-AATTGGAAGATTAGTAATATTAGCTGCTATAACTAAAAGAGCTCAGATTCC\n-+\n-@@CFFDEDHHFFHIACGIJGIJIGIIGGHGGGHGIIJGHHGIJJIIJIJHH\n-@ERR1044075.661472 HWI-ST790:248:H0G15ADXX:1:1106:13982:63648/1\n-TACAAATCATAAAGATATCGGAACTTTATATTTTATTTTTGGAGCTTGAGC\n-+\n-CCCFFFFFHHHHHJIJJJJJJJJJJJJJIIJJJJIJJJJJIIJJIJJGIJI\n-@ERR1044075.661879 HWI-ST790:248:H0G15ADXX:1:1106:7696:64091/1\n-TTCATGTAAAGTAGCTAATCAACTAAAAATTTTAATTCCAGTAGGAACTGC\n-+\n-@BBDFEBDFHHHHIIIJJIHIJIJGIJJJJIJIJGIIIIJIEFHHIJJIII\n-@ERR1044075.662140 HWI-ST790:248:H0G15ADXX:1:1106:8516:64305/1\n-CAGCAATTATATTAGCAGTTAATCGAACAGCTAATGTTCCAGGTCGAATAA\n-+\n-@@CFFFFFFHFHHJJBEHGCGHGCHIJEHG>FGIGHEDHHJHI??F@BDHH\n-@ERR1044075.662813 HWI-ST790:248:H0G15ADXX:1:1106:21170:64761/1\n-CCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACAT\n-+\n-?@BF?DEAFFDDFIJJJIJIGJIIIJIHHJGHHIJJJIJJIIGIJCHDFDD\n-@ERR1044075.663073 HWI-ST790:248:H0G15ADXX:1:1106:5648:65498/1\n-GATAAACTTCTGTGAAAAAAAGCTCAAAAAAATCTCACAAAAAATAAAAAT\n-+\n-?@<DDD>DF4CFACFBEEGH:G)@:?DGGGG<F9B?F4C>=@C@CCEGH##\n-@ERR1044075.663162 HWI-ST790:248:H0G15ADXX:1:1106:11759:65389/1\n-CAGAATATCTATGTTCAGCTGGTGGAGTATTTTGGTATCATTCAATTGATG\n-+\n-CCCFFFFFHHHHHIJJJJJJJJHHIHJFGHIJJJJFHIIJIJIJIIJJIJJ\n-@ERR1044075.663390 HWI-ST790:248:H0G15ADXX:1:1106:10400:65584/1\n-CAACCATTCATTCCAGCCTTCAATTAAAAGACTAATGATTATGCTACCTTT\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJIJJJJIJGIJJ\n-@ERR1044075.663400 HWI-ST790:248:H0G15ADXX:1:1106:11192:65654/1\n-ATTGAAGCTCCATTTACTATTGCAGACTCAATTTATGGATCAACATTTTTT\n-+\n-@CCFFFFBHHHHGJJJJJJIIIIIEGIIIFHIIHFIIJGHGIIIJIJJJJJ\n-@ERR1044075.664278 HWI-ST790:248:H0G15ADXX:1:1106:20222:66346/1\n-CTAAAATTCGAATTTGTGAGTTTATGGGTAAAACTACTCGGTTATCAACAT\n-+\n-@@@FFFFFHGDHHIGIIIIGHHGIGIJJAFGHEGHIIEIJJEHIIJIJIJJ\n-@ERR1044075.664837 HWI-ST790:248:H0G15ADXX:1:1106:12794:67053/1\n-CATATATTTGCTCATTTAGTTCCTCAAGGAACACCCGCTATTCTTATACCT\n-+\n-@@CFFDEFHHHHHJJJJJJIIJJJJJJJJJJJJJJJJJJJJJIJJIIIJII\n-@ERR1044075.665607 HWI-ST790:248:H0G15ADXX:1:1106:15165:67769/1\n-CTCGTGATACATCTCGTCATCATTGATATACAGTTAAAATAGTAATAATAT\n-+\n-@?@DFDFDHHHFHIJIDEFEHCHIEHIIHIHIJIGGGGGDHIGHGGII@GG\n-@ERR1044075.665680 HWI-ST790:248:H0G15ADXX:1:1106:19772:67837/1\n-GTTAAATAATAAATGATTAAAAAGTCATTTCATTATTATATTTATTGGAGT\n-+\n-@?@DDFFFHHDHHGFFGIJECF>BBHEIJJJIIGAHHIIJIGGIGIHGAFG\n-@ERR1044075.665714 HWI-ST790:248:H0G15ADXX:1:1106:6180:68224/1\n-ATTTCCTAAAAGAGTTAATAATAAATGTCCAGCAATTATATTAGCAGTTAA\n-+\n-4114422=:CBFCEEFEAHH@4FFHCH<CAEF+A@E9C9:C?C<:?BFD@4\n-@ERR1044075.665736 HWI-ST790:248:H0G15ADXX:1:1106:7267:68163/1\n-AGAGAACCAAAAGTTTCCTTTTTTCCTGATTCTTGTCTAATAATATGAGAA\n-+\n-?@BDDFFFHHHHHJIJJJJJJJJJJGJEHIJGIJGHIGGECHHHGGADDHI\n-@ERR1044075.665878 HWI-ST790:248:H0G15ADXX:1:1106:16309:68134/1\n-CATGACCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAG\n-+\n-CCCFFFFFHHGHHJJIGHJJJJJJJJIJJJIJJJIHIJIFHGEGIJ9BGII\n-@ERR1044075.666310 HWI-ST790:248:H0G15ADXX:1:1106:13497:68695/1\n-TAAAAAAACAAATCCTAAAGCTCATAAAATAGCTGGAGAATAAGAAAGTTG\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJIJJJJJIIJJIJJJJJJJHII\n-@ERR1044075.666724 HWI-ST790:248:H0G15ADXX:1:1106:8127:69208/1\n-GCTCAAGTTACAGTAACTCCTGAAGCTAATAAAATAGCTGTATTTAATAAA\n-+\n-CCCFFFFFHHGHHIIJHJJJJJJJJIJJJJJJJJIJJJJJHHIJJJIGIJI\n' |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/Samp_R.fastq --- a/test-data/Samp_R.fastq Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,10000 +0,0 @@\n-@ERR1044075.680 HWI-ST790:248:H0G15ADXX:1:1101:10892:2723/2\n-ATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGAAATTGATTA\n-+\n-@<??DDADFFFFFDG@<G<F@GE??C:CG>FE*??0?DGFI<B>FDE<FFB\n-@ERR1044075.759 HWI-ST790:248:H0G15ADXX:1:1101:15792:2653/2\n-TGCTGCTTCAAAACCAAAATGATGATTTTTTGAGAAGTGATTATTTAAATG\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJIJJJJJJJGIIIJFGHIJGIJJJJIII\n-@ERR1044075.753 HWI-ST790:248:H0G15ADXX:1:1101:15644:2508/2\n-GGAACCTGTTTTTTAATCGATAATCCACGATGGACCTTACTTAAATTTGTA\n-+\n-@@CFFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJJJIHI\n-@ERR1044075.814 HWI-ST790:248:H0G15ADXX:1:1101:19529:2745/2\n-ATTTAATCCATTTCAAATTCCTTTATTAAATACAGCTATTTTATTAGCTTC\n-+\n-;@<DDFFFHHHFDHIIJIGHIHEGHIIIJJIJIJICHJIJIGIGJIE@GGE\n-@ERR1044075.946 HWI-ST790:248:H0G15ADXX:1:1101:8484:2908/2\n-ATTATATTAGCAGTTAATCGAACAGCTAATGTTCCAGGTCGAATAATATTT\n-+\n-CCCFFFFFHHGHHJJJJJJJJJJJJJJJJJJIJJJJIJGII?BBFHGGIIJ\n-@ERR1044075.818 HWI-ST790:248:H0G15ADXX:1:1101:19811:2591/2\n-GAGTATTTTGGTATCATTCAATTGATGAATTTAGTTGAATTGGGTAAATTA\n-+\n-@@BDDFFFHHGGHJJJIJIJIJIGIIJIGIJJDEHEHEGHJGGG:CGDHIE\n-@ERR1044075.978 HWI-ST790:248:H0G15ADXX:1:1101:10873:2966/2\n-AATTCATGTATTAATCGGAACAACTTTTTTATTAGTATGGTTACTACGACA\n-+\n-CCCFFFFFHHHHHJJJJJIJIJJIJJJJJJJJJIIHIJJIJJJIIFJJJJI\n-@ERR1044075.998 HWI-ST790:248:H0G15ADXX:1:1101:12703:2936/2\n-ATGTTCCTTCTCGTGATACATCTCGTCATCATTGATATACAGTTAAAATAG\n-+\n-CCCFFFFFHHHGHJJJJJJJJJJJJIJJJIJJJIGIIJJJJJJJIJJIJII\n-@ERR1044075.1137 HWI-ST790:248:H0G15ADXX:1:1101:1525:3138/2\n-GATAATAATAATATTAATTGTCCTAACCAAGAAGTTCTTAAGATAATATTA\n-+\n-@BCFFFFFHHFHHHJJJIIGHHHIJJFIHHHGGGGGGIDHGGI@GFC>DDI\n-@ERR1044075.1446 HWI-ST790:248:H0G15ADXX:1:1101:1567:3357/2\n-TGCAGCTATAGCTGCTCCTACACCTGTTTCTGCTTTAGTTCATTCTTCTAC\n-+\n-@@CDDDDDFHHHFHIIIJJJGGGCGJCHIIAHGIIEHIEE@FIIBHGHEHC\n-@ERR1044075.1652 HWI-ST790:248:H0G15ADXX:1:1101:16002:3269/2\n-CCGATTAATACATGAATTCCGTGAAATCCTGTTGCTATAAAAAATGTTGAT\n-+\n-@@BDDFFFHHHHHIIIIIJJIGHGIIEIGIIHIIIJGIIJJJIJIIGIEHI\n-@ERR1044075.2019 HWI-ST790:248:H0G15ADXX:1:1101:20598:3595/2\n-CTGCTCTTTCTTTACTATTAGTAAGTAGAATAGTTGAAAATGGGGCTGGGA\n-+\n-:41A:ADBFFDFFFBE4A<,<<CFCAF>,3<<FE4+9A?:<?E):?:?A=F\n-@ERR1044075.2025 HWI-ST790:248:H0G15ADXX:1:1101:1366:3788/2\n-AATTTATATGAAAAGTTTAAATAAAGAATTCGGCAAAAATAATATTCGCCT\n-+\n-CCCFFFFDHFBHFGIHIIHGGHIGGGAAFHHHGHIGGGGGGEGEDH4?FEI\n-@ERR1044075.2112 HWI-ST790:248:H0G15ADXX:1:1101:7863:3843/2\n-TGGAGATGATCAAATTTATAATGTAATTGTAACTGCACATGCTTTTATTAT\n-+\n-?