| Previous changeset 2:7a145c72d375 (2022-07-01) Next changeset 4:28e8d2bd6aba (2022-07-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0" |
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modified:
concoct.xml macros.xml |
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added:
test-data/clusters.csv test-data/composition.fa test-data/composition.fa.gz test-data/coverage test-data/ten_reads.fa test-data/ten_reads_two_contigs-s.bam test-data/two_contigs-cut1.fasta test-data/two_contigs-cut2-coverage.tabular test-data/two_contigs-cut2.bed test-data/two_contigs-cut2.fasta test-data/two_contigs.fa |
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removed:
coverage_table.py cut_up_fasta.py extract_fasta_bins.py merge_cut_up_clustering.py test-data/input.fasta.gz test-data/input1.fa.gz test-data/input1.tabular test-data/input_coverage_table.fasta.gz test-data/input_coverage_table.tabular test-data/input_merge_clusters.tabular test-data/inputcluster1.tabular test-data/output_coverage_table.tabular test-data/output_merge_clusters.tabular |
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| diff -r 7a145c72d375 -r 3842ef1b2f34 concoct.xml --- a/concoct.xml Fri Jul 01 14:14:44 2022 +0000 +++ b/concoct.xml Thu Jul 07 08:33:35 2022 +0000 |
| [ |
| b'@@ -1,99 +1,140 @@\n <tool id="concoct" name="CONCOCT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n- <description>metagenome binning</description>\n+ <description>for metagenome binning</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements"/>\n <command detect_errors="exit_code"><![CDATA[\n-#set pca_components_file_name = \'PCA_components_data_gt\' + str($advanced.length_threshold) + \'.csv\'\n-#set pca_transformed_file_name = \'PCA_transformed_data_gt\' + str($advanced.length_threshold) + \'.csv\'\n-#set clustering_file_name = \'clustering_gt\' + str($advanced.length_threshold) + \'.csv\'\n-\n ## CONCOCT doesn\'t handle gzipped files.\n #if $composition_file.ext.endswith(".gz")\n- gunzip -c \'$composition_file\' > composition_file.fa &&\n+ gunzip -c \'$composition_file\' > \'composition_file.fa\' &&\n #else:\n- ln -s \'$composition_file\' composition_file.fa &&\n+ ln -s \'$composition_file\' \'composition_file.fa\' &&\n #end if\n \n mkdir outdir &&\n concoct\n---coverage_file \'$coverage_file\'\n---composition_file composition_file.fa\n---clusters $advanced.clusters\n---kmer_length $advanced.kmer_length\n---threads \\${GALAXY_SLOTS:-4}\n---length_threshold $advanced.length_threshold\n---read_length $advanced.read_length\n---total_percentage_pca $advanced.total_percentage_pca\n---basename \'outdir/\'\n---seed $advanced.seed\n---iterations $advanced.iterations\n---epsilon $advanced.epsilon\n-$advanced.no_cov_normalization\n-$advanced.no_total_coverage\n---no_original_data\n-$advanced.converge_out\n-\n-## Convert all CONCOCT .csv outputs to tabular.\n-&& sed \'s/\\("\\([^"]*\\)"\\)\\?,/\\2\\t/g\' outdir/$pca_components_file_name > \'$output_pca_components\'\n-&& sed \'s/\\("\\([^"]*\\)"\\)\\?,/\\2\\t/g\' outdir/$pca_transformed_file_name > \'$output_pca_transformed\'\n-&& sed \'s/\\("\\([^"]*\\)"\\)\\?,/\\2\\t/g\' outdir/$clustering_file_name > \'$output_clustering\'\n-#if str($advanced.output_process_log) == \'yes\':\n- && mv outdir/log.txt \'$process_log\'\n-#end if\n+ --coverage_file \'$coverage_file\'\n+ --composition_file \'composition_file.fa\'\n+ --clusters $advanced.clusters\n+ --kmer_length $advanced.kmer_length\n+ --threads \\${GALAXY_SLOTS:-4}\n+ --length_threshold $advanced.length_threshold\n+ --read_length $advanced.read_length\n+ --total_percentage_pca $advanced.total_percentage_pca\n+ --basename \'outdir/\'\n+ --seed $advanced.seed\n+ --iterations $advanced.iterations\n+ $advanced.no_cov_normalization\n+ $output.no_total_coverage\n+ --no_original_data\n+ $output.converge_out\n ]]></command>\n <inputs>\n- <param argument="--coverage_file" type="data" format="tabular" label="Tabular coverage file" help="Columns correspond to samples and rows to contigs"/>\n- <param argument="--composition_file" type="data" format="fasta,fasta.gz" label="Fasta file" help="Used to calculate the kmer composition (the genomic signature) of each contig"/>\n+ <param argument="--coverage_file" type="data" format="tabular" label="Coverage file" help="Table where each row correspond to a contig, and each column correspond to a sample. The values are the average coverage for this contig in that sample"/>\n+ <param argument="--composition_file" type="data" format="fasta,fasta.gz" label="Composition file with sequences" help="It is named the composition file since it is used to calculate the kmer composition (the genomic signature) of each contig."/>\n <section name="advanced" title="Advanced options">\n- <param argument="--clusters" type="integer" value="400" label="Maximum number of clusters for the Variational Gaussian Mixture Model algorithm"/>\n- <param argument="--kmer_length" type="integer" value="4" label="Kmer length"/>\n- <param argument="--length_threshold" type="integer" value="1000" label="Sequence length threshold" help="Contigs shorter than this value will not be included"/>\n- <param argument="--read_length" type="integer" value='..b' <param name="log" value="true"/>\n+ </section>\n+ <output name="process_log" ftype="txt" compare="contains">\n <assert_contents>\n- <has_size value="367636"/>\n- <has_text text="7377051e-02"/>\n+ <has_size value="786"/>\n+ <has_text text="CONCOCT Finished"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_pca_components" ftype="csv">\n+ <assert_contents>\n+ <has_size value="362924" delta="10"/>\n+ <has_text text="-5.90697200e-02"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_pca_transformed" ftype="csv">\n+ <assert_contents>\n+ <has_size value="834200" delta="10"/>\n+ <has_text text="contig-21000001"/>\n </assert_contents>\n </output>\n- <output name="output_pca_transformed" ftype="tabular">\n+ <output name="output_clustering" ftype="csv">\n <assert_contents>\n- <has_size value="737926"/>\n- <has_text text="NODE_103_length_20202_cov_8.395357.0"/>\n+ <has_size value="6923" delta="10"/>\n+ <has_text text="contig-21000001,"/>\n </assert_contents>\n </output>\n- <output name="output_clustering" ftype="tabular">\n+ </test>\n+ <test expect_num_outputs="3">\n+ <param name="coverage_file" value="coverage" ftype="tabular"/>\n+ <param name="composition_file" value="composition.fa.gz" ftype="fasta.gz"/>\n+ <section name="advanced">\n+ <param name="clusters" value="400"/>\n+ <param name="kmer_length" value="4"/>\n+ <param name="length_threshold" value="1000"/>\n+ <param name="read_length" value="100"/>\n+ <param name="total_percentage_pca" value="100"/>\n+ <param name="seed" value="1"/>\n+ <param name="iterations" value="500"/>\n+ <param name="no_cov_normalization" value=""/>\n+ </section>\n+ <section name="output">\n+ <param name="no_total_coverage" value=""/>\n+ <param name="converge_out" value=""/>\n+ <param name="log" value="false"/>\n+ </section>\n+ <output name="output_pca_components" ftype="csv">\n <assert_contents>\n- <has_size value="12167"/>\n- <has_text text="NODE_103_length_20202_cov_8.395357"/>\n+ <has_size value="362924" delta="10"/>\n+ <has_text text="-5.90697200e-02"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_pca_transformed" ftype="csv">\n+ <assert_contents>\n+ <has_size value="834200" delta="10"/>\n+ <has_text text="contig-21000001"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_clustering" ftype="csv">\n+ <assert_contents>\n+ <has_size value="6923" delta="10"/>\n+ <has_text text="contig-21000001,"/>\n </assert_contents>\n </output>\n </test>\n@@ -103,7 +144,7 @@\n \n CONCOCT (Clustering cONtigs with COverage and ComposiTion) performs unsupervised binning of metagenomic contigs by\n using nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately\n-(up to species level) bin metagenomic contigs. \n+(up to species level) bin metagenomic contigs.\n \n The tool accepts 2 inputs; a tabular file where each row corresponds to a contig and each column corresponds to a\n sample (the values are the average coverage for this contig in that sample) and a file containing sequences in\n' |