@BBDBDFHHHHGIJJIJJJHJGJJIJJJFIIIIJIGIIGIGGIJIEIIII\n-@ERR1044075.2117 HWI-ST790:248:H0G15ADXX:1:1101:8122:3811/2\n-CTAAAATTGAAGAAATTCCTGCTAAATGTAGAGAAAAAATAGCTAAATCAA\n-+\n-CCCFFFFFHHGHHJJJJJJJJJJJJJJJHIJIIJJJJJJJJJJJJJJGIIJ\n-@ERR1044075.2555 HWI-ST790:248:H0G15ADXX:1:1101:1876:4399/2\n-GTAACTTTAAAAAGAATCGGCCATCAATGATATTGAAGTTACGAATATTCA\n-+\n-BB@FFFFFHHHHHJJJJJJJJJJJJJJJIIIIIIBHIIHIIJIIIDHIJII\n-@ERR1044075.3073 HWI-ST790:248:H0G15ADXX:1:1101:1378:4822/2\n-CTCCCGCTGGGTCAAAAAATGATGTATTTAAATTTCGATCTGTTAATAATA\n-+\n-CC@FFFFFHHHFHIJJJJIJJIIJGHIIIJJGJJJHIHJGIGIJJIIJIIG\n-@ERR1044075.3103 HWI-ST790:248:H0G15ADXX:1:1101:3753:4970/2\n-CTCCTGTTAATCCTCCTACTGTAAATAAAAAAACAAATCCTAAAGCTCATA\n-+\n-CCCFFFFFHHHHHJJJJIIJIHIJIIJJJJJJIGIJIIJJIJJJJGGGGHI\n-@ERR1044075.3115 HWI-ST790:248:H0G15ADXX:1:1101:4946:4934/2\n-AAAAAAGGAAACTTTTGGTTCTCTAGGAATAATTTATGCTATATTAGCTAT\n-+\n-CCCFFFFFHHHHHJJJJJHJJJJIJJJIIIJJJJJJJJJIIGGIIIIIIJI\n-@ERR1044075.3167 HWI-ST790:248:H0G15ADXX:1:1101:8133:4808/2\n-TGGAGCTTCAGTTGATTTAGCTATTTTTTCTCTACATTTAGCAGGAATTTC\n-+\n-CCCFFFFFHHHFHIFIJJJJJJJJJJJJJJJJJJJIIJJJIJJJJJJJJJI\n-@ERR1044075.3206 HWI-ST790:248:H0G15ADXX:1:1101:9789:4942/2\n-CTGTAAATAAAAAAACAAATCCTAAAGCTCATAAAATAGCTGGAGAATAAG\n-+\n-@@<;DDDDFHDFFDG<BEHFFF@E?FF:?FEC>BBFBB9?BBGH8?;*=F4\n-@ERR1044075.3251 HWI-ST790:248:H0G15ADXX:1:1101:12710:4758/2\n-GAATAAAACCTGCTATAATAGCAAATACAGCTCCTATAGATAAAACATAAT\n-+\n-CCCFFFFFHHHHHJJJJJJJIJJJJJJJJJJIJJJJJJGIIJJJJIJIJJJ\n-@ERR1044075.3552 HWI-ST790:248:H0G15ADXX:1:1101:10536:5030/2\n-CTGCTAAATGTAGAGAAAAAATAGCTAAATCAACTGAAGCTCCACCATGAG\n-+\n-B@CFFFFFHHFHHJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJIJIIJ\n-@ERR1044075.3658 HWI-ST790:248:H0G15ADXX:1:1101:18523:5017/2\n-CTC'..b'IIJJH\n-@ERR1044075.659985 HWI-ST790:248:H0G15ADXX:1:1106:11631:62123/2\n-CCACAGATTTATGAACATTGACCATAAAATAAACCCGGTCGATTAATAAAA\n-+\n-:1++2<A+<7,C?A>=ACA7<7@AAA7C?A<BACBAA@A<A0=B<?B77=>\n-@ERR1044075.660170 HWI-ST790:248:H0G15ADXX:1:1106:7215:62363/2\n-TGAAAATGGAGCTGGGACAGGATGAACTGTTTATCCACCTCTATCCGCTGG\n-+\n-@CCFFFFFHHHHHJJJIJJJJGGJIJJJIIJJJJJJJJJJIJGJJJJJJII\n-@ERR1044075.660255 HWI-ST790:248:H0G15ADXX:1:1106:12160:62309/2\n-AAAGAATCGGCCATCAATGATATTGAAGTTACGAATATTCAGATTTTAATA\n-+\n-@@@FDDDDDAHFHGGIEIEF@HGIJJIIGJIIGHEHIBG:??BHGGGEBDI\n-@ERR1044075.660247 HWI-ST790:248:H0G15ADXX:1:1106:11554:62387/2\n-TGTTGCTATAAAAAATGTTGATCCATAAATTGAGTCTGCAATAGTAAATGG\n-+\n-@CBFFFFFHHHHHJJJJIIJJJJJJJJJIJJJGGHIJJIJJGEGGIJJIIJ\n-@ERR1044075.660686 HWI-ST790:248:H0G15ADXX:1:1106:8134:62985/2\n-CTGGAATACCTCGACGTTATTCAGATTACCCAGATGCTTACACAACATGAA\n-+\n-@CCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJJIJJJJJJJJJJJIJJJJJ\n-@ERR1044075.661147 HWI-ST790:248:H0G15ADXX:1:1106:8314:63385/2\n-AGAAGAATGAACTAAAGCAGAAACAGGTGTAGGAGCAGCTATAGCTGCAGG\n-+\n-@@@FFFFDHHGHGJIJJIIIJIIIJGI<AFEGHHHIIHGDGEGII@GEHIJ\n-@ERR1044075.661472 HWI-ST790:248:H0G15ADXX:1:1106:13982:63648/2\n-CTCCAATTAATGCTCCAGGATGTCCTAATTCAGCTCGAATTAAAATTCTTA\n-+\n-BCCFFFFFHHHHHJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJIJJIJJJ\n-@ERR1044075.661879 HWI-ST790:248:H0G15ADXX:1:1106:7696:64091/2\n-GATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATGTAGATA\n-+\n-CCCFFFFFHHHHHJJJJJJIIJIJHJJJJHJIJIIJJGHJIG@DHDDHDGH\n-@ERR1044075.662140 HWI-ST790:248:H0G15ADXX:1:1106:8516:64305/2\n-TATGATTATGTTTTATATTATATGGATGAATTAATCATACACAACATATAT\n-+\n-@@@FDDFFHGDHHJJIEIJGHEIIJIJIJIJGHEHGIFHIACGIGAGGFDI\n-@ERR1044075.662813 HWI-ST790:248:H0G15ADXX:1:1106:21170:64761/2\n-CTTTAATTCCTTATTCATCTTTTGCTCATATAGGAATTTTTCTGTCAGGAC\n-+\n-@@@FFFFD,2AC?GHBFIEGIE<3:<FEHGEGC+?E3C*@CE**:?DC??D\n-@ERR1044075.663073 HWI-ST790:248:H0G15ADXX:1:1106:5648:65498/2\n-TTTGTATTAGGTAATATTATTACTATTTTAACTGTATATCAATGATGACGA\n-+\n-@@BFFFFFHHHCFHIJJJJJJJJIJJJJJJJIJJHIJIJJJIJIEHDIIJI\n-@ERR1044075.663162 HWI-ST790:248:H0G15ADXX:1:1106:11759:65389/2\n-ATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGA\n-+\n-CCCFFFFEHHHHHJJJJJJJJJJJJJJJJJJIJJJJJJJJJGIJJIIJJJA\n-@ERR1044075.663390 HWI-ST790:248:H0G15ADXX:1:1106:10400:65584/2\n-ATTCGCCTGTTTAACAAAAACATGTCTTTTTGAATTATATATAAAGTCTAA\n-+\n-CCCFFFFFHHGHHJJJJJJJIJJJJJJJJJJJJIJIJJIJIIJJJHIHHIJ\n-@ERR1044075.663400 HWI-ST790:248:H0G15ADXX:1:1106:11192:65654/2\n-CCTCATCAGTAAATTGTGATATATAAAAATAATCAAACTACATCGACAAAA\n-+\n-C@CFFFDEHFFHHIIJFHHHIIIJJGJHGGHHIFHGIGEGFEDDGCFGIHF\n-@ERR1044075.664278 HWI-ST790:248:H0G15ADXX:1:1106:20222:66346/2\n-AATTATTTTACTATTTATTGCTCTTCCTTCTTTACGTTTACTTTATTTATT\n-+\n-<@@FFFFFHGFGFGHIJEHHEGEHECHGHEHGIGEHHHIDHIHIGIIJHIG\n-@ERR1044075.664837 HWI-ST790:248:H0G15ADXX:1:1106:12794:67053/2\n-ATTTCCTAAAAGAGTTAATAATAAATGTCCAGCAATTATATTAGCAGTTAA\n-+\n-CCCFFFFFHHHHGJJIJJJJIIJIJJJHGGGJIJIJJJIGJJJJJIIIIHI\n-@ERR1044075.665607 HWI-ST790:248:H0G15ADXX:1:1106:15165:67769/2\n-TTTTCATTTAGTGGATTATAGTCCATGACCATTAACAGGAGCTATCGGAGC\n-+\n-@@CFFFFFHHHCFHHIIIJJJJIJJIJJJJIJJJIIJJIIIIJIJGIJIJJ\n-@ERR1044075.665680 HWI-ST790:248:H0G15ADXX:1:1106:19772:67837/2\n-CATCTGGGTAATCTGAATAACGTCGAGGTATTCCAGCCAATCCTAAAAAAT\n-+\n-@C@FFFFFDHHHFIIHGFHIIIFHIHJJ:EGIJIGHFHIHJIICGIGHIIJ\n-@ERR1044075.665714 HWI-ST790:248:H0G15ADXX:1:1106:6180:68224/2\n-GGAACACCCGCTATTCTTATACCTTTTATAGTATGTATTGAAACTATTAGA\n-+\n-CCCFFFFFHHHHHJJJJJIIJIJJJJJJJJJIIIIFHIIDHHHIIIJIJJJ\n-@ERR1044075.665736 HWI-ST790:248:H0G15ADXX:1:1106:7267:68163/2\n-ATTTTATACCAACATTTATTTTGATTTTTTGGTCATCCTGAAGTTTATATT\n-+\n-CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJGHIIJIJIJIJJJIHGAGI\n-@ERR1044075.665878 HWI-ST790:248:H0G15ADXX:1:1106:16309:68134/2\n-CGTGATACATCTCGTCATCATTGATATACAGTTAAAATAGTAATAATATTA\n-+\n-B@@DFFFFHHHGHJGIIIJJHHIJIIJJJIIIIJJJIIJIDEHGIJJIGJJ\n-@ERR1044075.666310 HWI-ST790:248:H0G15ADXX:1:1106:13497:68695/2\n-CTCATATTATTAGACAAGAATCAGGAAAAAAGGAAACTTTTGGTTCTCTAG\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJIIIIJJJ\n-@ERR1044075.666724 HWI-ST790:248:H0G15ADXX:1:1106:8127:69208/2\n-CATACTTATGCAGTAACTATTGGTTTACGATGAGGAATAATTCTATTTATT\n-+\n-CCCFFFFFHHHHHJJJJJJJJJJHJJJJJIJIHIJIJIJIIJ<FFIIIGIJ\n' |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/Samp_class_fraction_counts.tabular --- a/test-data/Samp_class_fraction_counts.tabular Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -Low_complexity 0.0 -Simple_repeat 98.0 -rRNA 772.0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/Samp_family_fraction_counts.tabular --- a/test-data/Samp_family_fraction_counts.tabular Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -Low_complexity 0.0 -Simple_repeat 98.0 -rRNA 772.0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/Samp_fraction_counts.tabular --- a/test-data/Samp_fraction_counts.tabular Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -A-rich Low_complexity Low_complexity 0 -LSU-rRNA_Cel rRNA rRNA 772 -_ATA_n Simple_repeat Simple_repeat 0 -_ATTTAT_n Simple_repeat Simple_repeat 0 -_ATT_n Simple_repeat Simple_repeat 9 -_AT_n Simple_repeat Simple_repeat 0 -_CTAATT_n Simple_repeat Simple_repeat 7 -_TAT_n Simple_repeat Simple_repeat 0 -_TA_n Simple_repeat Simple_repeat 0 -_TTA_n Simple_repeat Simple_repeat 82 -_T_n Simple_repeat Simple_repeat 0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/aligned_353.tab --- a/test-data/aligned_353.tab Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -# Total reads aligned to repeated sequences -15862067 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/aligned_354.tab --- a/test-data/aligned_354.tab Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -# Total reads aligned to repeated sequences -28421096 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/aligned_355.tab --- a/test-data/aligned_355.tab Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -# Total reads aligned to repeated sequences -10808170 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/aligned_356.tab --- a/test-data/aligned_356.tab Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -# Total reads aligned to repeated sequences -29256707 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/aligned_reads.tab --- a/test-data/aligned_reads.tab Mon Mar 18 09:39:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -# Total reads aligned to repeated sequences - -2510 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/chrY-1-500k.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrY-1-500k.fa Tue Apr 02 21:16:37 2024 +0000 |
| b |
| b"@@ -0,0 +1,10001 @@\n+>chrY range=chrY:1-500000 5'pad=0 3'pad=0 strand=+ repeatMasking=none\n+GCGTTGTGAGCAACGACACTGAAAGCAACAATAATATTGTTAATTACTGC\n+TCAAAACTATAACACATTTAATCACTTACACAATTTACACACGCTTCCTG\n+CCTAGGAGTTGTGGGACCAGCTACCGATAATGCCAACAATACCGGGAAAC\n+GCGTCGCGGGACACCGATAACAATTTGGCGGTTAAAATGCTAGAACATCG\n+AGTACCAGACATGTTTTTCCTGCCGATATATCGAAGCCCAATAGCCCGCC\n+AACGCTCAAAACATAAATCGGAGTGTGAGACCAGATACCGAAGCCGTTAA\n+AAGCTTCGCGGTATATCGATAACAATTTGGCGGTAAAAATATTAGAACAT\n+CGAGTACCAACCATGTTTTTTTTTTCCTTCCGATTAATCGAAGTCAAACA\n+GCCCGCCAACGCTCCAAATTTAAATCGGAGTGTGAGACCAGCTACCGATG\n+CCGGTAAAAGCTTCGCGGGATATCGATAACAATCAGGTGGTTAAAAATAC\n+TATAACATCGAGTACCAGCCGTGTTTTTCCTGTCGATTTATCGAAGTCCA\n+ACAGCCCGCCTTCGCTCCGAACACAAATCGACAAGTCAGTAGCTTTTTTA\n+ACCCGGCAGTGGCGCCTGTGCAGCAGCTATTTAAAGTGAAAAACACGAAA\n+CGCAACAACAAAATGGACGGCCATAATGGAGACATAAATGAAGGATGGGC\n+AACAGTACTATCTATCTCGTCGGATGATAGTAACCAACTTTCGTCGCCGG\n+CGTCATTATAGTCTCATCGCTGGACACCACGCCAACGCCTGTCTAATGCA\n+AATCAACTTACATATTACTCTAAAATCTACTTATAACTGTCCCCTCTAAT\n+GATAAGCAATTTTTATGTTTACTTTAAACTTAAACCGATACCTTAAACTA\n+TGGCGCGCAAAATGACTACCAAGAAATCTAAAACTGTAAATTGTTGCAAA\n+CTATTTCTCCTAGTAATGTTAAATTTAAATGCGCGCATAATCGCAGCCAA\n+GTTAACCAAAAATGTCTCTCGTAAATGTAATTCCTAAATTAACACTTGTA\n+ACTAAGCGCGTATAAATACCGCAAATCCAAAAATGTAAATATGCCATAAA\n+TTGTTACTATATATTTTTTATAAAAAAATCAGAGTACAATAAAAATGCCA\n+GCGTCTATTAGGCGTTGAAAATTTAAAAAAAAAAAAAAAAAACTGAACTC\n+CCCACCCTGCTGAGACTAGAGGAAGAGGAGGCAGAGCTCAAAAGAATAAA\n+AAAACAGGAAGAGAGGGAAAGAAGGGAAAGGGAAAACCAAAAGTGGCCTC\n+CAGATAGGTGGTGTGAATTGGAAATAAACCGATATAATAAAAAATATAGA\n+AATGGCGATCTAACCAGGCAGGAAATTATAGAAAAATTCCGAGGGCAACC\n+ATTAAATGTACAACGAATAATCCTACCCGACTACGAAGGTGACTAAAAGT\n+AAATCAAAACAAACTAGGGTCGGAGCATAAAGCAGAAATANNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNN"..b'CAGATGAGGCTGACAAAAAATAGTACATTTTGAATTATTCAACAGA\n+CAACTAGACCGATTTATTTCCAGACATACCCAGTGGATGGCGTCTAAGAT\n+AACATTTCTTGTTAGTGATTTTAAAAACTGCAAGACACCACACCAAATGG\n+GACGCCAAAACTTATCTTACCAAAAAGCAGGAGAAAGATTAAAAAGGAAA\n+CTGGTGATCACGACAAAAGTCTTTTGATTCATGCAGCAACTGTTTTTGCT\n+AGAAAAGAATGTAATAGGGAACCTTTAAAAAAAACAGAATTTCCAAGCGA\n+ATCACCAGATGAAGCTCTAGCTTATCTCCTGAAAAACACGCTGACAAAAC\n+AGCAATATATAAGCACCAGGCTTTTAAATAAAAGCCATAACAGCGACATA\n+TATCCGCCATATAATGTAGTTATCGAAGGAAAATTACAGTGCCGACCAGA\n+AGTAATGGAAAACACTGCTCAAGTGCTATTAAGAAATCGCTTGGCTCATA\n+CAGCGCAAAGATTAATTAAGTTGCAATCTGATGTTTTCAAGCAATTTTCA\n+GATGTCTTTAAAATAAAATTAATTCGCAGCTATGGATTTGATGGGACAAC\n+TGGTAATAGTGCTAACAAGCAGAAATTTGAGACTGAAGCACTTGGCACAC\n+CAATTTCTGATCAATCTTTATTTGTAACTTCTGTAATACTTTATTTATGA\n+CAGTGGTCTACAGTTCTCGCTGCCATATGCCCGCAATAGTTCCTTGATAT\n+ATTGCGAATGGCCCAAAGTGATTTCTCCAAGGTCGCCATCTCGTTGCACC\n+TCCATGCCTAAGAACAAATGCAGTGGACCCTTGTCCGTGCACTCGAAAGA\n+CTCTGAAATCTTAGCTTTCAGATCTTCTCTTGACTGGCACGCTAGAATTA\n+AATCATCAACATATACTAAGATGAGCATCAGATTACCTTGACCACTTTGC\n+TGATAAAGACATGGTTCATGATTACAGGCCTTAAATCCCAAGTCTTTTAG\n+AACACCGTCGAGCTTGGAGTTCCACTCTCTGCCGGNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATAATCTTATTTTTG\n+AAGTATTTTATTTGATTTCAAATTATTACTAGTTTATTAATTTTTCCTTT\n+GTCGGAAAATTCAACGATTCTTTGATCCCAAGCTACATAAACTTCCTTCA\n+CCAATTACCGTTTCGGTTTTAAATACTTTTTGTTCACCAATGTATTTTTT\n+ATAATAGAATCTTTTAACGCAAGAGCATTTTTTCCCCAATCAAACACAAA\n+TTTCCTCATTTTCGGATTCTAAACCTTCTATTTCATAAAATAGATGTTTT\n+GTTTCAAATATTGTTAATATTTTATAATTGAGTATCCATAAACTGTAGAT\n+ACTCCTTTGAATGTGGGCAATTCTTTTTTATTTTCATAAATTCCCATTTA\n+GCAACTCTGGTGGGTTTAGAGAAAAGACTGTTTCTGAGATTGAACCGCTC\n+ATTGTTTTATTCGTTTCCTTGGCTTTTTCTTATGAGTATTTTTTTTATTT\n+ATGAGTAATGTCATTTTCAAGTTTACTTCGTTGTAGAATTCTGTAATACT\n+TAAACGTCCCTGTCCATGGTTGCATATTTCTGATTCGAGGATATTGAGTG\n+GTCGATTATCGTTACAAATAAAAATCAATTGCTTGTAAGTTTAAAACTTT\n+ACCATGGATAGTTAAAGCGTCATTACTGCCCCCATGATTTTATTACTTAG\n+AATTGTTCAAGCAATAAAATATTGTTCGCTTTTAATTTTATATTTCTTTT\n+CTGCTGCTTCTCTCCAGACTACATATTGGATCATTTCACCTGTGAACTTT\n+GGTAAAGATTTAACTACAGGTTAGTTTCGCATTTTATAGTTGGGTCAAGT\n+GCTCGGATTTTATAATCTTCCACTTTATTTCTGATAGCGTTTAACTGCCC\n+TTCTATCCCTTCAATTTGTCTGGTCACTTAACCCAATTGTACATTTATTA\n+ATCGGTTAACTAATTCCATTGTCAGATTTGTGGCGCTGGGTATCCCGCCC\n+GCAGAATAGGGTGGTGCTGAACCTCCATTTGCCATTGTTAAATTTAAATC\n+TTCAAAACTATTTAATAATCTTTTCAGATTGATTTCTTTAATTAATTGTT\n+AAAACTGATTTTGTAATGTTTAATTTTAAACTTCATAATATTCCCTGTAT\n+CTTCCTCTTATTTTAATGATTTCTTTTAATTCTTTCTTTCTTTCTTTTCT\n+TCAACCTCGGCGTGAAAATTTTCTTTAGAAACTTCTTGAACTTTCAATTA\n+TGTTTATTGTAAACAGCTTTCCGCTGAAATTGTTGTACTGCATTGTGGAA\n+TTGAAATTTGCTGTCTGATGCAGTTTGATTGAAGCGGAAGCTGGCAAAGG\n+TAATGACAAAAACGAAGACAAAGGAAATGCCGCCGAGATTCGAATTTGAA\n+ATTTGTTTATAAACTGAAATTTTAAATCGATTTATAAACTGGAGTAGAGT\n+GCTATGTTTTCGGGTTTTTAATTTGTCTGAATATTGCAGAAATTTTTGTT\n+CAGCAACAATAATGACTCGGCTATTGATCGTGATCAAGAAAATATATATT\n+TGACATGATCGGAAACGTTTTCGTCTGCCTTCCTTTCTCAACGAGTAAGG\n+GGTATAAATAGTGCTGCGTTTACATCTTAATAATCTATATACTTCCCGGA\n+GATCTCAGTTCTCATACGTGCAGAAACGGTTATAACCTTTTCAACGAACC\n+TTCTACTGCACGAGTAATAAATAGATTTCATAAATTTATTTTTTATTATT\n+TTTAGGATGGCCAAAACGTGGAGTCAATGAGACAATTTTTGAGTACTATG\n+TGGATGATAACGGAAACTGGCAACACTGGAGCACACGCGTTGAAGAATTT\n+CGATATCCAGAAGATGAAATTCCAGAGTTTTCATCTATTTTAGTTCCGAA\n+TGTAGATAATGTGCGCACTGCTTTCCTTTTACATAATATTGCTAAGCAGC\n+TCAAGCAAGTTCTTTTAATTGGTGAGCAGGGTACTGCTAAGACAGTGATG\n+ATAAAGGCCTATATGGGTCATTACGATCCCGAAGTTCACATTTTTAAATC\n+CTTTAATTTTTCATCCGCTACCACGCCTAACATGTACCAGGTAAAATCAA\n+TGCATTTTTTATATAATATGTATAATTAAATGTTTGCAATATGTGAAAGT\n+GAAAAAAATATAATTTTTATTTCAGAAGAACACCAACATATTACAATTAG\n+GTCTCAAACTGAACTCTGATAATTATTCTGATTTCATTGACGTTCAAGCC\n+TCGGTATCGAGCTTTTCTGATATGGGTTCGGATCATGAAGAGAAAAAACC\n+TTGCGTTTCTCTTGGATTCAAGTGCATTCGCTCTTGGATACAAGTGCTCT\n+TATATTCTTATAATTTCTTTATTGAAATCGATACTTTTGTTTTTCGGGAT\n+TTAAATTAGGGGACGGATGTTTAGTCTACCTGTGGGTGACTTATCTAGAG\n+TTGGGGCTTTTCCACTCTCGAGGATCATGTGACAATCTTATTCTTATCTG\n+CTATCTGTTGGGTTATATGCTTTATACAGAGTCAAACTAATTATTATTAT\n+GACAGAAGTTGTAATGCATATAATTTAGAAAAATATATAATGTTTTACAT\n+GGGATTCTACCATTTCTCTCGTTTTTAAGTGATTTATTGGTTTTAAACGT\n+GTGACATTGTTGGTGATATAAATTGTTTGTTAAAGTCTGCTAGATTATTG\n+GAGATTAGGAATTCATATGTTGCTTAGATCGGCAGCTAAAAAAAATTCGG\n' |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/chrY-1-500k.fa.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrY-1-500k.fa.out Tue Apr 02 21:16:37 2024 +0000 |
| b |
| b'@@ -0,0 +1,672 @@\n+ 192 10.4 9.8 2.2 chrY 1 256 (3667096) + TART_B1 LINE/Jockey 590 864 (9790) 120772\n+ 88 11.5 9.7 3.3 chrY 270 413 (3666939) + TART_B1 LINE/Jockey 712 864 (9790) 120772\n+ 631 14.8 8.1 4.6 chrY 426 1187 (3666165) + TART_B1 LINE/Jockey 9741 10528 (126) 120773\n+ 286 3.3 0.0 0.0 chrY 1192 1490 (3665862) + TART-A LINE/Jockey 9873 10171 (5405) 120774\n+ 448 7.4 0.0 0.5 chrY 8991 9409 (3657943) + HETA LINE/Jockey 5661 6077 (4) 120775\n+ 7 12.2 0.0 0.0 chrY 9408 9448 (3657904) C DNAREP1_DM RC/Helitron (217) 377 337 120776\n+ 38 19.9 15.5 1.8 chrY 9447 9543 (3657809) C DNAREP1_DM RC/Helitron (340) 254 145 120776\n+ 19 5.9 0.0 0.0 chrY 9560 9593 (3657759) C DNAREP1_DM RC/Helitron (551) 43 10 120777\n+ 167 19.0 32.1 0.7 chrY 10936 11253 (3656099) C DNAREP1_DM RC/Helitron (0) 594 178 120778\n+ 523 2.1 0.0 0.0 chrY 11410 11833 (3655519) + PROTOP_A DNA/P 1 424 (681) 120779\n+ 312 2.5 0.0 0.0 chrY 11821 12098 (3655254) C PROTOP_A DNA/P (645) 460 183 120780\n+ 15 18.1 2.6 0.0 chrY 12233 12270 (3655082) + (GCCTTT)n Simple_repeat 1 39 (0) 120781\n+ 14 26.9 1.5 4.5 chrY 12814 12881 (3654471) + A-rich Low_complexity 1 66 (0) 120782\n+ 229 30.4 3.5 9.6 chrY 13410 14042 (3653310) + Chouto_I-int LTR/Gypsy 854 1370 (4345) 120783\n+ 15 18.1 2.6 0.0 chrY 14385 14422 (3652930) + (GCCTTT)n Simple_repeat 1 39 (0) 120784\n+ 339 2.7 0.9 0.0 chrY 14819 15147 (3652205) C TC1-2_DM DNA/TcMar-Tc1 (0) 1644 1313 120785\n+ 182 25.8 2.3 4.7 chrY 15489 15748 (3651604) + Chouto_I-int LTR/Gypsy 1117 1370 (4345) 120786\n+ 316 2.2 0.0 0.0 chrY 16562 16839 (3650513) C PROTOP_A DNA/P (645) 460 183 120787\n+ 15 18.1 2.6 0.0 chrY 16974 17011 (3650341) + (GCCTTT)n Simple_repeat 1 39 (0) 120788\n+ 14 28.5 1.5 3.0 chrY 17555 17621 (3649731) + A-rich Low_complexity 1 66 (0) 120789\n+ 13 28.9 5.2 1.2 chrY 17622 17627 (3649725) + (AACACA)n Simple_repeat 5 80 (0) 120790\n+ 357 26.2 5.4 5.4 chrY 18175 18691 (3648661) + Chouto_I-int LTR/Gypsy 854 1370 (4345) 120791\n+ 717 34.9 4.9 4.8 chrY 19620 21544 (3645808) + GTWIN_I-int LTR/Gypsy 2720 4645 (1776) 120792\n+ 404 2.8 0.7 0.2 chrY 22648 23056 (3644296) + (TAATA)n Simple_repeat 1 411 (0) 120793\n+ 293 8.9 0.0 0.4 chrY 23057 23338 (3644014) C Baggins1 LINE/LOA (69) 5384 5104 120794\n+ 855 5.7 5.7 0.0 chrY 23356 24131 (3643221) C Baggins1 LINE/LOA (730) 4723 3904 120794\n+ 41 12.2 57.0 0.0 chrY 24134 24240 (3643112) C Baggins1 LINE/LOA (1656) 3797 3630 120794\n+ 87 17.3 24.9 0.0 chrY 25318 25490 (3641862) + DOC3_DM LINE/Jockey 4195 4410 (330) 120795\n+ 14 14.5 3.2 0.0 chrY 25604 25634 (3641718) + (TTC)n Simple_repeat 1 32 (0) 120796\n+ 232 12.5 34.0 0.9 chrY 25758 26095 (3641257) C DNAREP1_DM RC/Helitron (134) 460 12 120797\n+ 34 14.3 0.0 0.0 chrY 29452 29507 (3637845) C DNAREP1_DM RC/Helitron (0) 594 539 120798\n+ 39 14.7 0.0 0.0 chrY 29529 29596 (3637756) C DNAREP1_DM RC/Helitron (176) 418 351 120798\n+ 76 23.'