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| diff -r 7a145c72d375 -r 3842ef1b2f34 coverage_table.py --- a/coverage_table.py Fri Jul 01 14:14:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,83 +0,0 @@ -#!/usr/bin/env python - -import argparse -import gzip -from functools import partial - -from Bio import SeqIO - - -def generate_coverage_table(input_fasta, input_tabular, gzipped, output): - # Read input file into a dict and return everything - # in the table format required by CONCOCT. - gc_and_len_dict = get_gc_and_len_dict(input_fasta, gzipped) - assert(len(gc_and_len_dict) > 0) - bed_coverage_dict = get_bed_coverage_dict(input_tabular) - - with open(output, 'w') as fh: - # Output the header. - fh.write("contig\tlength") - t = tuple(range(len(bed_coverage_dict))) - fh.write("\tcov_mean_sample_%d\n" % len(t)) - # Output the content. - for acc in gc_and_len_dict: - # Fasta stats. - fh.write("%s\t%s" % (acc, gc_and_len_dict[acc]['length'])) - # Mean - try: - # Coverage mean - fh.write("\t%f" % (bed_coverage_dict[acc]["cov_mean"])) - except KeyError: - # No reads mapped to this contig - fh.write("\t0") - fh.write("\n") - - -def get_bed_coverage_dict(input_tabular): - # Ddetermine mean coverage and percentage covered - # for each contig, returning a dict with fasta id - # as key and percentage covered and cov_mean as keys - # for the inner dict. - out_dict = {} - - with open(input_tabular, 'r') as fh: - for line in fh: - line = line.rstrip('\r\n') - cols = line.split('\t') - try: - d = out_dict[cols[0]] - except KeyError: - d = {} - out_dict[cols[0]] = d - if int(cols[1]) == 0: - d["percentage_covered"] = 100 - float(cols[4]) * 100.0 - else: - d["cov_mean"] = d.get("cov_mean", 0) + int(cols[1]) * float(cols[4]) - return out_dict - - -def get_gc_and_len_dict(input_fasta, gzipped): - # Creates a dictionary with the fasta id as key - # and GC and length as keys for the inner dictionary. - if gzipped: - _open = partial(gzip.open, mode='rt') - else: - _open = open - - out_dict = {} - with _open(input_fasta) as input_fh: - for rec in SeqIO.parse(input_fh, "fasta"): - out_dict[rec.id] = {} - out_dict[rec.id]["length"] = len(rec.seq) - return out_dict - - -parser = argparse.ArgumentParser(description=__doc__) -parser.add_argument('--input_tabular', action='store', dest='input_tabular', help='bedtools genomeCoverageBed bed file') -parser.add_argument('--input_fasta', action='store', dest='input_fasta', help='Contigs fasta file') -parser.add_argument("--gzipped", action="store_true", dest="gzipped", default=False, help="input_fasta is gzipped") -parser.add_argument('--output', action='store', dest='output', help='Output file') - -args = parser.parse_args() - -generate_coverage_table(args.input_fasta, args.input_tabular, args.gzipped, args.output) |
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| diff -r 7a145c72d375 -r 3842ef1b2f34 cut_up_fasta.py --- a/cut_up_fasta.py Fri Jul 01 14:14:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,58 +0,0 @@ -#!/usr/bin/env python - -import argparse -import gzip -from functools import partial - -from Bio import SeqIO - - -def cut_up_fasta(input_fasta, chunk_size, overlap, merge_last, output_fasta, output_bed, gzipped): - if gzipped: - _open = partial(gzip.open, mode='rt') - else: - _open = open - - fasta_fh = open(output_fasta, 'w') - - if output_bed is not None: - bed_fh = open(output_bed, 'w') - - with _open(input_fasta) as input_fh: - for record in SeqIO.parse(input_fh, "fasta"): - if (not merge_last and len(record.seq) > chunk_size) or (merge_last and len(record.seq) >= 2 * chunk_size): - for index, split_seq in enumerate(chunks(record.seq, chunk_size, overlap, merge_last)): - fasta_fh.write(f">{record.id}.concoct_part_{index}\n{split_seq}\n") - if output_bed is not None: - bed_fh.write(f"{record.id}\t{chunk_size * index}\t{chunk_size * index + len(split_seq)}\t{record.id}.concoct_part_{index}\n") - else: - fasta_fh.write(f">{record.id}.concoct_part_0\n{record.seq}\n") - if output_bed is not None: - bed_fh.write(f"{record.id}\t0\t{len(record.seq)}\t{record.id}.concoct_part_0\n") - if output_bed is not None: - bed_fh.close() - - -def chunks(seq, chunk_size, overlap_size, merge_last): - # Yield successive chunk_size-sized chunks from seq - # with given overlap overlap_size between the chunks. - assert chunk_size > overlap_size - if merge_last: - for i in range(0, len(seq) - chunk_size + 1, chunk_size - overlap_size): - yield seq[i:i + chunk_size] if i + chunk_size + chunk_size - overlap_size <= len(seq) else seq[i:] - else: - for i in range(0, len(seq), chunk_size - overlap_size): - yield seq[i:i + chunk_size] - - -parser = argparse.ArgumentParser() -parser.add_argument("--input_fasta", action="store", dest="input_fasta", help="Fasta files with contigs") -parser.add_argument("--gzipped", action="store_true", dest="gzipped", help="Input file is gzipped") -parser.add_argument("--chunk_size", action="store", dest="chunk_size", type=int, help="Chunk size\n") -parser.add_argument("--overlap_size", action="store", dest="overlap_size", type=int, help="Overlap size\n") -parser.add_argument("--merge_last", default=False, action="store_true", dest="merge_last", help="Concatenate final part to last contig\n") -parser.add_argument("--output_bed", action="store", dest="output_bed", default=None, help="BED file to be created with exact regions of the original contigs corresponding to the newly created contigs") -parser.add_argument("--output_fasta", action="store", dest="output_fasta", help="Output fasta file with cut contigs") - -args = parser.parse_args() -cut_up_fasta(args.input_fasta, args.chunk_size, args.overlap_size, args.merge_last, args.output_fasta, args.output_bed, args.gzipped) |
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| diff -r 7a145c72d375 -r 3842ef1b2f34 extract_fasta_bins.py --- a/extract_fasta_bins.py Fri Jul 01 14:14:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,49 +0,0 @@ -#!/usr/bin/env python - -import argparse -import gzip -import os -import sys -from collections import defaultdict -from functools import partial - -import pandas as pd -from Bio import SeqIO - -parser = argparse.ArgumentParser(description=__doc__) - -parser.add_argument('--gzipped', action='store_true', dest='gzipped', help='Input files are gzipped') -parser.add_argument("--input_fasta", action="store", dest="input_fasta", help="Input Fasta file") -parser.add_argument("--input_cluster", action="store", dest="input_cluster", help="Concoct output cluster file") -parser.add_argument("--output_path", help="Output directory") - -args = parser.parse_args() - -all_seqs = {} -if args.gzipped: - _open = partial(gzip.open, mode='rt') -else: - _open = open - -with _open(args.input_fasta) as fh: - for seq in SeqIO.parse(fh, "fasta"): - all_seqs[seq.id] = seq - -# Make sure we're reading the file as tabular! -df = pd.read_csv(args.input_cluster, sep='\t') -try: - assert df.columns[0] == 'contig_id' - assert df.columns[1] == 'cluster_id' -except AssertionError: - sys.stderr.write("ERROR! Header line was not 'contig_id, cluster_id', please adjust your input file. Exiting!\n") - sys.exit(-1) - -cluster_to_contigs = defaultdict(list) -for i, row in df.iterrows(): - cluster_to_contigs[row['cluster_id']].append(row['contig_id']) - -for cluster_id, contig_ids in cluster_to_contigs.items(): - output_file = os.path.join(args.output_path, "{0}.fa".format(cluster_id)) - seqs = [all_seqs[contig_id] for contig_id in contig_ids] - with open(output_file, 'w') as ofh: - SeqIO.write(seqs, ofh, 'fasta') |
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| diff -r 7a145c72d375 -r 3842ef1b2f34 macros.xml --- a/macros.xml Fri Jul 01 14:14:44 2022 +0000 +++ b/macros.xml Thu Jul 07 08:33:35 2022 +0000 |
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| @@ -1,12 +1,11 @@ <macros> - <token name="@TOOL_VERSION@">1.0.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">1.1.0</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.01</token> <xml name="requirements"> <requirements> - <requirement type="package" version="1.79">biopython</requirement> <requirement type="package" version="@TOOL_VERSION@">concoct</requirement> - <requirement type="package" version="0.19.2">pandas</requirement> + <yield/> </requirements> </xml> <token name="@HELP_OVERVIEW@"> |