..b' 4126 4250 (226) 121171\n+ 318 17.3 14.7 4.3 chrY 475840 476261 (3191091) + Gypsy_LTR LTR/Gypsy 1 464 (18) 121172\n+ 139 11.3 32.4 1.3 chrY 476281 476459 (3190893) + MICROPIA_I-int LTR/Gypsy 4243 4476 (0) 121171\n+ 277 14.2 8.6 8.6 chrY 476463 476846 (3190506) + MICROPIA_LTR LTR/Gypsy 93 476 (0) 121173\n+ 63 24.3 20.9 2.4 chrY 476847 476928 (3190424) C DNAREP1_DM RC/Helitron (478) 116 10 121174\n+ 12 21.6 2.5 2.5 chrY 477485 477524 (3189828) + A-rich Low_complexity 1 40 (0) 121175\n+ 401 7.1 0.3 3.0 chrY 478056 478432 (3188920) + ROVER-LTR_DM LTR/Gypsy 1 367 (0) 121176\n+ 802 8.9 2.0 8.5 chrY 478432 479782 (3187570) + ROVER-I_DM LTR/Gypsy 1 1396 (5188) 121176\n+ 2679 12.1 0.9 0.0 chrY 479777 482273 (3185079) + ROVER-I_DM LTR/Gypsy 1776 4295 (2289) 121176\n+ 1510 12.8 0.7 0.9 chrY 482275 485215 (3182137) + ROVER-I_DM LTR/Gypsy 3532 6584 (0) 121177\n+ 431 23.1 18.6 1.4 chrY 485353 485488 (3181864) C QUASIMODO_I-int LTR/Gypsy (223) 5837 5661 121178\n+ 30 4.8 2.2 2.2 chrY 485489 485533 (3181819) + (TTA)n Simple_repeat 1 45 (0) 121179\n+ 431 23.1 18.6 1.4 chrY 485534 486301 (3181051) C QUASIMODO_I-int LTR/Gypsy (400) 5660 4781 121178\n+ 95 21.6 5.9 0.5 chrY 486311 486496 (3180856) C QUASIMODO_I-int LTR/Gypsy (1447) 4613 4418 121178\n+ 6 33.1 22.4 0.6 chrY 486491 486633 (3180719) C QUASIMODO_I-int LTR/Gypsy (1826) 4234 4061 121178\n+ 40 38.1 0.0 0.0 chrY 486609 486742 (3180610) + FROGGER_I-int LTR/Copia 662 795 (1282) 121180\n+ 178 38.9 19.0 1.4 chrY 486794 487481 (3179871) + Copia1-I_DM LTR/Copia 3239 4046 (78) 121181\n+ 184 16.1 24.1 0.0 chrY 487537 487785 (3179567) C DNAREP1_DM RC/Helitron (284) 310 2 121182\n+ 14 18.6 8.2 0.0 chrY 487882 487930 (3179422) + (TATAA)n Simple_repeat 1 53 (0) 121183\n+ 12 26.8 0.0 5.8 chrY 488005 488059 (3179293) + A-rich Low_complexity 1 52 (0) 121184\n+ 403 13.4 9.2 10.3 chrY 492159 492758 (3174594) + IDEFIX_LTR LTR/Gypsy 1 594 (0) 121185\n+ 1507 14.8 11.1 1.2 chrY 492969 494609 (3172743) C IDEFIX_I-int LTR/Gypsy (3461) 2167 365 121186\n+ 363 5.7 1.8 0.0 chrY 494610 494996 (3172356) C TRANSIB1 DNA/CMC-Transib (0) 3014 2621 121187\n+ 90 4.8 1.9 0.0 chrY 495001 495103 (3172249) C TRANSIB1 DNA/CMC-Transib (504) 2510 2406 121187\n+ 225 21.8 4.3 1.6 chrY 495086 495388 (3171964) C IDEFIX_I-int LTR/Gypsy (5316) 312 2 121186\n+ 206 9.6 0.4 10.3 chrY 495783 496037 (3171315) C IDEFIX_LTR LTR/Gypsy (72) 522 291 121188\n+ 841 5.9 15.4 0.0 chrY 496013 496839 (3170513) + TRANSIB2 DNA/CMC-Transib 514 1467 (1377) 121189\n+ 406 0.9 2.7 0.0 chrY 496853 497185 (3170167) C DM1731_I-int LTR/Copia (760) 3216 2875 121190\n+ 127 32.9 11.5 1.2 chrY 497647 498067 (3169285) C BURDOCK_I-int LTR/Gypsy (4378) 1337 631 121191\n+ 15 7.5 0.0 6.7 chrY 498420 498451 (3168901) + (TTTC)n Simple_repeat 1 30 (0) 121192\n+ 50 14.7 47.4 0.0 chrY 498763 498857 (3168495) C DNAREP1_DM RC/Helitron (454) 140 1 121193\n+ 265 8.5 17.8 0.1 chrY 499374 499971 (3167381) C IDEFIX_LTR LTR/Gypsy (0) 594 99 121194\n+ 269 5.2 19.8 0.9 chrY 499964 500407 (3166945) + DMCR1A LINE/CR1 891 1418 (3052) 121195\n' |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/chrY-500k.R1.fastqsanger.gz |
| b |
| Binary file test-data/chrY-500k.R1.fastqsanger.gz has changed |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/chrY-500k.R2.fastqsanger.gz |
| b |
| Binary file test-data/chrY-500k.R2.fastqsanger.gz has changed |
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| diff -r 89e05f831259 -r 530626b0757c test-data/chrY_paired_class_fraction_counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrY_paired_class_fraction_counts.tab Tue Apr 02 21:16:37 2024 +0000 |
| b |
| @@ -0,0 +1,6 @@ +DNA 53.0 +LINE 197.0 +LTR 22125.0 +Low_complexity 0.0 +RC 0.0 +Simple_repeat 77.0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/chrY_paired_family_fraction_counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrY_paired_family_fraction_counts.tab Tue Apr 02 21:16:37 2024 +0000 |
| b |
| @@ -0,0 +1,13 @@ +CMC-Transib 18.0 +CR1 0.0 +Copia 21226.0 +Gypsy 876.0 +Helitron 0.0 +Jockey 91.0 +LOA 0.0 +Low_complexity 0.0 +P 27.0 +Pao 23.0 +R1 106.0 +Simple_repeat 77.0 +TcMar-Tc1 8.0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/chrY_paired_fraction_counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrY_paired_fraction_counts.tab Tue Apr 02 21:16:37 2024 +0000 |
| b |
| @@ -0,0 +1,145 @@ +A-rich Low_complexity Low_complexity 0.0 +ACCORD2_I-int LTR Gypsy 0.0 +ACCORD2_LTR LTR Gypsy 0.0 +ACCORD_I-int LTR Gypsy 0.0 +BARI1 DNA TcMar-Tc1 0.0 +BATUMI_LTR LTR Pao 0.0 +BS LINE Jockey 0.0 +BS2 LINE Jockey 50.0 +BURDOCK_I-int LTR Gypsy 0.0 +Baggins1 LINE LOA 0.0 +Bica_I-int LTR Gypsy 36.0 +Bica_LTR LTR Gypsy 1.0 +CIRCE LTR Gypsy 0.0 +Chouto_I-int LTR Gypsy 3.0 +Copia1-I_DM LTR Copia 0.0 +Copia_I-int LTR Copia 20956.0 +Copia_LTR LTR Copia 270.0 +DIVER2_I-int LTR Pao 0.0 +DIVER2_LTR LTR Pao 1.0 +DM1731_I-int LTR Copia 0.0 +DM1731_LTR LTR Copia 0.0 +DM176_I-int LTR Gypsy 0.0 +DM412 LTR Gypsy 2.0 +DM412B_LTR LTR Gypsy 0.0 +DMCR1A LINE CR1 0.0 +DMLTR5 LTR Gypsy 0.0 +DMRT1A LINE R1 0.0 +DMRT1B LINE R1 106.0 +DMRT1C LINE R1 0.0 +DNAREP1_DM RC Helitron 0.0 +DOC2_DM LINE Jockey 0.0 +DOC3_DM LINE Jockey 0.0 +FB4_DM DNA TcMar-Tc1 4.0 +FROGGER_I-int LTR Copia 0.0 +FW2_DM LINE Jockey 0.0 +G3_DM LINE Jockey 0.0 +G5A_DM LINE Jockey 0.0 +G5_DM LINE Jockey 0.0 +G6_DM LINE Jockey 0.0 +GA-rich Low_complexity Low_complexity 0.0 +GTWIN_I-int LTR Gypsy 9.0 +G_DM LINE Jockey 0.0 +Gypsy11_I-int LTR Gypsy 0.0 +Gypsy11_LTR LTR Gypsy 0.0 +Gypsy12_LTR LTR Gypsy 0.0 +Gypsy2-I_DM LTR Gypsy 0.0 +Gypsy2-LTR_DM LTR Gypsy 0.0 +Gypsy3_LTR LTR Gypsy 0.0 +Gypsy4_I-int LTR Gypsy 0.0 +Gypsy5_I-int LTR Gypsy 0.0 +Gypsy6A_LTR LTR Gypsy 1.0 +Gypsy6_I-int LTR Gypsy 26.0 +Gypsy8_I-int LTR Gypsy 0.0 +Gypsy8_LTR LTR Gypsy 0.0 +Gypsy9_I-int LTR Gypsy 0.0 +Gypsy_I-int LTR Gypsy 24.0 +Gypsy_LTR LTR Gypsy 0.0 +HELENA_RT LINE Jockey 0.0 +HETA LINE Jockey 24.0 +HMSBEAGLE_I-int LTR Gypsy 0.0 +IDEFIX_I-int LTR Gypsy 1.0 +IDEFIX_LTR LTR Gypsy 0.0 +Invader1_I-int LTR Gypsy 0.0 +Invader1_LTR LTR Gypsy 0.0 +Invader2_I-int LTR Gypsy 0.0 +Invader4_I-int LTR Gypsy 0.0 +Invader4_LTR LTR Gypsy 0.0 +Invader5_I-int LTR Gypsy 0.0 +Invader5_LTR LTR Gypsy 0.0 +Invader6_I-int LTR Gypsy 0.0 +Invader6_LTR LTR Gypsy 0.0 +MAX_I-int LTR Pao 22.0 +MAX_LTR LTR Pao 0.0 +MDG1_I-int LTR Gypsy 0.0 +MDG1_LTR LTR Gypsy 0.0 +MDG3_I-int LTR Gypsy 92.0 +MDG3_LTR LTR Gypsy 1.0 +MICROPIA_I-int LTR Gypsy 40.0 +MICROPIA_LTR LTR Gypsy 2.0 +Mariner2_DM DNA TcMar-Tc1 0.0 +NINJA_I-int LTR Pao 0.0 +NOMAD_I-int LTR Gypsy 0.0 +PROTOP_A DNA P 27.0 +PROTOP_B DNA P 0.0 +QUASIMODO2-I_DM LTR Gypsy 24.0 +QUASIMODO2-LTR_DM LTR Gypsy 0.0 +QUASIMODO_I-int LTR Gypsy 85.5 +QUASIMODO_LTR LTR Gypsy 14.5 +R1_DM LINE R1 0.0 +ROOA_I-int LTR Pao 0.0 +ROOA_LTR LTR Pao 0.0 +ROVER-I_DM LTR Gypsy 286.0 +ROVER-LTR_DM LTR Gypsy 2.0 +S2_DM DNA TcMar-Tc1 0.0 +STALKER4_I-int LTR Gypsy 133.0 +STALKER4_LTR LTR Gypsy 22.0 +S_DM DNA TcMar-Tc1 4.0 +Stalker2_I-int LTR Gypsy 69.0 +Stalker2_LTR LTR Gypsy 2.0 +TART-A LINE Jockey 4.0 +TART_B1 LINE Jockey 13.0 +TC1-2_DM DNA TcMar-Tc1 0.0 +TC1_DM DNA TcMar-Tc1 0.0 +TLD2 LTR Gypsy 0.0 +TRANSIB1 DNA CMC-Transib 0.0 +TRANSIB2 DNA CMC-Transib 18.0 +ZAM_I-int LTR Gypsy 0.0 +_AACACA_n Simple_repeat Simple_repeat 0.0 +_AAT_n Simple_repeat Simple_repeat 0.0 +_ACAATAG_n Simple_repeat Simple_repeat 0.0 +_ACC_n Simple_repeat Simple_repeat 0.0 +_AGAGAAG_n Simple_repeat Simple_repeat 2.5 +_AGAGA_n Simple_repeat Simple_repeat 33.5 +_ATAAT_n Simple_repeat Simple_repeat 0.0 +_ATATATT_n Simple_repeat Simple_repeat 0.0 +_ATATTAT_n Simple_repeat Simple_repeat 0.0 +_ATTTTT_n Simple_repeat Simple_repeat 0.0 +_ATT_n Simple_repeat Simple_repeat 0.0 +_AT_n Simple_repeat Simple_repeat 0.0 +_A_n Simple_repeat Simple_repeat 0.0 +_CATA_n Simple_repeat Simple_repeat 0.0 +_CTTTT_n Simple_repeat Simple_repeat 0.0 +_GAGAA_n Simple_repeat Simple_repeat 38.0 +_GCCTTT_n Simple_repeat Simple_repeat 3.0 +_TAATAT_n Simple_repeat Simple_repeat 0.0 +_TAATA_n Simple_repeat Simple_repeat 0.0 +_TATAAAA_n Simple_repeat Simple_repeat 0.0 +_TATAA_n Simple_repeat Simple_repeat 0.0 +_TATCATG_n Simple_repeat Simple_repeat 0.0 +_TA_n Simple_repeat Simple_repeat 0.0 +_TGTTG_n Simple_repeat Simple_repeat 0.0 +_TTATATA_n Simple_repeat Simple_repeat 0.0 +_TTATAT_n Simple_repeat Simple_repeat 0.0 +_TTATA_n Simple_repeat Simple_repeat 0.0 +_TTA_n Simple_repeat Simple_repeat 0.0 +_TTCTT_n Simple_repeat Simple_repeat 0.0 +_TTC_n Simple_repeat Simple_repeat 0.0 +_TTTAT_n Simple_repeat Simple_repeat 0.0 +_TTTA_n Simple_repeat Simple_repeat 0.0 +_TTTC_n Simple_repeat Simple_repeat 0.0 +_TTTGA_n Simple_repeat Simple_repeat 0.0 +_TTTTAG_n Simple_repeat Simple_repeat 0.0 +_TTTTCTT_n Simple_repeat Simple_repeat 0.0 +_TTTTC_n Simple_repeat Simple_repeat 0.0 +_T_n Simple_repeat Simple_repeat 0.0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/chrY_single_class_fraction_counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrY_single_class_fraction_counts.tab Tue Apr 02 21:16:37 2024 +0000 |
| b |
| @@ -0,0 +1,6 @@ +DNA 72.0 +LINE 121.0 +LTR 13181.0 +Low_complexity 0.0 +RC 0.0 +Simple_repeat 89.0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/chrY_single_family_fraction_counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrY_single_family_fraction_counts.tab Tue Apr 02 21:16:37 2024 +0000 |
| b |
| @@ -0,0 +1,13 @@ +CMC-Transib 12.0 +CR1 2.0 +Copia 12453.0 +Gypsy 701.0 +Helitron 0.0 +Jockey 51.0 +LOA 0.0 +Low_complexity 0.0 +P 27.0 +Pao 27.0 +R1 68.0 +Simple_repeat 89.0 +TcMar-Tc1 33.0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/chrY_single_fraction_counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrY_single_fraction_counts.tab Tue Apr 02 21:16:37 2024 +0000 |
| b |
| @@ -0,0 +1,145 @@ +A-rich Low_complexity Low_complexity 0.0 +ACCORD2_I-int LTR Gypsy 0.0 +ACCORD2_LTR LTR Gypsy 0.0 +ACCORD_I-int LTR Gypsy 0.0 +BARI1 DNA TcMar-Tc1 0.0 +BATUMI_LTR LTR Pao 0.0 +BS LINE Jockey 0.0 +BS2 LINE Jockey 29.0 +BURDOCK_I-int LTR Gypsy 0.0 +Baggins1 LINE LOA 0.0 +Bica_I-int LTR Gypsy 25.0 +Bica_LTR LTR Gypsy 0.0 +CIRCE LTR Gypsy 0.0 +Chouto_I-int LTR Gypsy 2.0 +Copia1-I_DM LTR Copia 0.0 +Copia_I-int LTR Copia 12327.0 +Copia_LTR LTR Copia 123.0 +DIVER2_I-int LTR Pao 1.0 +DIVER2_LTR LTR Pao 1.0 +DM1731_I-int LTR Copia 3.0 +DM1731_LTR LTR Copia 0.0 +DM176_I-int LTR Gypsy 0.0 +DM412 LTR Gypsy 8.0 +DM412B_LTR LTR Gypsy 0.0 +DMCR1A LINE CR1 2.0 +DMLTR5 LTR Gypsy 0.0 +DMRT1A LINE R1 0.0 +DMRT1B LINE R1 68.0 +DMRT1C LINE R1 0.0 +DNAREP1_DM RC Helitron 0.0 +DOC2_DM LINE Jockey 0.0 +DOC3_DM LINE Jockey 0.0 +FB4_DM DNA TcMar-Tc1 12.0 +FROGGER_I-int LTR Copia 0.0 +FW2_DM LINE Jockey 0.0 +G3_DM LINE Jockey 0.0 +G5A_DM LINE Jockey 0.0 +G5_DM LINE Jockey 0.0 +G6_DM LINE Jockey 0.0 +GA-rich Low_complexity Low_complexity 0.0 +GTWIN_I-int LTR Gypsy 8.0 +G_DM LINE Jockey 0.0 +Gypsy11_I-int LTR Gypsy 0.0 +Gypsy11_LTR LTR Gypsy 0.0 +Gypsy12_LTR LTR Gypsy 0.0 +Gypsy2-I_DM LTR Gypsy 3.0 +Gypsy2-LTR_DM LTR Gypsy 0.0 +Gypsy3_LTR LTR Gypsy 0.0 +Gypsy4_I-int LTR Gypsy 0.0 +Gypsy5_I-int LTR Gypsy 0.0 +Gypsy6A_LTR LTR Gypsy 0.0 +Gypsy6_I-int LTR Gypsy 16.0 +Gypsy8_I-int LTR Gypsy 0.0 +Gypsy8_LTR LTR Gypsy 0.0 +Gypsy9_I-int LTR Gypsy 0.0 +Gypsy_I-int LTR Gypsy 16.0 +Gypsy_LTR LTR Gypsy 0.0 +HELENA_RT LINE Jockey 0.0 +HETA LINE Jockey 12.0 +HMSBEAGLE_I-int LTR Gypsy 1.0 +IDEFIX_I-int LTR Gypsy 3.0 +IDEFIX_LTR LTR Gypsy 1.0 +Invader1_I-int LTR Gypsy 0.0 +Invader1_LTR LTR Gypsy 0.0 +Invader2_I-int LTR Gypsy 0.0 +Invader4_I-int LTR Gypsy 0.0 +Invader4_LTR LTR Gypsy 0.0 +Invader5_I-int LTR Gypsy 0.0 +Invader5_LTR LTR Gypsy 0.0 +Invader6_I-int LTR Gypsy 0.0 +Invader6_LTR LTR Gypsy 0.0 +MAX_I-int LTR Pao 24.0 +MAX_LTR LTR Pao 1.0 +MDG1_I-int LTR Gypsy 0.0 +MDG1_LTR LTR Gypsy 0.0 +MDG3_I-int LTR Gypsy 67.0 +MDG3_LTR LTR Gypsy 2.0 +MICROPIA_I-int LTR Gypsy 45.0 +MICROPIA_LTR LTR Gypsy 2.0 +Mariner2_DM DNA TcMar-Tc1 0.0 +NINJA_I-int