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| diff -r 7a145c72d375 -r 3842ef1b2f34 merge_cut_up_clustering.py --- a/merge_cut_up_clustering.py Fri Jul 01 14:14:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,56 +0,0 @@ -#!/usr/bin/env python - -import argparse -import re -import sys -from collections import Counter -from collections import defaultdict - - -CONTIG_PART_EXPR = re.compile(r'(.*)\.concoct_part_([0-9]*)') - - -def original_contig_name_special(contig_id): - try: - original_id, part_index = CONTIG_PART_EXPR.match(contig_id).group(1, 2) - return original_id, part_index - except AttributeError: - # No matches for concoct_part regex. - return contig_id, 0 - - -parser = argparse.ArgumentParser() -parser.add_argument("--input", action="store", dest="input", help="Tabular file with cut up clusters") -parser.add_argument("--output", action="store", dest="output", help="Output file with merged clusters") - -args = parser.parse_args() - -# Get cut up clusters -all_seqs = {} -all_originals = defaultdict(dict) -with open(args.input, 'r') as ifh: - for i, line in enumerate(ifh): - if i == 0: - if 'contig_id' not in line: - sys.stderr.write("ERROR nvalid clustering file, 'contig_id' is not found in the header.") - sys.exit(-1) - # Skip header. - continue - line = line.rstrip('\r\n') - contig_id, cluster_id = line.split('\t') - original_contig_name, part_id = original_contig_name_special(contig_id) - all_originals[original_contig_name][part_id] = cluster_id - -# Merge cut up clusters. -with open(args.output, 'w') as ofh: - ofh.write("contig_id\tcluster_id\n") - for original_contig_id, part_ids_d in all_originals.items(): - if len(part_ids_d) > 1: - c = Counter(part_ids_d.values()) - cluster_id = c.most_common(1)[0][0] - c_string = [(a, b) for a, b in c.items()] - # Here if len(c.values()) > 1, - # then no cluster for contig. - else: - cluster_id = list(part_ids_d.values())[0] - ofh.write(f"{original_contig_id}\t{cluster_id}\n") |
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| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/clusters.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clusters.csv Thu Jul 07 08:33:35 2022 +0000 |
| b |
| @@ -0,0 +1,350 @@ +contig_id,cluster_id +contig-21000001,39 +contig-75000034,53 +contig-2482000051,39 +contig-194000040,39 +contig-600000042,39 +contig-1619000036,37 +contig-20000017,39 +contig-750000028,39 +contig-80000059,39 +contig-1349000009,37 +contig-216000039,17 +contig-447000020,39 +contig-21000060,39 +contig-2440000038,39 +contig-223000034,39 +contig-28000057,39 +contig-25000027,39 +contig-90000033,39 +contig-421000040,49 +contig-85000005,39 +contig-135000029,23 +contig-2453000058,39 +contig-37000022,39 +contig-278000010,39 +contig-223000058,0 +contig-554000017,24 +contig-51000051,39 +contig-176000044,39 +contig-334000016,39 +contig-561000035,39 +contig-986000004,39 +contig-1105000038,39 +contig-22000004,39 +contig-721000030,39 +contig-1264000040,39 +contig-2538000050,39 +contig-213000005,39 +contig-85000031,39 +contig-6000035,39 +contig-913000037,39 +contig-44000020,39 +contig-96000008,39 +contig-161000004,52 +contig-973000053,39 +contig-241000057,39 +contig-2452000034,39 +contig-101000036,11 +contig-99000027,39 +contig-119000019,45 +contig-1000023,39 +contig-61000022,39 +contig-53000052,17 +contig-142000043,39 +contig-173000038,39 +contig-2487000030,39 +contig-73000046,39 +contig-39000006,39 +contig-77000037,39 +contig-57000048,39 +contig-70000056,39 +contig-38000053,3 +contig-2000036,39 +contig-422000003,39 +contig-13000028,39 +contig-70000037,39 +contig-355000043,39 +contig-118000028,41 +contig-844000015,29 +contig-74000016,39 +contig-59000020,39 +contig-2510000020,39 +contig-332000045,39 +contig-126000012,13 +contig-70000052,39 +contig-114000018,39 +contig-418000042,23 +contig-80000004,39 +contig-145000030,39 +contig-1258000044,39 +contig-734000047,40 +contig-498000018,39 +contig-62000044,39 +contig-26000030,39 +contig-279000032,15 +contig-606000057,39 +contig-31000047,39 +contig-313000032,39 +contig-505000034,39 +contig-25000059,39 +contig-6000001,39 +contig-587000030,39 +contig-201000051,39 +contig-2557000045,39 +contig-71000056,39 +contig-145000057,16 +contig-1512000010,48 +contig-73000020,15 +contig-1319000017,39 +contig-483000045,6 +contig-245000032,39 +contig-86000038,39 +contig-9000012,39 +contig-208000005,39 +contig-168000042,39 +contig-720000009,39 +contig-82000009,39 +contig-129000060,39 +contig-168000018,40 +contig-61000049,39 +contig-83000052,39 +contig-104000034,39 +contig-114000022,39 +contig-133000010,39 +contig-301000036,39 +contig-1393000034,39 +contig-849000019,39 +contig-1869000048,39 +contig-421000055,39 +contig-295000035,39 +contig-2354000041,9 +contig-52,39 +contig-123000003,39 +contig-203000050,39 +contig-1909000043,37 +contig-1624000019,39 +contig-1552000031,39 +contig-148000050,39 +contig-2326000025,39 +contig-55000036,39 +contig-252000038,39 +contig-186000043,39 +contig-365000045,39 +contig-101000041,39 +contig-396000006,39 +contig-83000059,39 +contig-41000033,39 +contig-53000041,39 +contig-71000017,39 +contig-524000001,39 +contig-2500000026,39 +contig-74000043,39 +contig-12000026,39 +contig-118000009,7 +contig-100000043,39 +contig-358000029,39 +contig-154000061,39 +contig-2513000037,39 +contig-1361000032,39 +contig-96000006,21 +contig-397000044,37 +contig-1581000051,39 +contig-518000031,35 +contig-2316000002,39 +contig-2576000045,39 +contig-48000025,17 +contig-2444000058,39 +contig-360000059,39 +contig-33000003,39 +contig-1167000007,39 +contig-1067000006,5 +contig-813000012,39 +contig-1086000039,39 +contig-104000009,48 +contig-257000051,39 +contig-94000000,39 +contig-122000019,39 +contig-2497000034,39 +contig-36000028,39 +contig-920000003,39 +contig-169000025,39 +contig-1758000047,47 +contig-44000014,39 +contig-10000029,39 +contig-397000046,39 +contig-575000037,39 +contig-118000021,39 +contig-1861000019,39 +contig-112000056,39 +contig-214000004,34 +contig-80000060,39 +contig-13000026,39 +contig-660000045,41 +contig-54000007,39 +contig-2516000046,39 +contig-177000043,25 +contig-923000027,39 +contig-3000003,39 +contig-130000015,51 +contig-340000039,22 +contig-129000036,39 +contig-112000030,39 +contig-150000030,39 +contig-1062000011,48 +contig-268000020,39 +contig-2000043,39 +contig-490000060,39 +contig-197000051,39 +contig-262000026,39 +contig-304000048,30 +contig-497000050,39 +contig-3000044,39 +contig-173000042,10 +contig-185000039,39 +contig-228000052,39 +contig-48000030,39 +contig-101000023,39 +contig-157000027,39 +contig-97000040,39 +contig-193000061,39 +contig-545000000,39 +contig-132000015,39 +contig-433000030,39 +contig-59000035,39 +contig-322000050,39 +contig-609000006,39 +contig-693000042,39 +contig-62000015,39 +contig-189000003,39 +contig-284000009,39 +contig-432000046,39 +contig-384000046,39 +contig-113000037,40 +contig-161000048,39 +contig-33000020,39 +contig-44000021,39 +contig-1861000057,39 +contig-274000008,39 +contig-1343000001,39 +contig-44000044,39 +contig-177000026,9 +contig-913000044,39 +contig-334000007,39 +contig-186000025,31 +contig-77000008,39 +contig-177000037,50 +contig-91000012,1 +contig-508000060,39 +contig-166000020,27 +contig-131000060,4 +contig-106000039,39 +contig-40000045,39 +contig-106000038,20 +contig-1234000040,39 +contig-862000002,39 +contig-17000055,39 +contig-2464000022,39 +contig-193000056,13 +contig-131000027,39 +contig-71000048,39 +contig-195000056,15 +contig-71000058,39 +contig-42000030,39 +contig-148000052,39 +contig-71000043,39 +contig-1088000058,39 +contig-297000000,39 +contig-289000050,39 +contig-7000000,39 +contig-61000046,14 +contig-99000012,39 +contig-258000054,39 +contig-788000040,37 +contig-49000052,52 +contig-140000037,39 +contig-9000050,39 +contig-126000014,18 +contig-2050000048,39 +contig-1219000041,39 +contig-327000030,39 +contig-205000060,39 +contig-58000040,39 +contig-203000046,36 +contig-263000008,42 +contig-202000053,39 +contig-2555000050,39 +contig-114000039,39 +contig-173000043,44 +contig-2571000015,39 +contig-40000056,39 +contig-755000024,39 +contig-60,39 +contig-2531000029,39 +contig-142000011,7 +contig-39000033,13 +contig-314000057,39 +contig-52000025,39 +contig-135000052,39 +contig-362000043,39 +contig-1981000047,39 +contig-2522000033,39 +contig-138000012,39 +contig-138000058,39 +contig-49000002,37 +contig-102000024,39 +contig-1731000047,39 +contig-1815000037,39 +contig-534000020,39 +contig-54000014,39 +contig-120000027,39 +contig-111000016,39 +contig-344000022,2 +contig-202000024,39 +contig-388000011,39 +contig-316000015,39 +contig-524000047,39 +contig-73000009,39 +contig-558000012,12 +contig-2479000045,39 +contig-28000027,39 +contig-513000043,39 +contig-740000015,39 +contig-197000042,39 +contig-318000039,8 +contig-1730000050,39 +contig-284000007,30 +contig-171000032,19 +contig-1140000053,39 +contig-526000010,39 +contig-127000026,43 +contig-86000030,39 +contig-85000045,12 +contig-1256000020,39 +contig-229000014,39 +contig-207000061,41 +contig-64000040,33 +contig-126000041,39 +contig-377000024,39 +contig-294000057,46 +contig-411000013,39 +contig-497000014,38 +contig-2518000016,39 +contig-766000005,35 +contig-128000004,2 +contig-108000038,39 +contig-842000017,37 +contig-343000039,39 +contig-1142000053,32 +contig-40000039,39 +contig-109000013,33 +contig-338000005,26 +contig-20000011,39 +contig-129000002,39 +contig-106000034,39 +contig-529000024,39 +contig-246000052,36 +contig-1374000055,39 +contig-27000055,39 +contig-109000031,30 +contig-200000042,28 |
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/composition.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/composition.fa Thu Jul 07 08:33:35 2022 +0000 |
| b |
| b'@@ -0,0 +1,17599 @@\n+>contig-21000001 9998 nucleotides\n+GACCATCCGGTGGAGATTTCTCCTCTGACCAAGAGAAAACCGGAGGATCCTGACTATACG\n+GAGCGTTTTGAGCTGTTTATCACGAAGCGTGAGATGGCTAACGCTTACTCTGAGTTAAAC\n+GATCCGATTGACCAGAGACTTCGTTTTGAGGCGCAGGAAGTGTTAAAGGCCGCAGGCGAT\n+GAGGAAGCCAACTCCATGGATGAGGACTTCTTAAATGCGCTGATGATCGGTATGCCTCCG\n+ACAGGCGGCATCGGCATCGGCATCGACCGTTTCGTTATGCTGCTGACTGATTCCTATGCA\n+ATTCGTGACGTTCTGCTGTTCCCGACCATGAAGACGCTGGGCAGTTCTGATAATAGCAGG\n+AAGGCAGAGAAGGCCGCTCCGGCCGCTGCTTCTGCTCCGGCTGCTGAGAACGTGAAAGCC\n+GCGGTGGAGATTGATTTTTCCAATGTGAAGATTGAGCCGCTGTTTGAAGAGATGGTGGAT\n+TTTGAGACTTTCTCAAAGTCTGATTACCGTGCAGTGAAGATCAAAGACTGCGTGGCAGTG\n+CCGAAGAGCAAGAAGCTTCTCCAGTTTACTCTGGACGATGGAAGCGGCACAGACCGCACG\n+ATTTTAAGCGGAATTCATGAGTACTACGAGCCGGAGGATCTGATTGGTAAGACAGCCATC\n+GCCATCGTGAATCTGCCGCCAAGAAAGATGATGGGAATTGACTCCTGCGGTATGCTGATT\n+TCAGCCGTGCATGAGGAAGACGGACATGAGGGACTGAATCTGCTGATGGTGGATGATAGG\n+ATTCCGGCGGGGGCGAAGTTGTATTAAAATACAACAAAAGAACCGTTTTTCAGGATAGTA\n+GGAATTCAATAACAAAAGTTGTTACCCCCAATTTTGTTAACATTGAAAAATGTAGATGTG\n+TTTGAACAGAAGTGGCGCTTACTGATATAATGATAAGAAATTAGGACTCTATGACATTAG\n+TCATAGAGTCCTTTTTTCTGTTTTGAAATCAAATTGTTTAGAATATGCTTGAAAGTAAAC\n+AAAATTAAACAAGAAATAGATGAATAGTAAACAAAACGTTGACCATAAAGCTTTTTAATG\n+GTATAATAACTATCAAAGCAAAGGAGGATAAGACCATGTACGCAATGGATTTCGCTCTGG\n+TAGGAGCTAACATACAAAATAAATTAGTTGAAAAGGAAATGACACAACAGAGTTTGGCGG\n+ATGCTCTTGGTATATCAAAGCAGGTTATGAACAAAATCATTAAAGGAAGCAAGGCGATCA\n+ATGTGAATGAGCTTGCAAGAATTGCGGATATCCTGAACACATCTGCAGATGAATTACTTA\n+CAGTTGGGACTGAACCAGCTACTGTTGACAGCCTGAGCTTTATGGGAGATGTTTACGATG\n+AGGTTACACGGGAACGTATTAACTTCATCAGATCTGCGATTGATGAGATTCATATGCTGG\n+AGGATTTACTGGATGACTAATGACTTAAATGAATTAGAAGTAAATGAAATAAAGAATCAT\n+GCAATAGAAAAGTTAGGACTGTGCAGAAAAGGAAATGATATTATAGGGACACAGATTTTT\n+TCAATCCTTGGTTTGTATGCCAGAGTAATTTACTATCCTCTGGGAAAAAATGCACCTTGG\n+GGATTTACCAGAATCAGCGGTTCTAGAAATGATGCCTCATTGGAGAAGCCATTTGTTGCC\n+CTTAATTCTTCTATTCCGGTGGACTGCCAGGTGTTTGCAGCGGCACACGAATTATACCAT\n+ATTTGGTATGAACAAAATCCGGATATGCTTCCTTCTGATTTGTTGAATGAACACGATAAA\n+AAGACAAGTGAGAAAAAAGCAAATAGATTTGCAGCAGAATTTCTTGTGGATGAATTATTG\n+CTGAAACAGGAAATCGAGTTATATAAAATTAAGAAGCTTACAATAAAAAGCATATTACAA\n+TTAGCAGAACTGTTTACGGTTCCATACAGGACAATGGTGAAGCGGCTGGGAGAAATTGGA\n+GTAATTGAGGATGCGGATCTAAATAGATTTCTCGCAGAGTCAGAGGATTCTGTTGAAAAA\n+TATAAGAAGAGATATTCCATACCATCTCAGAAATCTGATGGTCGGATTATCATGGATAAC\n+CTGGTTGAGTTAGCCGTCGCCGCTTATGAAGCCGGGTACATTACATATGAGAAACTGGAA\n+TATTTGCTGAGAATCAGTACCTTAAAGCCAGAGGATTTAGGCATTGAAAAGAAAACTGCC\n+TGCGAATTCCCTTCTGATGATGAATTAGATCGTATTATGGAGGAATGAGTATGGTAGAAA\n+AATAATTATTGATGCAGATTTATGTATCAAGTTGGGAGGAAGTAATAAGTATAGATATTT\n+GCATGATGTGCTTCCTTTGATTGCAAAAGAGATTTATATGCATACACACGCCTTTGGAGA\n+GGTGTTGATGCCTGCCAGTGCAGTCAGCCAGTTAAAGGATTTGATTACGGAAAATAAAGT\n+GGTTCTTGTTAACGAAAGTGGTTTGGACAGCAAGGTACGAGCAATCTATGATGCAGCTTA\n+TCGTAATCTTGAGAGAGTTATGATTGATGCAACGAGACCAAACAAGAATAAAGGAGAGAT\n+GTGTTCGCTCGCATATGCAAAAGCAGCGAGCATACCTATCTTTGCAACAGATGAAAAAGA\n+CCTACAGCCTATCATTGATAAGCAATTGAATACGGGAATGGATGATATAACCTGCATAAG\n+AATTACAGATATTATTACGAAGGCTAAGGAGGGGGAAATAGCGGTACCGAGAAAGATTGC\n+AAAGGCACTTTGGATCGTGGCCGGAAAGAGAAAAGAAGTATTTGATAATGAGATATGGCC\n+GGTAACGGCTGAATGATACATATGAAAGGAGCCTGTTTGGGACAAAGGAATACCGCCTTG\n+TCCCAAACAGGCTATTACTGGAAGCAGAGGCTTCGTGGACTGCCTGGAAACGGTGATGAA\n+GATTCATTACACCAGCATTTCAACAAACTCAACCGGATACATAGTCCGTTTGGACACTTC\n+CTCAACCGCTAGTCCCTGGCTGAGAAAACGCCTGATGACGCACTCCATGCTTTCTGCTGC\n+CTCAATGATATATTTATCAAAATCATAAAACCGCATACTCCGCTGGCCCCAGGGATATTC\n+CGTCGGGTGATGGATAAATTCCACTCCTTCGATGGCCTCCAGCTTTCTCTCCCAGTCGTC\n+GATCCGGTCTGTTTCAAAATAGAGCTGAAAGTTATTTGCTGCTGTCTTTCTGTTCAGTGA\n+TTTACCGATCATTGCTTCGTAGTTTGCCTGCAGGCTGAGGCCATTGTCCAATGAGACGTG\n+TTCTCCTAAATCCATGAGGACTTTTTGCTCCAGGATTGTTTCGTAAAAATATTTTGATTT\n+TTCCATATCATCAACTATAAGCAATGTGCCTCCGTATTTCATATGGATACCTCCTCTTTT\n+TTTCTCAATTATAGCCTAAAACTTTGCGATCGCACTGTAAAAATCGGACAAGTTGTTTCG\n+GTATTCCTGAGGAGTAACGCCGCATACGGCCCTAAAATCCCTGATAAAGTGAGAAATATC\n+ATAAAACCCGGATTCGGCAGATATATAATCGAGGCTGTAGCTCGTATGGTGCAGCAGATA\n+AATGGCTTTGTTGATACGCACGATTCGGGAAAAATGTTTCAGGTTAAATCCTAAATAGTG\n+ATTGGAAAGCCTGTTTAAATGACGTTCACTGTAAAATGTTTTTTCTGTTATTTCTTTGAG\n+ACTTATGTTACCGTTACTCTGAATGATCAGCTGCACGGCCAGACGGAATTCAGCCGGGTA\n+TTGGCTGCATTGGCTGCAAAGCAGCAGACTCTCGATT'..b'TAACA\n+AGTACAAACGGGCAGTGAGCGAGATTCATACCCAGCAAGCTGAAACGGATAGTCTCCTTG\n+CCTATCTGGAAAGTCTTGACGCGTCCCTGGATACAGCCATCACCAAAGGGGATGTTTCAG\n+AAATCAAGGAAGAAATCATTGCCCTTGGCCTCCTTCCCAAGCCCCGTAAAAAGATGGCGG\n+TCCAGTCCAAATCAGTTCCGCTTAAAGTCGTTCTTTCGGAAGACACCCTCCTTTATGTGG\n+GAAAAAACAACAAGCAGAATGACTATGTCACCTTCAAACTAGGACGCGCCCATGATCTTT\n+GGTTCCATGCCAAGAACATTCCGGGCTCCCATGTCATTCTGAAAACGACCCTTCCAAGCC\n+CCAGGGAAGAAGATATCCTGCGGGCTGCTCAAATCGCCGCTTACTACAGCAAAGGACGCT\n+TTTCCAGCCGCGTTTCCATCGACTGTACGCAGCGCCGCTATGTAAAAAAGCCAAACGGAG\n+CCAAGCCGGGCTTTGTCATTTTCACCAACCAAAAAACCATCAACGCGGAGCCAAAAAAAG\n+AACCGTGACCCAATGAAATGTACCCTCTTTACTAGACACCCAGTAAGGAGGGTACATTTT\n+GCGTTATACGAC\n+>contig-109000031 1241 nucleotides\n+GGCGCCCGCCGTGAGTCCTATACGCAGGATTCGCGCAAACCGCAGGTCGAGGCGGGCACG\n+CTCGAAGACGACCAGCGCCGCCGCGACTTCACGATCAACGCCATGGCGTGGTCGCTCAAC\n+GCCGGTTCGTTCGGCGAGCTGGTCGACCCGTTCGACGGCATGGACGACCTCGAAGAGTGC\n+GTCATCCGCACGCCGTGCGATCCCGACGTTACCTTCTCGGACGACCCGCTGCGCATGATG\n+CGGGCCGTGCGCTTCGCGTCGCAGTTGGGGTTCACGATCGAAGGCGAGACCTTCGACGCC\n+ATCCGCCGCAATGCGCACCGCATCCGGATCGTGTCGCGCGAACGCATCGCTGCGGAACTT\n+AACAAGATCGTCCTTTCGCCCGTACCCTCGATGGGCTTCGAACTGCTGGAGCTGACGGGG\n+CTTCTGGAGCTGATTTTCCCGGAGATGCACAACCTCAAGGGCGTCGAGAAGCGGGGCGCG\n+CATGCCCATAAGGACAATTTTATCCATACGCTCAAGGTGCTGGACAACGTCGCCCGCCGC\n+AGCGGCGATCTGTGGCTGCGCTGGGCCGCCGTGCTGCACGACATCGCCAAGCCGCTGACG\n+AAGGCTTACGATCCCAAGGTCGGCTGGACGTTCCACGGCCACGAGGTCCTCGGCTCGAAG\n+ATGGTGCCGGCGATCTTCCGGCAGTTGAAGCTGCCGCTCAACGAGCATATGAAATTCGTG\n+CAGAAGCTGGTTTTCCTCCACCTGCGGCCGATCATCCTCTCCGAAGATCTGGTCACGGAC\n+TCGGCCGTGCGGCGTCTGCTGTTCGAGGCGGGCGACGACGTGGAGCAGCTGATGATCCTG\n+TGCGAAGCCGACATCACTTCGGGCATCGACGCCAAGGTCAAACGCTATCTGGCCAATTTC\n+GAGCTGGTGCGCCGCAAGATGAAGGATTTGGAGGAGCGCGACCGCATCCGCAACTTCCAG\n+CCGCCGATCACGGGCGAGATCATCATGCAGACCTACGGCATCGGTCCCTGCCGTGCCATC\n+GGCGACATCAAGGAGGTGATCAAGAACGCCATTCTCGACGGCGAAATTCCCAACGATTAC\n+GACGCGGCCTACGCCCTGATGGAGCGGCTGGCGGCGGAGAAGGGGCTGACGAAGGCCGGG\n+GGGCAGAACCCGTAGAATGGGGCCCGGCCGTCCGGGGCGTATTCGTGAATCGAAAGGTTG\n+GGCCGCTGCGGCTCAACCTTTTTTCATGCCCGCTTCCGCCT\n+>contig-78000025 3759 nucleotides\n+CGATATTCTTTATTGAGAAAATATCCGGCCGATAAGATATCCCATGTTTTTCCGTCATAG\n+AGCAGTTTTCCGTCACGGGTGAATTCGTAGATTACTTTTCCGGATAATCCTTTCACCCAT\n+TTCTGATAAACACGGTCGGGCAATGTAAGGGGAGTGAGCGGTTCCGTGTGGTCGGGGACT\n+TGCTTGCGGATACAGTTCTTCGGCTCTTTCCAGCCTTTGTACCAGATGGTGGCGGCGTCA\n+TTGCCGGTAGGTGTGATACGGAATTCCGTCGTATCTCCTTTCTGATTGCGTAAATGGAAG\n+AAGTAGCTGCCGTCAGCTTCCTGTTTTATCTGTTCGGCATAAAAAACGACATAATAGTTC\n+TCTACGAAATTCTCTCCGATGAGCGGACCGTTCCAGTCAGACACATTGTCTGCTTTAAAT\n+TGCCAGTAGCCTCGCAAAGATTCGGGAATTGTCTGATAAGTGCCGGATTGGGCGAAAGCG\n+ATAGTCTGTGTACTGCATAAAAGCAAAAGACCTATCAGGAGAAAACAGTAGGGGGGTCTC\n+ATGGTGTGTTTTTATTTAAGTTAGTATTTCGATTTATGACAAAGGTATTTTAATACCGGA\n+ATAATGAGGTGTGGTAAGTTTATTATTTGTAGTAGTTTAACTATTTTCTTCCCGATTCGT\n+ATCAAGATATTGAACTTGTCATTATCTTTGCAGCGTTATTTTAAACTCTTAATTTATATC\n+GTGTTATGAGAGCTAAGAAGTTTGCATGCTGTTTGATGGTCATGTCATTGCTGGCAGGTA\n+TTTCATTTATTTCCTGTGGCAATAGCTCCAGGGCGAAAGTAGAAAGTGAAGCAGCACAGA\n+CAGGAGAAGATTTCAAGTCG\n+>contig-200000042 1043 nucleotides\n+CAACTTCATCAGTCTGCTCTACTACTTCGGAATGCTCACCATCAGCGGCACGCACGAAGG\n+TAAGACAAAACTCTCCATCCCCAACATGGCGGTTCGCGTCACTCTCCATTAAACTCGTAT\n+CGAAAATGTGTGAAACATCACATTTCCGGTATGAAAATATGATTGACTATGTTCGGCAGG\n+ACTGTTTACTTGACACGCAAACGTTTTCGTAGATTAACCGTGTTTTTTCGTTACACTTGG\n+TCTATCGGCTTCTTTTTCTTCTCTATCTTTGAATCAAGTAATAATTTGAAAATCTAATAG\n+TATGAAGAAGATTAAGTTTCTTTCTTTTTTCTTATTTAGTGTGTTTTCATTCTGCTTGGT\n+AGCTTGCAGTGATGATAATGGTACTATACCTACACCGGAACCGGAACCTGAGCCGGAACC\n+TACGCCGTCAGAATGGACTGCGATTGCTGCATCTCCTGCTGATTGGGATGGGGAAAAACG\n+TGCGGACATCTCTTATCAGTTATTGGTTTACTCCTTTTCCGATGGCAATGGTGACGGTTA\n+TGGTGACATAAATGGCTTAATTTCTAAATTGGATTACATCAACTCTTTGGGTGTGAAGGC\n+TATCTGGCTTTCTCCTATTCATCCGTCGCCTTCGTATCATGGCTATGATGTGACGGATTA\n+TACGAAGGTGAATCAAAAGTTTGGTACAGAGAGTGACTTCGACAGGTTGGTTGCCGAAGC\n+ACACAGTCGGGGCATCAAGGTTTATTTGGATTATGTGTTGAACCACACGAGTGCGGAACA\n+TCCGTGGTTTCTGGCAGCAAAAGCTTCTACTGAGAGCGAATATCGCAATTACTACATATT\n+CTCTCAAGACCCGGAAGCTGACATCAAGGCAGGAAAAATTGATATGATTTCCAGTGAAGG\n+GGGAAACGGATATAATTCGGGAGAATGGTATTCTACGACAGCTTCAACAGATGTCGTAAG\n+CGGATGTTATAAATTTGTACTCGATTGGTCGAATGCTTCAAAACCTACGGTGACGGTGAG\n+CGTTGCAGAAAAGGCGGATACGG\n' |
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/composition.fa.gz |
| b |
| Binary file test-data/composition.fa.gz has changed |
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/coverage --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage Thu Jul 07 08:33:35 2022 +0000 |
| b |
| b'@@ -0,0 +1,351 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| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/input1.tabular --- a/test-data/input1.tabular Fri Jul 01 14:14:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/input_coverage_table.fasta.gz |
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| Binary file test-data/input_coverage_table.fasta.gz has changed |
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| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/input_coverage_table.tabular --- a/test-data/input_coverage_table.tabular Fri Jul 01 14:14:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/input_merge_clusters.tabular --- a/test-data/input_merge_clusters.tabular Fri Jul 01 14:14:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,330 +0,0 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|
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/inputcluster1.tabular --- a/test-data/inputcluster1.tabular Fri Jul 01 14:14:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -contig_id cluster_id -NODE_1_length_2054_cov_17.474684 77 -NODE_2_length_16156_cov_8.219856 93 |
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/output_coverage_table.tabular --- a/test-data/output_coverage_table.tabular Fri Jul 01 14:14:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,447 +0,0 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|
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/output_merge_clusters.tabular --- a/test-data/output_merge_clusters.tabular Fri Jul 01 14:14:44 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,306 +0,0 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|
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/ten_reads.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ten_reads.fa Thu Jul 07 08:33:35 2022 +0000 |
| b |
| @@ -0,0 +1,75 @@ +>contig-21000001_read_0 contig-21000001 9998 nucleotides +TTTCTCTCCCAGTCGTCGATCCGGTCTGTTTCAAAATAGAGCTGAAAGTTATTTGCTGCT +GTCTTTCTGTTCAGTGATTTACCGATCATTGCTTCGTAGT +>contig-21000001_read_1 contig-21000001 9998 nucleotides +GAGTCAGTCAGACGGCTGGCCCCGGAAATACCAGCAGCAATGGAGAAAATCCATCCTCCC +CGCCTGGAAGCGAAAGCAGAAATGACCAAATACCAGCGGC +>contig-21000001_read_2 contig-21000001 9998 nucleotides +TTTCAGAGAGGCTGTTTGAGTACTCCCATCCCCTGGGGGACAGAGGGCAGATTCTGGCCG +CTTCCCGGTGGCTGCAGCGGTTTGGCCTGGAGGCCAATGA +>contig-21000001_read_3 contig-21000001 9998 nucleotides +ACGATCACAAAAGGTCATTACGGCTGGCTGATTGATAAGGAGGCGGAAACGGAGGCTCTG +TTGGAAATAATCAGATCCGGTGAAAGTCAGGAGCGGGAGC +>contig-21000001_read_4 contig-21000001 9998 nucleotides +TAAAATGGTGCTGTTTCATGGATTCAACCATCTGTTCGATCTCATCCTCCATGGACAGGG +CCTGGTCGGAGGCAATGATGTGCAGATACTCCTCTTCACA +>contig-21000001_read_5 contig-21000001 9998 nucleotides +CAGTGCAGTCAGCCAGTTAAAGGATTTGATTACGGAAAATAAAGTGGTTCTTGTTAACGA +AAGTGGTTTGGACAGCAAGGTACGAGCAATCTATGATGCA +>contig-21000001_read_6 contig-21000001 9998 nucleotides +AGTGAGAAAAAAGCAAATAGATTTGCAGCAGAATTTCTTGTGGATGAATTATTGCTGAAA +CAGGAAATCGAGTTATATAAAATTAAGAAGCTTACAATAA +>contig-21000001_read_7 contig-21000001 9998 nucleotides +TGGTAGAAAAATAATTATTGATGCAGATTTATGTATCAAGTTGGGAGGAAGTAATAAGTA +TAGATATTTGCATGATGTGCTTCCTTTGATTGCAAAAGAG +>contig-21000001_read_8 contig-21000001 9998 nucleotides +TTTTCCAATGTGAAGATTGAGCCGCTGTTTGAAGAGATGGTGGATTTTGAGACTTTCTCA +AAGTCTGATTACCGTGCAGTGAAGATCAAAGACTGCGTGG +>contig-21000001_read_9 contig-21000001 9998 nucleotides +TCCACTCCTTCGATGGCCTCCAGCTTTCTCTCCCAGTCGTCGATCCGGTCTGTTTCAAAA +TAGAGCTGAAAGTTATTTGCTGCTGTCTTTCTGTTCAGTG +>contig-75000034_read_0 contig-75000034 1615 nucleotides +TTTTACCTTCATCACAAGAAAAGATAACTACGATGTCACAAAACAGACGGAGGTTATCCT +AAGGGCGGTCAAAAAGCTGGGTGTAAATGCAGAACGGACC +>contig-75000034_read_1 contig-75000034 1615 nucleotides +CAGGATTTACAGGATCTGGTCTGCGATATGATGTAGTGCTGTGCCGTCGATTCACAGACG +CGCCTGAGAGAACAGGAGGATTGGATGGAAAAACATTATG +>contig-75000034_read_2 contig-75000034 1615 nucleotides +GGAAATACGGCAGGAAGATCCCGTTCAGCGATGAAGCCGCCGCCCGTTTTACCTGGGGGG +AGGCCCAGGTGCTGGTCCATGTGGAAGAGGGGCGTGTCCG +>contig-75000034_read_3 contig-75000034 1615 nucleotides +ATTGTCCACGAGGCCCTGATGGTGGAGCCGACGGAGACGGAATCAAAGGAGAACTTAGAT +GAACTGATCGCCGTGTTCCACGAGATCTATGAGACGGCGA +>contig-75000034_read_4 contig-75000034 1615 nucleotides +ATCCCAATTTCGGCATGGAGGAGTATTTGCTTTACGATGTGGAAGAAGAGGAATGCATTC +TCTACCTGTGGCAGAATGAGAAAACCGTGGTCATAGGCAG +>contig-75000034_read_5 contig-75000034 1615 nucleotides +TACCCCTATCCCAATTTCGGCATGGAGGAGTATTTGCTTTACGATGTGGAAGAAGAGGAA +TGCATTCTCTACCTGTGGCAGAATGAGAAAACCGTGGTCA +>contig-75000034_read_6 contig-75000034 1615 nucleotides +ATCAAAGGAGAACTTAGATGAACTGATCGCCGTGTTCCACGAGATCTATGAGACGGCGAA +GCGTGATCCCGAATATATCCGGAGCTCCCCCCACATCACC +>contig-75000034_read_7 contig-75000034 1615 nucleotides +TATCTCCACACCACCGGCCTTTACCGGGAGGTGAAGAAGACAGAGGCCGCCGGCCTCCAT +ACGGAAGGCCTGCGCGTATCCATGGAGGAACTGAAGAAAC +>contig-75000034_read_8 contig-75000034 1615 nucleotides +CCTGTTTAAACTGCGGATGCATTCCTACGAAAACGTATCTCCACACCACCGGCCTTTACC +GGGAGGTGAAGAAGACAGAGGCCGCCGGCCTCCATACGGA +>contig-75000034_read_9 contig-75000034 1615 nucleotides +AAGGGCGGTCAAAAAGCTGGGTGTAAATGCAGAACGGACCGGCCGCAATGATATCACAGT +GGATGGCCGCAAGTTTTCCGGCAACGCGTACTACGAGACC +>contig-200000042_read_0 contig-200000042 1043 nucleotides +CATCCGTGGTTTCTGGCAGCAAAAGCTTCTACTGAGAGCGAATATCGCAATTACTACATA +TTCTCTCAAGACCCGGAAGCTGACATCAAGGCAGGAAAAA +>contig-200000042_read_1 contig-200000042 1043 nucleotides +ACTATGTTCGGCAGGACTGTTTACTTGACACGCAAACGTTTTCGTAGATTAACCGTGTTT +TTTCGTTACACTTGGTCTATCGGCTTCTTTTTCTTCTCTA +>contig-200000042_read_2 contig-200000042 1043 nucleotides +ACTCTCCATCCCCAACATGGCGGTTCGCGTCACTCTCCATTAAACTCGTATCGAAAATGT +GTGAAACATCACATTTCCGGTATGAAAATATGATTGACTA +>contig-200000042_read_3 contig-200000042 1043 nucleotides +ACTTCATCAGTCTGCTCTACTACTTCGGAATGCTCACCATCAGCGGCACGCACGAAGGTA +AGACAAAACTCTCCATCCCCAACATGGCGGTTCGCGTCAC +>contig-200000042_read_4 contig-200000042 1043 nucleotides +TGTGAAGGCTATCTGGCTTTCTCCTATTCATCCGTCGCCTTCGTATCATGGCTATGATGT +GACGGATTATACGAAGGTGAATCAAAAGTTTGGTACAGAG |
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/ten_reads_two_contigs-s.bam |
| b |
| Binary file test-data/ten_reads_two_contigs-s.bam has changed |
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/two_contigs-cut1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_contigs-cut1.fasta Thu Jul 07 08:33:35 2022 +0000 |
| b |