LTR Pao 0.0 +NOMAD_I-int LTR Gypsy 0.0 +PROTOP_A DNA P 27.0 +PROTOP_B DNA P 0.0 +QUASIMODO2-I_DM LTR Gypsy 19.0 +QUASIMODO2-LTR_DM LTR Gypsy 0.0 +QUASIMODO_I-int LTR Gypsy 94.0 +QUASIMODO_LTR LTR Gypsy 15.0 +R1_DM LINE R1 0.0 +ROOA_I-int LTR Pao 0.0 +ROOA_LTR LTR Pao 0.0 +ROVER-I_DM LTR Gypsy 203.0 +ROVER-LTR_DM LTR Gypsy 3.0 +S2_DM DNA TcMar-Tc1 0.0 +STALKER4_I-int LTR Gypsy 106.0 +STALKER4_LTR LTR Gypsy 22.0 +S_DM DNA TcMar-Tc1 21.0 +Stalker2_I-int LTR Gypsy 38.0 +Stalker2_LTR LTR Gypsy 2.0 +TART-A LINE Jockey 2.0 +TART_B1 LINE Jockey 8.0 +TC1-2_DM DNA TcMar-Tc1 0.0 +TC1_DM DNA TcMar-Tc1 0.0 +TLD2 LTR Gypsy 0.0 +TRANSIB1 DNA CMC-Transib 0.0 +TRANSIB2 DNA CMC-Transib 12.0 +ZAM_I-int LTR Gypsy 0.0 +_AACACA_n Simple_repeat Simple_repeat 0.0 +_AAT_n Simple_repeat Simple_repeat 0.0 +_ACAATAG_n Simple_repeat Simple_repeat 0.0 +_ACC_n Simple_repeat Simple_repeat 0.0 +_AGAGAAG_n Simple_repeat Simple_repeat 2.5 +_AGAGA_n Simple_repeat Simple_repeat 41.5 +_ATAAT_n Simple_repeat Simple_repeat 0.0 +_ATATATT_n Simple_repeat Simple_repeat 0.0 +_ATATTAT_n Simple_repeat Simple_repeat 0.0 +_ATTTTT_n Simple_repeat Simple_repeat 0.0 +_ATT_n Simple_repeat Simple_repeat 0.0 +_AT_n Simple_repeat Simple_repeat 0.0 +_A_n Simple_repeat Simple_repeat 0.0 +_CATA_n Simple_repeat Simple_repeat 0.0 +_CTTTT_n Simple_repeat Simple_repeat 0.0 +_GAGAA_n Simple_repeat Simple_repeat 44.0 +_GCCTTT_n Simple_repeat Simple_repeat 1.0 +_TAATAT_n Simple_repeat Simple_repeat 0.0 +_TAATA_n Simple_repeat Simple_repeat 0.0 +_TATAAAA_n Simple_repeat Simple_repeat 0.0 +_TATAA_n Simple_repeat Simple_repeat 0.0 +_TATCATG_n Simple_repeat Simple_repeat 0.0 +_TA_n Simple_repeat Simple_repeat 0.0 +_TGTTG_n Simple_repeat Simple_repeat 0.0 +_TTATATA_n Simple_repeat Simple_repeat 0.0 +_TTATAT_n Simple_repeat Simple_repeat 0.0 +_TTATA_n Simple_repeat Simple_repeat 0.0 +_TTA_n Simple_repeat Simple_repeat 0.0 +_TTCTT_n Simple_repeat Simple_repeat 0.0 +_TTC_n Simple_repeat Simple_repeat 0.0 +_TTTAT_n Simple_repeat Simple_repeat 0.0 +_TTTA_n Simple_repeat Simple_repeat 0.0 +_TTTC_n Simple_repeat Simple_repeat 0.0 +_TTTGA_n Simple_repeat Simple_repeat 0.0 +_TTTTAG_n Simple_repeat Simple_repeat 0.0 +_TTTTCTT_n Simple_repeat Simple_repeat 0.0 +_TTTTC_n Simple_repeat Simple_repeat 0.0 +_T_n Simple_repeat Simple_repeat 0.0 |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/edgeR_plots.pdf |
| b |
| Binary file test-data/edgeR_plots.pdf has changed |
| b |
| diff -r 89e05f831259 -r 530626b0757c test-data/edgeR_result_file.tab --- a/test-data/edgeR_result_file.tab Mon Mar 18 09:39:44 2024 +0000 +++ b/test-data/edgeR_result_file.tab Tue Apr 02 21:16:37 2024 +0000 |
| b |
| b'@@ -1,211 +1,211 @@\n TE_item\tlog2FC\tFDR\tClass\tType\n-DM297_I-int\t 2.69047105\t4.4945e-21\tLTR\tGypsy\n-DM297_LTR\t 1.74961921\t1.3397e-18\tLTR\tGypsy\n-Gypsy1-I_DM\t 2.37388633\t4.4803e-16\tLTR\tGypsy\n-NOF_FB\t-2.79644759\t4.4803e-16\tDNA\tMULE-NOF\n-G7_DM\t 3.25987375\t1.5530e-15\tLINE\tJockey\n-Gypsy_I-int\t 1.74702180\t4.3525e-12\tLTR\tGypsy\n-LINEJ1_DM\t 1.94429218\t5.1807e-12\tLINE\tJockey\n-TOM_I-int\t 1.33935222\t6.6923e-12\tLTR\tGypsy\n-GTWIN_LTR\t 1.89490932\t8.8059e-12\tLTR\tGypsy\n-Gypsy_LTR\t 1.56024436\t2.9985e-11\tLTR\tGypsy\n-DM1731_I-int\t 1.53134430\t6.4921e-10\tLTR\tCopia\n-Gypsy6_LTR\t 1.53023046\t1.0751e-06\tLTR\tGypsy\n-LOOPER1_DM\t-2.46983670\t1.6192e-06\tDNA\tPiggyBac\n-TIRANT_LTR\t 1.12203469\t1.7801e-06\tLTR\tGypsy\n-Gypsy12_I-int\t-1.12204057\t2.1949e-06\tLTR\tGypsy\n-R2_DM\t 1.67889583\t2.7304e-06\tLINE\tR2\n-TRANSPAC_LTR\t 1.49364968\t2.9021e-06\tLTR\tGypsy\n-Copia_LTR\t 1.66649088\t1.1860e-05\tLTR\tCopia\n-ACCORD_LTR\t 1.37240595\t1.7595e-05\tLTR\tGypsy\n-TIRANT_I-int\t 1.17728139\t2.0469e-05\tLTR\tGypsy\n-TART_B1\t-1.14695346\t3.0966e-05\tLINE\tJockey\n-TRANSIB1\t-1.39021194\t6.1650e-05\tDNA\tCMC-Transib\n-DM412B_LTR\t 0.80309005\t1.2443e-04\tLTR\tGypsy\n-MICROPIA_LTR\t-1.29556276\t1.2985e-04\tLTR\tGypsy\n-G6_DM\t-1.05894869\t1.3831e-04\tLINE\tJockey\n-NINJA_I-int\t-0.87426452\t1.5554e-04\tLTR\tPao\n-R1_DM\t 0.95590515\t1.8985e-04\tLINE\tR1\n-Invader6_LTR\t-1.18865109\t2.1299e-04\tLTR\tGypsy\n-Copia_I-int\t 1.93316905\t2.2313e-04\tLTR\tCopia\n-BLASTOPIA_LTR\t 1.34881959\t3.6488e-04\tLTR\tGypsy\n-LSU-rRNA_Hsa\t 2.61189118\t8.0160e-04\trRNA\trRNA\n-TRANSPAC_I-int\t 1.16122218\t8.4531e-04\tLTR\tGypsy\n-G4_DM\t-0.74970144\t9.1437e-04\tLINE\tJockey\n-SSU-rRNA_Hsa\t 1.12389968\t1.0426e-03\trRNA\trRNA\n-DOC5_DM\t-0.80987287\t1.6241e-03\tLINE\tJockey\n-Invader1_I-int\t 0.74972783\t1.9892e-03\tLTR\tGypsy\n-TRANSIB4\t-1.00230688\t2.0605e-03\tDNA\tCMC-Transib\n-MICROPIA_I-int\t-0.75119303\t2.9293e-03\tLTR\tGypsy\n-PLACW_DM\t 1.16310826\t3.0518e-03\tDNA\tP\n-TABOR_I-int\t 0.73770219\t3.5495e-03\tLTR\tGypsy\n-I_DM\t 1.04141382\t4.5715e-03\tLINE\tI\n-Gypsy3_I-int\t 0.58659480\t5.3315e-03\tLTR\tGypsy\n-DOC\t 0.94015336\t5.5212e-03\tLINE\tJockey\n-Helitron1_DM\t-5.10401049\t6.3658e-03\tRC\tHelitron\n-Invader5_I-int\t-0.97342264\t6.6603e-03\tLTR\tGypsy\n-ACCORD_I-int\t 0.59304769\t7.0136e-03\tLTR\tGypsy\n-LSU-rRNA_Dme\t 0.90220479\t1.0210e-02\trRNA\trRNA\n-DM412\t 0.77597081\t1.0808e-02\tLTR\tGypsy\n-NINJA_LTR\t-0.92340817\t1.0956e-02\tLTR\tPao\n-BATUMI_I-int\t-0.56286761\t1.4855e-02\tLTR\tPao\n-DMRT1C\t-0.66474417\t1.7456e-02\tLINE\tR1\n-TAHRE\t-0.50950303\t1.9854e-02\tLINE\tJockey\n-Gypsy8_I-int\t-0.57827690\t2.4898e-02\tLTR\tGypsy\n-BLASTOPIA_I-int\t 0.79698775\t3.0182e-02\tLTR\tGypsy\n-DM176_LTR\t-0.69138467\t4.3254e-02\tLTR\tGypsy\n-DMRT1A\t-0.50960841\t4.3254e-02\tLINE\tR1\n-Gypsy11_I-int\t-0.73463462\t4.3254e-02\tLTR\tGypsy\n-QUASIMODO2-I_DM\t 0.47005794\t4.4414e-02\tLTR\tGypsy\n-MuDR-1_DEl\t 1.35524443\t5.3232e-02\tDNA\tMULE-NOF\n-DM1731_LTR\t 0.75223818\t5.4013e-02\tLTR\tCopia\n-FROGGER_I-int\t-0.60531971\t5.4013e-02\tLTR\tCopia\n-MAX_I-int\t-0.51645609\t6.4340e-02\tLTR\tPao\n-BURDOCK_I-int\t 