| b'@@ -0,0 +1,24 @@\n+>contig-21000001.concoct_part_0\n+GACCATCCGGTGGAGATTTCTCCTCTGACCAAGAGAAAACCGGAGGATCCTGACTATACGGAGCGTTTTGAGCTGTTTATCACGAAGCGTGAGATGGCTAACGCTTACTCTGAGTTAAACGATCCGATTGACCAGAGACTTCGTTTTGAGGCGCAGGAAGTGTTAAAGGCCGCAGGCGATGAGGAAGCCAACTCCATGGATGAGGACTTCTTAAATGCGCTGATGATCGGTATGCCTCCGACAGGCGGCATCGGCATCGGCATCGACCGTTTCGTTATGCTGCTGACTGATTCCTATGCAATTCGTGACGTTCTGCTGTTCCCGACCATGAAGACGCTGGGCAGTTCTGATAATAGCAGGAAGGCAGAGAAGGCCGCTCCGGCCGCTGCTTCTGCTCCGGCTGCTGAGAACGTGAAAGCCGCGGTGGAGATTGATTTTTCCAATGTGAAGATTGAGCCGCTGTTTGAAGAGATGGTGGATTTTGAGACTTTCTCAAAGTCTGATTACCGTGCAGTGAAGATCAAAGACTGCGTGGCAGTGCCGAAGAGCAAGAAGCTTCTCCAGTTTACTCTGGACGATGGAAGCGGCACAGACCGCACGATTTTAAGCGGAATTCATGAGTACTACGAGCCGGAGGATCTGATTGGTAAGACAGCCATCGCCATCGTGAATCTGCCGCCAAGAAAGATGATGGGAATTGACTCCTGCGGTATGCTGATTTCAGCCGTGCATGAGGAAGACGGACATGAGGGACTGAATCTGCTGATGGTGGATGATAGGATTCCGGCGGGGGCGAAGTTGTATTAAAATACAACAAAAGAACCGTTTTTCAGGATAGTAGGAATTCAATAACAAAAGTTGTTACCCCCAATTTTGTTAACATTGAAAAATGTAGATGTGTTTGAACAGAAGTGGCGCTTACTGATATAATGATAAGAAATTAGGACTCTATGACATTAGTCATAGAGTCCTTTTTTCTGTTTTGAAATCAAATTGTTTA\n+>contig-21000001.concoct_part_1\n+GAATATGCTTGAAAGTAAACAAAATTAAACAAGAAATAGATGAATAGTAAACAAAACGTTGACCATAAAGCTTTTTAATGGTATAATAACTATCAAAGCAAAGGAGGATAAGACCATGTACGCAATGGATTTCGCTCTGGTAGGAGCTAACATACAAAATAAATTAGTTGAAAAGGAAATGACACAACAGAGTTTGGCGGATGCTCTTGGTATATCAAAGCAGGTTATGAACAAAATCATTAAAGGAAGCAAGGCGATCAATGTGAATGAGCTTGCAAGAATTGCGGATATCCTGAACACATCTGCAGATGAATTACTTACAGTTGGGACTGAACCAGCTACTGTTGACAGCCTGAGCTTTATGGGAGATGTTTACGATGAGGTTACACGGGAACGTATTAACTTCATCAGATCTGCGATTGATGAGATTCATATGCTGGAGGATTTACTGGATGACTAATGACTTAAATGAATTAGAAGTAAATGAAATAAAGAATCATGCAATAGAAAAGTTAGGACTGTGCAGAAAAGGAAATGATATTATAGGGACACAGATTTTTTCAATCCTTGGTTTGTATGCCAGAGTAATTTACTATCCTCTGGGAAAAAATGCACCTTGGGGATTTACCAGAATCAGCGGTTCTAGAAATGATGCCTCATTGGAGAAGCCATTTGTTGCCCTTAATTCTTCTATTCCGGTGGACTGCCAGGTGTTTGCAGCGGCACACGAATTATACCATATTTGGTATGAACAAAATCCGGATATGCTTCCTTCTGATTTGTTGAATGAACACGATAAAAAGACAAGTGAGAAAAAAGCAAATAGATTTGCAGCAGAATTTCTTGTGGATGAATTATTGCTGAAACAGGAAATCGAGTTATATAAAATTAAGAAGCTTACAATAAAAAGCATATTACAATTAGCAGAACTGTTTACGGTTCCATACAGGACAATGGTGAAGCGGCTGGGAGAAATTGGAGTAATTGAGGATGCGGATCT\n+>contig-21000001.concoct_part_2\n+AAATAGATTTCTCGCAGAGTCAGAGGATTCTGTTGAAAAATATAAGAAGAGATATTCCATACCATCTCAGAAATCTGATGGTCGGATTATCATGGATAACCTGGTTGAGTTAGCCGTCGCCGCTTATGAAGCCGGGTACATTACATATGAGAAACTGGAATATTTGCTGAGAATCAGTACCTTAAAGCCAGAGGATTTAGGCATTGAAAAGAAAACTGCCTGCGAATTCCCTTCTGATGATGAATTAGATCGTATTATGGAGGAATGAGTATGGTAGAAAAATAATTATTGATGCAGATTTATGTATCAAGTTGGGAGGAAGTAATAAGTATAGATATTTGCATGATGTGCTTCCTTTGATTGCAAAAGAGATTTATATGCATACACACGCCTTTGGAGAGGTGTTGATGCCTGCCAGTGCAGTCAGCCAGTTAAAGGATTTGATTACGGAAAATAAAGTGGTTCTTGTTAACGAAAGTGGTTTGGACAGCAAGGTACGAGCAATCTATGATGCAGCTTATCGTAATCTTGAGAGAGTTATGATTGATGCAACGAGACCAAACAAGAATAAAGGAGAGATGTGTTCGCTCGCATATGCAAAAGCAGCGAGCATACCTATCTTTGCAACAGATGAAAAAGACCTACAGCCTATCATTGATAAGCAATTGAATACGGGAATGGATGATATAACCTGCATAAGAATTACAGATATTATTACGAAGGCTAAGGAGGGGGAAATAGCGGTACCGAGAAAGATTGCAAAGGCACTTTGGATCGTGGCCGGAAAGAGAAAAGAAGTATTTGATAATGAGATATGGCCGGTAACGGCTGAATGATACATATGAAAGGAGCCTGTTTGGGACAAAGGAATACCGCCTTGTCCCAAACAGGCTATTACTGGAAGCAGAGGCTTCGTGGACTGCCTGGAAACGGTGATGAAGATTCATTACACCAGCATTTCAACAAACTCAACCGGATACATAGTCCGTTTGGACACTTC\n+>contig-21000001.concoct_part_3\n+CTCAACCGCTAGTCCCTGGCTGAGAAAACGCCTGATGACGCACTCCATGCTTTCTGCTGCCTCAATGATATATTTATCAAAATCATAAAACCGCATACTCCGCTGGCCCCAGGGATATTCCGTCGGGTGATGGATAAATTCCACTCCTTCGATGGCCTCCAGCTTTCTCTCCCAGTCGTCGATCCGGTCTGTTTCAAAATAGAGCTGAAAGTTATTTGCTGCTGTCTTTCTGTTCAGTGATTTACCGATCATTGCTTCGTAGTTTGCCTGCAGGCTGAGGCCATTGTCCAATGAGACGTGTTCTCCTAAATCCATGAGGACTTTTTGCTCCAGGATTGTTTCGTAAAAATATTTTGATTTTTCCATATCATCAACTATAAGCAATGTGCCTCCGTATTTCATATGGATACCTCCTCTTTTTTTCTCAATTATAGCCTAAAACTTTGCGATCGCACTGTAAAAATCGGACAAGTTGTTTCGGTATTCCTGAGGAGTAACGCCGCATACGGCCCTAAAATCCCTGATAAAGTGAGAAATATCATAAAACCCGGATTCGGCAGATATATAATCGAGGCTGTAGCTCGTATGGTGCAGCAGATAAATGGCTTTGTTGATACGCACGATTCGGGAAAAATGTTTCAGGTTAAATCCTAAATAGTGATTGGAAAGCCTGTTTAAATGACGTTCACTGTAAAATGTTTTTTCTGTTATTTCTTTGAGACTTATGTTACCGTTACTCTGAATGATCAGCTGCACGGCCAGACGGAATTCAGCCGGGTATTGGCTGCATTGGCTGCAAAGCAGCAGACTCTCGATTCTGGTCAGCAGTTCTTCCGCGGTTCC'..b'CTTTTTTCCTGACCGCGAACTTTGCATGGAATCGTATTATCAGTGGCTGGAACTCCCGGAGCATTTAACCGGAAGGCTGTGTGAGGCCGAGCTCTCCGGCAGGGGAGTCAGCGTATTCGGCGCAGAGCGCTTCTATGTTGGAAAACAGCTGAAAGCAAATGCCGTCAGAGTGGCAACCAGCTCGGCGGAAAGTGACGAACAACTCCGCCGGGGGCTGGAGGTACTGCAGAATTTTATCCGGCAGC\n+>contig-21000001.concoct_part_8\n+GGGATGCGGGGCCTTTATTCATCGTCTAGTTTTTGACCGGAATCACGATTCGTGTAATGTATTCGTCAATGGAATTGATGGTCATCTCGTTTACCCCTGTTTCGTAGGCGTATCCGAAAAGTGTGAGGCCGTGCTGCTTCGCATAGTCCAGGATTTCCGAATATCGCTGCGGAAGCCTGTCCCAGCTTCCCGTACAGTAGGCGCACAGATAGCTGCCGCTCGGCTTTTTATGGATTTCATTTACAGAAGCTGTGTGGGAAACCTTCATAAACAGGCCGTCATACTGGTCAAACTCGGAATGGAGCAGGTGGGAGACGGAGATCAGGGAGCCGTAAGTGGTATCGTGGAGACTCTTAAAATGGTGCTGTTTCATGGATTCAACCATCTGTTCGATCTCATCCTCCATGGACAGGGCCTGGTCGGAGGCAATGATGTGCAGATACTCCTCTTCACATTCGACAACGTCGATCCGGGTCAGATCGGTGTTCAGTAAATCGGTGAAGGTACCGCATTGGTCCGTCAGCATATCACGGATCGTGTTCAGCTTTTCTATTTCACGGTCCACGTCCTGAATCTTTTTATGCAGAAGCTGAACGTAGGCTTCTGCCCCACGCCTGTCTAAAAACTCTTTGATCTCAGGAATTCCCATATTCAGTTCCCGCAAAACCAGAATCGTCTCCAGCAAAGAGCTCTGATAGTAGGTGTAATAGCGGTAGCCGTTCTCTTTTACGACCGCCGGCTTGAATAAGCCGATCTCATCGTACCACATCAGAGTCTTTTTGTTGATGTTATGAAGGGCTGCAAATTGGCCGATCGTAAATAGTTTTTCTCTTTCCATAAAAAAATCCCCTTTTCCTCTTTACCGTACAGTTACTGTATGGATTATTATACAGGTAAGACAGTACAAATACAAGAAAAAAGGAGAATAGAATCATGAATTCAGAACATATTACACTGCGCCCCATCACACGAAAGGATTATCCGTTTATAGAGGATATCA\n+>contig-21000001.concoct_part_9\n+TACGCAAGACGTGGAAATACGACGCGCTGAGCAGCAATCCGAAGGATGCAAAGCATATGGCAAGGCTGTATCTGCGTTCCTGTCTGCTGCGGGCGACATTTTCCTGTGTCGCGGCTGTGGATGGAAAGGTGCTGGGAGTTATTCTGGCCGGGAGTAAAAAATCCGTTCCGAAATTCGCCCTTCGCCGCACCCTGGCTCAGCTCTGGTCCATTGCGCTGCTGTTTACAACGAAAACCGGAAGAGGAATCGGTAAATTTTTCAGTACCTTCGACCAAACGGACGAAGAACTGCTGAAAAATGCAGGAAATGCTTTTGACGCGGAAATCTGTTTCTTTGCCGTGGATGAGAGTACAAGGGGAACCGGAATCGGAAAAATGCTTTTTGCCCAGGCCCTTGATTATCTGGAACAGGAAGGGGTAAAGACCCTGTACCTCTTCACGGATTCCAGCTGTACTTACCAGTTTTACGAGAAGCGGGGAATGCAGCGGCTGGGAGAGAAGACGGTGGAATTCAGCCCCCATACAGACTACCGCCTGAATATGTTTATCTATGGCCTGGAATTGCAGGCGGCCAGTTAAGGCCGCTCTGCAATTCAGACCGCACTGCTTCGCTGCCCGCAGGCCGGCGCATCGATGACCCGGTCATACCGGTAGGCCGAGAAGATAAATCCCAGCAGAAGCATATTTACGAGGATGCTGATACTGCCCTCCGAAACCATGGGAAGATTAGTAAAGCTGCCATACTGGAAACCAAAATTCCCAAGTATATAGAGCACGCTCTGAAACAGCAGGCACAGGCCGCAGTGAAAGGACACCGCTCCGGCGAGCGCGCCGTGTATCCTTCGGATGCAGGAGAAGAGGACTGCGTAGAAGGCGGCCATAACTGCAAGAAACAGAATTCCGGCCAGCCAGCCGAACTGTAGTATGAATACGGCCAGGAGATAGTTGTTCGCGTAATGCTGGGGCAGAATGTTCCATAAAGTGACATCTGACGGATCG\n+>contig-75000034.concoct_part_0\n+CATCCGCCGACCATGTACTTCCCGCTGATTGTCCACGAGGCCCTGATGGTGGAGCCGACGGAGACGGAATCAAAGGAGAACTTAGATGAACTGATCGCCGTGTTCCACGAGATCTATGAGACGGCGAAGCGTGATCCCGAATATATCCGGAGCTCCCCCCACATCACCATGGTGAAGCGCCTGGATGAAGTAAATGCGGCCCGGAATCCGAAGCTGCATTACGCATTCGGGGAGGAAAGCGCAGAGGGGGAAGAGGCGTGATCCGCCGACTGACCCTGGCCCTGGGGCCGGGGTCATACCCCTATCCCAATTTCGGCATGGAGGAGTATTTGCTTTACGATGTGGAAGAAGAGGAATGCATTCTCTACCTGTGGCAGAATGAGAAAACCGTGGTCATAGGCAGGAATCAGAACGCATGGAAGGAGTGCCGCAGAGAGGAACTGGAGGCGGCCGGAGGTCATCTGGTGAGACGGCTGTCGGGAGGCGGCGCCGTATTCCACGACCTGGGCAATTTAAATTTTACCTTCATCACAAGAAAAGATAACTACGATGTCACAAAACAGACGGAGGTTATCCTAAGGGCGGTCAAAAAGCTGGGTGTAAATGCAGAACGGACCGGCCGCAATGATATCACAGTGGATGGCCGCAAGTTTTCCGGCAACGCGTACTACGAGACCGGGGACTTCTGCTATCATCACGGGACCATTCTGCTCTCCGTGGACAAAGAAGAGATGGCCCGCTATCTAAACGTTTCCAGGGAAAAACTGAGATCCAAAAGCGTGGATTCCGTCAAAAGCCGTGTGGCCAATTTAATCGAATTCGTACCGGATCTGACGGTTAGACGCATGAGAGACAGTCTGGAGGAAAGCTTCGGCGAGGTCTACGGCCTTCCCGCAGGCCCATTTCCTCCGGAACGGCTTTGCGAAGACGAGGTAAGGGAGCGGACGGAGCGGTTTGCCTCCTGGGAGTGGAAATACGGCAGGAAGATCCCGTTCAGCGA\n+>contig-75000034.concoct_part_1\n+TGAAGCCGCCGCCCGTTTTACCTGGGGGGAGGCCCAGGTGCTGGTCCATGTGGAAGAGGGGCGTGTCCGGGAAGGAAAGATCTGGTCCGACGCCCTGGATACGGATTTTATCAAAGCTACGGAAGACATTCTGACCGGCATGATCTGGAACAGAAAGGCAGCGGCAGACCGTTTTGCAGCCCTGTCCTGCGGCACTCCGGTTCAGGAGGCGATGCGGCAGGATTTACAGGATCTGGTCTGCGATATGATGTAGTGCTGTGCCGTCGATTCACAGACGCGCCTGAGAGAACAGGAGGATTGGATGGAAAAACATTATGATCTCGTCGTAATCGGCGCGGGGCCGGGCGGCTATATGACGGCCCTGTACGCGTCGAAGGCGGGAAAAAGAACGGCCGTGATCGAACGGTCCCATGTGGGGGGCACCTGTTTAAACTGCGGATGCATTCCTACGAAAACGTATCTCCACACCACCGGCCTTTACCGGGAGGTGAAGAAGACAGAGGCCGCCGGCCTCCATACGGAAGGCCTGCGCGTATCCATGGAGGAACTGAAGAAACGCAAAGACGCCGTGGTGGAAGAATTGCGCGCCGGCATCGAGAAGCAGCTGGCCGCCGC\n' |
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/two_contigs-cut2-coverage.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_contigs-cut2-coverage.tabular Thu Jul 07 08:33:35 2022 +0000 |
| b |
| @@ -0,0 +1,11 @@ +contig cov_mean_sample_ten_reads_two_contigs-s +contig-21000001.concoct_part_0 0.100 +contig-21000001.concoct_part_1 0.100 +contig-21000001.concoct_part_2 0.200 +contig-21000001.concoct_part_3 0.200 +contig-21000001.concoct_part_4 0.000 +contig-21000001.concoct_part_5 0.100 +contig-21000001.concoct_part_6 0.100 +contig-21000001.concoct_part_7 0.100 +contig-21000001.concoct_part_8 0.050 +contig-75000034.concoct_part_0 0.619 |
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/two_contigs-cut2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_contigs-cut2.bed Thu Jul 07 08:33:35 2022 +0000 |
| b |
| @@ -0,0 +1,10 @@ +contig-21000001 0 1000 contig-21000001.concoct_part_0 +contig-21000001 1000 2000 contig-21000001.concoct_part_1 +contig-21000001 2000 3000 contig-21000001.concoct_part_2 +contig-21000001 3000 4000 contig-21000001.concoct_part_3 +contig-21000001 4000 5000 contig-21000001.concoct_part_4 +contig-21000001 5000 6000 contig-21000001.concoct_part_5 +contig-21000001 6000 7000 contig-21000001.concoct_part_6 +contig-21000001 7000 8000 contig-21000001.concoct_part_7 +contig-21000001 8000 9998 contig-21000001.concoct_part_8 +contig-75000034 0 1615 contig-75000034.concoct_part_0 |
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/two_contigs-cut2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_contigs-cut2.fasta Thu Jul 07 08:33:35 2022 +0000 |
| b |
| b'@@ -0,0 +1,20 @@\n+>contig-21000001.concoct_part_0\n+GACCATCCGGTGGAGATTTCTCCTCTGACCAAGAGAAAACCGGAGGATCCTGACTATACGGAGCGTTTTGAGCTGTTTATCACGAAGCGTGAGATGGCTAACGCTTACTCTGAGTTAAACGATCCGATTGACCAGAGACTTCGTTTTGAGGCGCAGGAAGTGTTAAAGGCCGCAGGCGATGAGGAAGCCAACTCCATGGATGAGGACTTCTTAAATGCGCTGATGATCGGTATGCCTCCGACAGGCGGCATCGGCATCGGCATCGACCGTTTCGTTATGCTGCTGACTGATTCCTATGCAATTCGTGACGTTCTGCTGTTCCCGACCATGAAGACGCTGGGCAGTTCTGATAATAGCAGGAAGGCAGAGAAGGCCGCTCCGGCCGCTGCTTCTGCTCCGGCTGCTGAGAACGTGAAAGCCGCGGTGGAGATTGATTTTTCCAATGTGAAGATTGAGCCGCTGTTTGAAGAGATGGTGGATTTTGAGACTTTCTCAAAGTCTGATTACCGTGCAGTGAAGATCAAAGACTGCGTGGCAGTGCCGAAGAGCAAGAAGCTTCTCCAGTTTACTCTGGACGATGGAAGCGGCACAGACCGCACGATTTTAAGCGGAATTCATGAGTACTACGAGCCGGAGGATCTGATTGGTAAGACAGCCATCGCCATCGTGAATCTGCCGCCAAGAAAGATGATGGGAATTGACTCCTGCGGTATGCTGATTTCAGCCGTGCATGAGGAAGACGGACATGAGGGACTGAATCTGCTGATGGTGGATGATAGGATTCCGGCGGGGGCGAAGTTGTATTAAAATACAACAAAAGAACCGTTTTTCAGGATAGTAGGAATTCAATAACAAAAGTTGTTACCCCCAATTTTGTTAACATTGAAAAATGTAGATGTGTTTGAACAGAAGTGGCGCTTACTGATATAATGATAAGAAATTAGGACTCTATGACATTAGTCATAGAGTCCTTTTTTCTGTTTTGAAATCAAATTGTTTA\n+>contig-21000001.concoct_part_1\n+GAATATGCTTGAAAGTAAACAAAATTAAACAAGAAATAGATGAATAGTAAACAAAACGTTGACCATAAAGCTTTTTAATGGTATAATAACTATCAAAGCAAAGGAGGATAAGACCATGTACGCAATGGATTTCGCTCTGGTAGGAGCTAACATACAAAATAAATTAGTTGAAAAGGAAATGACACAACAGAGTTTGGCGGATGCTCTTGGTATATCAAAGCAGGTTATGAACAAAATCATTAAAGGAAGCAAGGCGATCAATGTGAATGAGCTTGCAAGAATTGCGGATATCCTGAACACATCTGCAGATGAATTACTTACAGTTGGGACTGAACCAGCTACTGTTGACAGCCTGAGCTTTATGGGAGATGTTTACGATGAGGTTACACGGGAACGTATTAACTTCATCAGATCTGCGATTGATGAGATTCATATGCTGGAGGATTTACTGGATGACTAATGACTTAAATGAATTAGAAGTAAATGAAATAAAGAATCATGCAATAGAAAAGTTAGGACTGTGCAGAAAAGGAAATGATATTATAGGGACACAGATTTTTTCAATCCTTGGTTTGTATGCCAGAGTAATTTACTATCCTCTGGGAAAAAATGCACCTTGGGGATTTACCAGAATCAGCGGTTCTAGAAATGATGCCTCATTGGAGAAGCCATTTGTTGCCCTTAATTCTTCTATTCCGGTGGACTGCCAGGTGTTTGCAGCGGCACACGAATTATACCATATTTGGTATGAACAAAATCCGGATATGCTTCCTTCTGATTTGTTGAATGAACACGATAAAAAGACAAGTGAGAAAAAAGCAAATAGATTTGCAGCAGAATTTCTTGTGGATGAATTATTGCTGAAACAGGAAATCGAGTTATATAAAATTAAGAAGCTTACAATAAAAAGCATATTACAATTAGCAGAACTGTTTACGGTTCCATACAGGACAATGGTGAAGCGGCTGGGAGAAATTGGAGTAATTGAGGATGCGGATCT\n+>contig-21000001.concoct_part_2\n+AAATAGATTTCTCGCAGAGTCAGAGGATTCTGTTGAAAAATATAAGAAGAGATATTCCATACCATCTCAGAAATCTGATGGTCGGATTATCATGGATAACCTGGTTGAGTTAGCCGTCGCCGCTTATGAAGCCGGGTACATTACATATGAGAAACTGGAATATTTGCTGAGAATCAGTACCTTAAAGCCAGAGGATTTAGGCATTGAAAAGAAAACTGCCTGCGAATTCCCTTCTGATGATGAATTAGATCGTATTATGGAGGAATGAGTATGGTAGAAAAATAATTATTGATGCAGATTTATGTATCAAGTTGGGAGGAAGTAATAAGTATAGATATTTGCATGATGTGCTTCCTTTGATTGCAAAAGAGATTTATATGCATACACACGCCTTTGGAGAGGTGTTGATGCCTGCCAGTGCAGTCAGCCAGTTAAAGGATTTGATTACGGAAAATAAAGTGGTTCTTGTTAACGAAAGTGGTTTGGACAGCAAGGTACGAGCAATCTATGATGCAGCTTATCGTAATCTTGAGAGAGTTATGATTGATGCAACGAGACCAAACAAGAATAAAGGAGAGATGTGTTCGCTCGCATATGCAAAAGCAGCGAGCATACCTATCTTTGCAACAGATGAAAAAGACCTACAGCCTATCATTGATAAGCAATTGAATACGGGAATGGATGATATAACCTGCATAAGAATTACAGATATTATTACGAAGGCTAAGGAGGGGGAAATAGCGGTACCGAGAAAGATTGCAAAGGCACTTTGGATCGTGGCCGGAAAGAGAAAAGAAGTATTTGATAATGAGATATGGCCGGTAACGGCTGAATGATACATATGAAAGGAGCCTGTTTGGGACAAAGGAATACCGCCTTGTCCCAAACAGGCTATTACTGGAAGCAGAGGCTTCGTGGACTGCCTGGAAACGGTGATGAAGATTCATTACACCAGCATTTCAACAAACTCAACCGGATACATAGTCCGTTTGGACACTTC\n+>contig-21000001.concoct_part_3\n+CTCAACCGCTAGTCCCTGGCTGAGAAAACGCCTGATGACGCACTCCATGCTTTCTGCTGCCTCAATGATATATTTATCAAAATCATAAAACCGCATACTCCGCTGGCCCCAGGGATATTCCGTCGGGTGATGGATAAATTCCACTCCTTCGATGGCCTCCAGCTTTCTCTCCCAGTCGTCGATCCGGTCTGTTTCAAAATAGAGCTGAAAGTTATTTGCTGCTGTCTTTCTGTTCAGTGATTTACCGATCATTGCTTCGTAGTTTGCCTGCAGGCTGAGGCCATTGTCCAATGAGACGTGTTCTCCTAAATCCATGAGGACTTTTTGCTCCAGGATTGTTTCGTAAAAATATTTTGATTTTTCCATATCATCAACTATAAGCAATGTGCCTCCGTATTTCATATGGATACCTCCTCTTTTTTTCTCAATTATAGCCTAAAACTTTGCGATCGCACTGTAAAAATCGGACAAGTTGTTTCGGTATTCCTGAGGAGTAACGCCGCATACGGCCCTAAAATCCCTGATAAAGTGAGAAATATCATAAAACCCGGATTCGGCAGATATATAATCGAGGCTGTAGCTCGTATGGTGCAGCAGATAAATGGCTTTGTTGATACGCACGATTCGGGAAAAATGTTTCAGGTTAAATCCTAAATAGTGATTGGAAAGCCTGTTTAAATGACGTTCACTGTAAAATGTTTTTTCTGTTATTTCTTTGAGACTTATGTTACCGTTACTCTGAATGATCAGCTGCACGGCCAGACGGAATTCAGCCGGGTATTGGCTGCATTGGCTGCAAAGCAGCAGACTCTCGATTCTGGTCAGCAGTTCTTCCGCGGTTCC'..b'GCGGCCTGGCGTGGAAAATCATACAGAAAAAGAGAGCGGCGGCCGCGGAGCGCAATCAGATTTATGCCTCCTTTTTTCCTGACCGCGAACTTTGCATGGAATCGTATTATCAGTGGCTGGAACTCCCGGAGCATTTAACCGGAAGGCTGTGTGAGGCCGAGCTCTCCGGCAGGGGAGTCAGCGTATTCGGCGCAGAGCGCTTCTATGTTGGAAAACAGCTGAAAGCAAATGCCGTCAGAGTGGCAACCAGCTCGGCGGAAAGTGACGAACAACTCCGCCGGGGGCTGGAGGTACTGCAGAATTTTATCCGGCAGC\n+>contig-21000001.concoct_part_8\n+GGGATGCGGGGCCTTTATTCATCGTCTAGTTTTTGACCGGAATCACGATTCGTGTAATGTATTCGTCAATGGAATTGATGGTCATCTCGTTTACCCCTGTTTCGTAGGCGTATCCGAAAAGTGTGAGGCCGTGCTGCTTCGCATAGTCCAGGATTTCCGAATATCGCTGCGGAAGCCTGTCCCAGCTTCCCGTACAGTAGGCGCACAGATAGCTGCCGCTCGGCTTTTTATGGATTTCATTTACAGAAGCTGTGTGGGAAACCTTCATAAACAGGCCGTCATACTGGTCAAACTCGGAATGGAGCAGGTGGGAGACGGAGATCAGGGAGCCGTAAGTGGTATCGTGGAGACTCTTAAAATGGTGCTGTTTCATGGATTCAACCATCTGTTCGATCTCATCCTCCATGGACAGGGCCTGGTCGGAGGCAATGATGTGCAGATACTCCTCTTCACATTCGACAACGTCGATCCGGGTCAGATCGGTGTTCAGTAAATCGGTGAAGGTACCGCATTGGTCCGTCAGCATATCACGGATCGTGTTCAGCTTTTCTATTTCACGGTCCACGTCCTGAATCTTTTTATGCAGAAGCTGAACGTAGGCTTCTGCCCCACGCCTGTCTAAAAACTCTTTGATCTCAGGAATTCCCATATTCAGTTCCCGCAAAACCAGAATCGTCTCCAGCAAAGAGCTCTGATAGTAGGTGTAATAGCGGTAGCCGTTCTCTTTTACGACCGCCGGCTTGAATAAGCCGATCTCATCGTACCACATCAGAGTCTTTTTGTTGATGTTATGAAGGGCTGCAAATTGGCCGATCGTAAATAGTTTTTCTCTTTCCATAAAAAAATCCCCTTTTCCTCTTTACCGTACAGTTACTGTATGGATTATTATACAGGTAAGACAGTACAAATACAAGAAAAAAGGAGAATAGAATCATGAATTCAGAACATATTACACTGCGCCCCATCACACGAAAGGATTATCCGTTTATAGAGGATATCATACGCAAGACGTGGAAATACGACGCGCTGAGCAGCAATCCGAAGGATGCAAAGCATATGGCAAGGCTGTATCTGCGTTCCTGTCTGCTGCGGGCGACATTTTCCTGTGTCGCGGCTGTGGATGGAAAGGTGCTGGGAGTTATTCTGGCCGGGAGTAAAAAATCCGTTCCGAAATTCGCCCTTCGCCGCACCCTGGCTCAGCTCTGGTCCATTGCGCTGCTGTTTACAACGAAAACCGGAAGAGGAATCGGTAAATTTTTCAGTACCTTCGACCAAACGGACGAAGAACTGCTGAAAAATGCAGGAAATGCTTTTGACGCGGAAATCTGTTTCTTTGCCGTGGATGAGAGTACAAGGGGAACCGGAATCGGAAAAATGCTTTTTGCCCAGGCCCTTGATTATCTGGAACAGGAAGGGGTAAAGACCCTGTACCTCTTCACGGATTCCAGCTGTACTTACCAGTTTTACGAGAAGCGGGGAATGCAGCGGCTGGGAGAGAAGACGGTGGAATTCAGCCCCCATACAGACTACCGCCTGAATATGTTTATCTATGGCCTGGAATTGCAGGCGGCCAGTTAAGGCCGCTCTGCAATTCAGACCGCACTGCTTCGCTGCCCGCAGGCCGGCGCATCGATGACCCGGTCATACCGGTAGGCCGAGAAGATAAATCCCAGCAGAAGCATATTTACGAGGATGCTGATACTGCCCTCCGAAACCATGGGAAGATTAGTAAAGCTGCCATACTGGAAACCAAAATTCCCAAGTATATAGAGCACGCTCTGAAACAGCAGGCACAGGCCGCAGTGAAAGGACACCGCTCCGGCGAGCGCGCCGTGTATCCTTCGGATGCAGGAGAAGAGGACTGCGTAGAAGGCGGCCATAACTGCAAGAAACAGAATTCCGGCCAGCCAGCCGAACTGTAGTATGAATACGGCCAGGAGATAGTTGTTCGCGTAATGCTGGGGCAGAATGTTCCATAAAGTGACATCTGACGGATCG\n+>contig-75000034.concoct_part_0\n+CATCCGCCGACCATGTACTTCCCGCTGATTGTCCACGAGGCCCTGATGGTGGAGCCGACGGAGACGGAATCAAAGGAGAACTTAGATGAACTGATCGCCGTGTTCCACGAGATCTATGAGACGGCGAAGCGTGATCCCGAATATATCCGGAGCTCCCCCCACATCACCATGGTGAAGCGCCTGGATGAAGTAAATGCGGCCCGGAATCCGAAGCTGCATTACGCATTCGGGGAGGAAAGCGCAGAGGGGGAAGAGGCGTGATCCGCCGACTGACCCTGGCCCTGGGGCCGGGGTCATACCCCTATCCCAATTTCGGCATGGAGGAGTATTTGCTTTACGATGTGGAAGAAGAGGAATGCATTCTCTACCTGTGGCAGAATGAGAAAACCGTGGTCATAGGCAGGAATCAGAACGCATGGAAGGAGTGCCGCAGAGAGGAACTGGAGGCGGCCGGAGGTCATCTGGTGAGACGGCTGTCGGGAGGCGGCGCCGTATTCCACGACCTGGGCAATTTAAATTTTACCTTCATCACAAGAAAAGATAACTACGATGTCACAAAACAGACGGAGGTTATCCTAAGGGCGGTCAAAAAGCTGGGTGTAAATGCAGAACGGACCGGCCGCAATGATATCACAGTGGATGGCCGCAAGTTTTCCGGCAACGCGTACTACGAGACCGGGGACTTCTGCTATCATCACGGGACCATTCTGCTCTCCGTGGACAAAGAAGAGATGGCCCGCTATCTAAACGTTTCCAGGGAAAAACTGAGATCCAAAAGCGTGGATTCCGTCAAAAGCCGTGTGGCCAATTTAATCGAATTCGTACCGGATCTGACGGTTAGACGCATGAGAGACAGTCTGGAGGAAAGCTTCGGCGAGGTCTACGGCCTTCCCGCAGGCCCATTTCCTCCGGAACGGCTTTGCGAAGACGAGGTAAGGGAGCGGACGGAGCGGTTTGCCTCCTGGGAGTGGAAATACGGCAGGAAGATCCCGTTCAGCGATGAAGCCGCCGCCCGTTTTACCTGGGGGGAGGCCCAGGTGCTGGTCCATGTGGAAGAGGGGCGTGTCCGGGAAGGAAAGATCTGGTCCGACGCCCTGGATACGGATTTTATCAAAGCTACGGAAGACATTCTGACCGGCATGATCTGGAACAGAAAGGCAGCGGCAGACCGTTTTGCAGCCCTGTCCTGCGGCACTCCGGTTCAGGAGGCGATGCGGCAGGATTTACAGGATCTGGTCTGCGATATGATGTAGTGCTGTGCCGTCGATTCACAGACGCGCCTGAGAGAACAGGAGGATTGGATGGAAAAACATTATGATCTCGTCGTAATCGGCGCGGGGCCGGGCGGCTATATGACGGCCCTGTACGCGTCGAAGGCGGGAAAAAGAACGGCCGTGATCGAACGGTCCCATGTGGGGGGCACCTGTTTAAACTGCGGATGCATTCCTACGAAAACGTATCTCCACACCACCGGCCTTTACCGGGAGGTGAAGAAGACAGAGGCCGCCGGCCTCCATACGGAAGGCCTGCGCGTATCCATGGAGGAACTGAAGAAACGCAAAGACGCCGTGGTGGAAGAATTGCGCGCCGGCATCGAGAAGCAGCTGGCCGCCGC\n' |