0.41822333\t6.9121e-02\tLTR\tGypsy\n-FROGGER_LTR\t 0.88832640\t7.0636e-02\tLTR\tCopia\n-DIVER_I-int\t 0.57905223\t7.3816e-02\tLTR\tPao\n-Chouto_I-int\t-0.55102999\t8.1512e-02\tLTR\tGypsy\n-DM176_I-int\t 0.38700877\t9.1864e-02\tLTR\tGypsy\n-Invader4_I-int\t 0.53274705\t9.4896e-02\tLTR\tGypsy\n-G3_DM\t-0.60764816\t1.0316e-01\tLINE\tJockey\n-Gypsy4_LTR\t 0.67676363\t1.0531e-01\tLTR\tGypsy\n-BATUMI_LTR\t-0.62559888\t1.1233e-01\tLTR\tPao\n-Gypsy2-I_DM\t 0.41886069\t1.2754e-01\tLTR\tGypsy\n-Invader3_LTR\t-0.55372613\t1.3023e-01\tLTR\tGypsy\n-MDG3_I-int\t 0.41719543\t1.3084e-01\tLTR\tGypsy\n-SSU-rRNA_Dme\t 0.50182621\t1.3084e-01\trRNA\trRNA\n-G5A_DM\t-0.46837522\t1.4239e-01\tLINE\tJockey\n-S2_DM\t-0.57644415\t1.5438e-01\tDNA\tTcMar-Tc1\n-Stalker2_I-int\t-0.42481708\t1.5792e-01\tLTR\tGypsy\n-BLOOD_LTR\t 0.49499975\t1.5864e-01\tLTR\tGypsy\n-Invader5_LTR\t-0.67598409\t1.5864e-01\tLTR\tGypsy\n-R1-2_DM\t-0.61185323\t1.5864e-01\tLINE\tR1\n-Transib5\t-0.51646991\t1.5864e-01\tDNA\tCMC-Transib\n-TLD2\t-1.24823549\t1.5867e-01\tLTR\tGypsy\n-TC1_DM\t 0.40057291\t1.6763e-01\tDNA\tTcMar-Tc1\n-BS2\t-0.33138649\t1.8548e-01\tLINE\tJockey\n-ROVER-LTR_DM\t-0.52968179\t1.8874e-01\tLTR\tGypsy\n-ACCORD2_I-int\t-0.35057261\t1.9179e-01\tLTR\tGypsy\n-Gypsy12A_LTR\t-0.354465'..b'.2455e-01\tLTR\tGypsy\n+Chouto_LTR\t-0.4338500\t4.3619e-01\tLTR\tGypsy\n+Chimpo_I-int\t-0.3314691\t4.5127e-01\tLTR\tGypsy\n+NOMAD_LTR\t-0.3209878\t4.5127e-01\tLTR\tGypsy\n+DIVER2_I-int\t-0.2289981\t4.5378e-01\tLTR\tPao\n+DOC3_DM\t-0.2381738\t4.6852e-01\tLINE\tJockey\n+Gypsy2_LTR\t 0.3263404\t4.9330e-01\tLTR\tGypsy\n+S_DM\t 0.1820634\t4.9593e-01\tDNA\tTcMar-Tc1\n+Gypsy6_I-int\t 0.2334889\t5.0030e-01\tLTR\tGypsy\n+Invader6_I-int\t-0.2164593\t5.0656e-01\tLTR\tGypsy\n+ROOA_I-int\t-0.2055700\t5.0656e-01\tLTR\tPao\n+BURDOCK_LTR\t 0.3163693\t5.2334e-01\tLTR\tGypsy\n+MAX_LTR\t-0.2697259\t5.2334e-01\tLTR\tPao\n+ROO_I-int\t 0.2651464\t5.2334e-01\tLTR\tPao\n+XDMR\t 0.2389322\t5.2334e-01\tUnknown\tUnknown\n+BEL_I-int\t 0.2260271\t5.4960e-01\tLTR\tPao\n+Gypsy10_I-int\t-0.2003926\t5.4960e-01\tLTR\tGypsy\n+Gypsy11_LTR\t-0.3153869\t5.4960e-01\tLTR\tGypsy\n+Gypsy8_LTR\t-0.2405647\t5.4960e-01\tLTR\tGypsy\n+Transib-N1_DM\t-0.2959361\t5.4960e-01\tDNA\tCMC-Transib\n+DIVER_LTR\t 0.2596569\t5.5142e-01\tLTR\tPao\n+DOC6_DM\t 0.2109295\t5.5744e-01\tLINE\tJockey\n+GTWIN_I-int\t 0.1824941\t5.5998e-01\tLTR\tGypsy\n+MDG1_LTR\t-0.2338760\t5.6341e-01\tLTR\tGypsy\n+ARS406_DM\t-0.2643500\t5.7901e-01\tUnknown\tUnknown\n+Invader3_I-int\t-0.1497623\t5.7901e-01\tLTR\tGypsy\n+TRANSIB2\t-0.1574346\t5.7901e-01\tDNA\tCMC-Transib\n+Gypsy9_LTR\t-0.3531528\t6.2010e-01\tLTR\tGypsy\n+Invader2_I-int\t-0.1629423\t6.2495e-01\tLTR\tGypsy\n+Jockey2\t-0.1743865\t6.2495e-01\tLINE\tJockey\n+MDG3_LTR\t-0.2003640\t6.2495e-01\tLTR\tGypsy\n+POGO\t-0.1617454\t6.2495e-01\tDNA\tTcMar-Pogo\n+FW2_DM\t 0.1701777\t6.5086e-01\tLINE\tJockey\n+Baggins1\t-0.1467398\t6.5429e-01\tLINE\tLOA\n+PROTOP_A\t 0.1182439\t6.7517e-01\tDNA\tP\n+TART-A\t 0.1256629\t6.7517e-01\tLINE\tJockey\n+Stalker3_LTR\t-0.1859830\t6.8046e-01\tLTR\tGypsy\n+Bica_LTR\t-0.2144653\t6.8233e-01\tLTR\tGypsy\n+NTS_DM\t-0.1893877\t6.8404e-01\tOther\tOther\n+G5_DM\t-0.1234155\t6.8736e-01\tLINE\tJockey\n+TABOR_LTR\t-0.2553509\t6.8736e-01\tLTR\tGypsy\n+FB4_DM\t-0.1257960\t7.3366e-01\tDNA\tTcMar-Tc1\n+HMSBEAGLE_I-int\t 0.1271561\t7.3366e-01\tLTR\tGypsy\n+DMRT1B\t-0.1232374\t7.3586e-01\tLINE\tR1\n+NOMAD_I-int\t-0.1496694\t7.3586e-01\tLTR\tGypsy\n+ZAM_LTR\t 0.1743412\t7.3586e-01\tLTR\tGypsy\n+Gypsy10_LTR\t-0.1653357\t7.4754e-01\tLTR\tGypsy\n+LmeSINE1c\t-0.2373454\t7.4754e-01\tSINE\ttRNA-Deu-L2\n+QUASIMODO2-LTR_DM\t-0.1678274\t7.4754e-01\tLTR\tGypsy\n+BEL_LTR\t 0.1413744\t7.6869e-01\tLTR\tPao\n+QUASIMODO_I-int\t 0.1147817\t7.6929e-01\tLTR\tGypsy\n+Invader1_LTR\t 0.1285521\t7.7711e-01\tLTR\tGypsy\n+IVK_DM\t-0.0922152\t7.8193e-01\tLINE\tI\n+BS4_DM\t-0.2651727\t7.9393e-01\tLINE\tJockey\n+Copia2_LTR_DM\t 0.1351925\t7.9393e-01\tLTR\tCopia\n+Gypsy12_LTR\t-0.0944692\t7.9977e-01\tLTR\tGypsy\n+Gypsy5_I-int\t-0.0889119\t8.0188e-01\tLTR\tGypsy\n+Gypsy6A_LTR\t-0.1275535\t8.1055e-01\tLTR\tGypsy\n+PROTOP_B\t-0.0857822\t8.1067e-01\tDNA\tP\n+Copia1-LTR_DM\t-0.1081470\t8.2869e-01\tLTR\tCopia\n+G_DM\t 0.0788783\t8.3480e-01\tLINE\tJockey\n+LSU-rRNA_Cel\t-0.1045374\t8.4508e-01\trRNA\trRNA\n+IDEFIX_I-int\t 0.0667804\t8.6328e-01\tLTR\tGypsy\n+DMRP1\t 0.0889793\t8.7188e-01\tUnknown\tUnknown\n+Gypsy4_I-int\t-0.0632668\t8.8199e-01\tLTR\tGypsy\n+QUASIMODO_LTR\t-0.0758141\t8.8199e-01\tLTR\tGypsy\n+Gypsy5_LTR\t-0.0832238\t8.8416e-01\tLTR\tGypsy\n+Gypsy7_I-int\t 0.0709106\t8.8416e-01\tLTR\tGypsy\n+TC1-2_DM\t 0.0485761\t8.8416e-01\tDNA\tTcMar-Tc1\n+ROVER-I_DM\t-0.0523539\t8.8501e-01\tLTR\tGypsy\n+Stalker2_LTR\t-0.0636566\t8.8501e-01\tLTR\tGypsy\n+MDG1_I-int\t-0.0527394\t9.0541e-01\tLTR\tGypsy\n+DMLTR5\t 0.0615033\t9.2259e-01\tLTR\tGypsy\n+Gypsy2_I-int\t-0.0370213\t9.2289e-01\tLTR\tGypsy\n+Gypsy2-LTR_DM\t 0.0531394\t9.2289e-01\tLTR\tGypsy\n+ALA_DM\t-0.1255824\t9.2725e-01\tUnknown\tUnknown\n+Gypsy3_LTR\t-0.0416825\t9.5360e-01\tLTR\tGypsy\n+M4DM\t-0.0286022\t9.5845e-01\tDNA\tCMC-Transib\n+DNAREP1_DM\t 0.0280918\t9.6629e-01\tRC\tHelitron\n+BARI_DM\t 0.0258962\t9.7189e-01\tDNA\tTcMar-Tc1\n+DMTOM1_LTR\t 0.0238942\t9.7754e-01\tLTR\tGypsy\n+MINOS\t 0.0226472\t9.8823e-01\tDNA\tTcMar-Tc1\n+STALKER4_I-int\t 0.0128051\t9.8873e-01\tLTR\tGypsy\n+G2_DM\t 0.0110450\t9.9427e-01\tLINE\tJockey\n+IDEFIX_LTR\t 0.0103925\t9.9427e-01\tLTR\tGypsy\n+ROOA_LTR\t-0.0111583\t9.9548e-01\tLTR\tPao\n+BS\t-0.0065436\t9.9758e-01\tLINE\tJockey\n+Invader4_LTR\t 0.0049712\t9.9758e-01\tLTR\tGypsy\n+Copia1-I_DM\t 0.0012652\t1.0000e+00\tLTR\tCopia\n+FTZ_DM\t 0.0000000\t1.0000e+00\tUnknown\tUnknown\n+FUSHI_DM\t 0.0000000\t1.0000e+00\tUnknown\tUnknown\n' |