| b |
| diff -r 7a145c72d375 -r 3842ef1b2f34 test-data/two_contigs.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_contigs.fa Thu Jul 07 08:33:35 2022 +0000 |
| b |
| b'@@ -0,0 +1,196 @@\n+>contig-21000001 9998 nucleotides\n+GACCATCCGGTGGAGATTTCTCCTCTGACCAAGAGAAAACCGGAGGATCCTGACTATACG\n+GAGCGTTTTGAGCTGTTTATCACGAAGCGTGAGATGGCTAACGCTTACTCTGAGTTAAAC\n+GATCCGATTGACCAGAGACTTCGTTTTGAGGCGCAGGAAGTGTTAAAGGCCGCAGGCGAT\n+GAGGAAGCCAACTCCATGGATGAGGACTTCTTAAATGCGCTGATGATCGGTATGCCTCCG\n+ACAGGCGGCATCGGCATCGGCATCGACCGTTTCGTTATGCTGCTGACTGATTCCTATGCA\n+ATTCGTGACGTTCTGCTGTTCCCGACCATGAAGACGCTGGGCAGTTCTGATAATAGCAGG\n+AAGGCAGAGAAGGCCGCTCCGGCCGCTGCTTCTGCTCCGGCTGCTGAGAACGTGAAAGCC\n+GCGGTGGAGATTGATTTTTCCAATGTGAAGATTGAGCCGCTGTTTGAAGAGATGGTGGAT\n+TTTGAGACTTTCTCAAAGTCTGATTACCGTGCAGTGAAGATCAAAGACTGCGTGGCAGTG\n+CCGAAGAGCAAGAAGCTTCTCCAGTTTACTCTGGACGATGGAAGCGGCACAGACCGCACG\n+ATTTTAAGCGGAATTCATGAGTACTACGAGCCGGAGGATCTGATTGGTAAGACAGCCATC\n+GCCATCGTGAATCTGCCGCCAAGAAAGATGATGGGAATTGACTCCTGCGGTATGCTGATT\n+TCAGCCGTGCATGAGGAAGACGGACATGAGGGACTGAATCTGCTGATGGTGGATGATAGG\n+ATTCCGGCGGGGGCGAAGTTGTATTAAAATACAACAAAAGAACCGTTTTTCAGGATAGTA\n+GGAATTCAATAACAAAAGTTGTTACCCCCAATTTTGTTAACATTGAAAAATGTAGATGTG\n+TTTGAACAGAAGTGGCGCTTACTGATATAATGATAAGAAATTAGGACTCTATGACATTAG\n+TCATAGAGTCCTTTTTTCTGTTTTGAAATCAAATTGTTTAGAATATGCTTGAAAGTAAAC\n+AAAATTAAACAAGAAATAGATGAATAGTAAACAAAACGTTGACCATAAAGCTTTTTAATG\n+GTATAATAACTATCAAAGCAAAGGAGGATAAGACCATGTACGCAATGGATTTCGCTCTGG\n+TAGGAGCTAACATACAAAATAAATTAGTTGAAAAGGAAATGACACAACAGAGTTTGGCGG\n+ATGCTCTTGGTATATCAAAGCAGGTTATGAACAAAATCATTAAAGGAAGCAAGGCGATCA\n+ATGTGAATGAGCTTGCAAGAATTGCGGATATCCTGAACACATCTGCAGATGAATTACTTA\n+CAGTTGGGACTGAACCAGCTACTGTTGACAGCCTGAGCTTTATGGGAGATGTTTACGATG\n+AGGTTACACGGGAACGTATTAACTTCATCAGATCTGCGATTGATGAGATTCATATGCTGG\n+AGGATTTACTGGATGACTAATGACTTAAATGAATTAGAAGTAAATGAAATAAAGAATCAT\n+GCAATAGAAAAGTTAGGACTGTGCAGAAAAGGAAATGATATTATAGGGACACAGATTTTT\n+TCAATCCTTGGTTTGTATGCCAGAGTAATTTACTATCCTCTGGGAAAAAATGCACCTTGG\n+GGATTTACCAGAATCAGCGGTTCTAGAAATGATGCCTCATTGGAGAAGCCATTTGTTGCC\n+CTTAATTCTTCTATTCCGGTGGACTGCCAGGTGTTTGCAGCGGCACACGAATTATACCAT\n+ATTTGGTATGAACAAAATCCGGATATGCTTCCTTCTGATTTGTTGAATGAACACGATAAA\n+AAGACAAGTGAGAAAAAAGCAAATAGATTTGCAGCAGAATTTCTTGTGGATGAATTATTG\n+CTGAAACAGGAAATCGAGTTATATAAAATTAAGAAGCTTACAATAAAAAGCATATTACAA\n+TTAGCAGAACTGTTTACGGTTCCATACAGGACAATGGTGAAGCGGCTGGGAGAAATTGGA\n+GTAATTGAGGATGCGGATCTAAATAGATTTCTCGCAGAGTCAGAGGATTCTGTTGAAAAA\n+TATAAGAAGAGATATTCCATACCATCTCAGAAATCTGATGGTCGGATTATCATGGATAAC\n+CTGGTTGAGTTAGCCGTCGCCGCTTATGAAGCCGGGTACATTACATATGAGAAACTGGAA\n+TATTTGCTGAGAATCAGTACCTTAAAGCCAGAGGATTTAGGCATTGAAAAGAAAACTGCC\n+TGCGAATTCCCTTCTGATGATGAATTAGATCGTATTATGGAGGAATGAGTATGGTAGAAA\n+AATAATTATTGATGCAGATTTATGTATCAAGTTGGGAGGAAGTAATAAGTATAGATATTT\n+GCATGATGTGCTTCCTTTGATTGCAAAAGAGATTTATATGCATACACACGCCTTTGGAGA\n+GGTGTTGATGCCTGCCAGTGCAGTCAGCCAGTTAAAGGATTTGATTACGGAAAATAAAGT\n+GGTTCTTGTTAACGAAAGTGGTTTGGACAGCAAGGTACGAGCAATCTATGATGCAGCTTA\n+TCGTAATCTTGAGAGAGTTATGATTGATGCAACGAGACCAAACAAGAATAAAGGAGAGAT\n+GTGTTCGCTCGCATATGCAAAAGCAGCGAGCATACCTATCTTTGCAACAGATGAAAAAGA\n+CCTACAGCCTATCATTGATAAGCAATTGAATACGGGAATGGATGATATAACCTGCATAAG\n+AATTACAGATATTATTACGAAGGCTAAGGAGGGGGAAATAGCGGTACCGAGAAAGATTGC\n+AAAGGCACTTTGGATCGTGGCCGGAAAGAGAAAAGAAGTATTTGATAATGAGATATGGCC\n+GGTAACGGCTGAATGATACATATGAAAGGAGCCTGTTTGGGACAAAGGAATACCGCCTTG\n+TCCCAAACAGGCTATTACTGGAAGCAGAGGCTTCGTGGACTGCCTGGAAACGGTGATGAA\n+GATTCATTACACCAGCATTTCAACAAACTCAACCGGATACATAGTCCGTTTGGACACTTC\n+CTCAACCGCTAGTCCCTGGCTGAGAAAACGCCTGATGACGCACTCCATGCTTTCTGCTGC\n+CTCAATGATATATTTATCAAAATCATAAAACCGCATACTCCGCTGGCCCCAGGGATATTC\n+CGTCGGGTGATGGATAAATTCCACTCCTTCGATGGCCTCCAGCTTTCTCTCCCAGTCGTC\n+GATCCGGTCTGTTTCAAAATAGAGCTGAAAGTTATTTGCTGCTGTCTTTCTGTTCAGTGA\n+TTTACCGATCATTGCTTCGTAGTTTGCCTGCAGGCTGAGGCCATTGTCCAATGAGACGTG\n+TTCTCCTAAATCCATGAGGACTTTTTGCTCCAGGATTGTTTCGTAAAAATATTTTGATTT\n+TTCCATATCATCAACTATAAGCAATGTGCCTCCGTATTTCATATGGATACCTCCTCTTTT\n+TTTCTCAATTATAGCCTAAAACTTTGCGATCGCACTGTAAAAATCGGACAAGTTGTTTCG\n+GTATTCCTGAGGAGTAACGCCGCATACGGCCCTAAAATCCCTGATAAAGTGAGAAATATC\n+ATAAAACCCGGATTCGGCAGATATATAATCGAGGCTGTAGCTCGTATGGTGCAGCAGATA\n+AATGGCTTTGTTGATACGCACGATTCGGGAAAAATGTTTCAGGTTAAATCCTAAATAGTG\n+ATTGGAAAGCCTGTTTAAATGACGTTCACTGTAAAATGTTTTTTCTGTTATTTCTTTGAG\n+ACTTATGTTACCGTTACTCTGAATGATCAGCTGCACGGCCAGACGGAATTCAGCCGGGTA\n+TTGGCTGCATTGGCTGCAAAGCAGCAGACTCTCGATTCT'..b'GCATGGAATCGTATTATCAGTG\n+GCTGGAACTCCCGGAGCATTTAACCGGAAGGCTGTGTGAGGCCGAGCTCTCCGGCAGGGG\n+AGTCAGCGTATTCGGCGCAGAGCGCTTCTATGTTGGAAAACAGCTGAAAGCAAATGCCGT\n+CAGAGTGGCAACCAGCTCGGCGGAAAGTGACGAACAACTCCGCCGGGGGCTGGAGGTACT\n+GCAGAATTTTATCCGGCAGCGGGATGCGGGGCCTTTATTCATCGTCTAGTTTTTGACCGG\n+AATCACGATTCGTGTAATGTATTCGTCAATGGAATTGATGGTCATCTCGTTTACCCCTGT\n+TTCGTAGGCGTATCCGAAAAGTGTGAGGCCGTGCTGCTTCGCATAGTCCAGGATTTCCGA\n+ATATCGCTGCGGAAGCCTGTCCCAGCTTCCCGTACAGTAGGCGCACAGATAGCTGCCGCT\n+CGGCTTTTTATGGATTTCATTTACAGAAGCTGTGTGGGAAACCTTCATAAACAGGCCGTC\n+ATACTGGTCAAACTCGGAATGGAGCAGGTGGGAGACGGAGATCAGGGAGCCGTAAGTGGT\n+ATCGTGGAGACTCTTAAAATGGTGCTGTTTCATGGATTCAACCATCTGTTCGATCTCATC\n+CTCCATGGACAGGGCCTGGTCGGAGGCAATGATGTGCAGATACTCCTCTTCACATTCGAC\n+AACGTCGATCCGGGTCAGATCGGTGTTCAGTAAATCGGTGAAGGTACCGCATTGGTCCGT\n+CAGCATATCACGGATCGTGTTCAGCTTTTCTATTTCACGGTCCACGTCCTGAATCTTTTT\n+ATGCAGAAGCTGAACGTAGGCTTCTGCCCCACGCCTGTCTAAAAACTCTTTGATCTCAGG\n+AATTCCCATATTCAGTTCCCGCAAAACCAGAATCGTCTCCAGCAAAGAGCTCTGATAGTA\n+GGTGTAATAGCGGTAGCCGTTCTCTTTTACGACCGCCGGCTTGAATAAGCCGATCTCATC\n+GTACCACATCAGAGTCTTTTTGTTGATGTTATGAAGGGCTGCAAATTGGCCGATCGTAAA\n+TAGTTTTTCTCTTTCCATAAAAAAATCCCCTTTTCCTCTTTACCGTACAGTTACTGTATG\n+GATTATTATACAGGTAAGACAGTACAAATACAAGAAAAAAGGAGAATAGAATCATGAATT\n+CAGAACATATTACACTGCGCCCCATCACACGAAAGGATTATCCGTTTATAGAGGATATCA\n+TACGCAAGACGTGGAAATACGACGCGCTGAGCAGCAATCCGAAGGATGCAAAGCATATGG\n+CAAGGCTGTATCTGCGTTCCTGTCTGCTGCGGGCGACATTTTCCTGTGTCGCGGCTGTGG\n+ATGGAAAGGTGCTGGGAGTTATTCTGGCCGGGAGTAAAAAATCCGTTCCGAAATTCGCCC\n+TTCGCCGCACCCTGGCTCAGCTCTGGTCCATTGCGCTGCTGTTTACAACGAAAACCGGAA\n+GAGGAATCGGTAAATTTTTCAGTACCTTCGACCAAACGGACGAAGAACTGCTGAAAAATG\n+CAGGAAATGCTTTTGACGCGGAAATCTGTTTCTTTGCCGTGGATGAGAGTACAAGGGGAA\n+CCGGAATCGGAAAAATGCTTTTTGCCCAGGCCCTTGATTATCTGGAACAGGAAGGGGTAA\n+AGACCCTGTACCTCTTCACGGATTCCAGCTGTACTTACCAGTTTTACGAGAAGCGGGGAA\n+TGCAGCGGCTGGGAGAGAAGACGGTGGAATTCAGCCCCCATACAGACTACCGCCTGAATA\n+TGTTTATCTATGGCCTGGAATTGCAGGCGGCCAGTTAAGGCCGCTCTGCAATTCAGACCG\n+CACTGCTTCGCTGCCCGCAGGCCGGCGCATCGATGACCCGGTCATACCGGTAGGCCGAGA\n+AGATAAATCCCAGCAGAAGCATATTTACGAGGATGCTGATACTGCCCTCCGAAACCATGG\n+GAAGATTAGTAAAGCTGCCATACTGGAAACCAAAATTCCCAAGTATATAGAGCACGCTCT\n+GAAACAGCAGGCACAGGCCGCAGTGAAAGGACACCGCTCCGGCGAGCGCGCCGTGTATCC\n+TTCGGATGCAGGAGAAGAGGACTGCGTAGAAGGCGGCCATAACTGCAAGAAACAGAATTC\n+CGGCCAGCCAGCCGAACTGTAGTATGAATACGGCCAGGAGATAGTTGTTCGCGTAATGCT\n+GGGGCAGAATGTTCCATAAAGTGACATCTGACGGATCG\n+>contig-75000034 1615 nucleotides\n+CATCCGCCGACCATGTACTTCCCGCTGATTGTCCACGAGGCCCTGATGGTGGAGCCGACG\n+GAGACGGAATCAAAGGAGAACTTAGATGAACTGATCGCCGTGTTCCACGAGATCTATGAG\n+ACGGCGAAGCGTGATCCCGAATATATCCGGAGCTCCCCCCACATCACCATGGTGAAGCGC\n+CTGGATGAAGTAAATGCGGCCCGGAATCCGAAGCTGCATTACGCATTCGGGGAGGAAAGC\n+GCAGAGGGGGAAGAGGCGTGATCCGCCGACTGACCCTGGCCCTGGGGCCGGGGTCATACC\n+CCTATCCCAATTTCGGCATGGAGGAGTATTTGCTTTACGATGTGGAAGAAGAGGAATGCA\n+TTCTCTACCTGTGGCAGAATGAGAAAACCGTGGTCATAGGCAGGAATCAGAACGCATGGA\n+AGGAGTGCCGCAGAGAGGAACTGGAGGCGGCCGGAGGTCATCTGGTGAGACGGCTGTCGG\n+GAGGCGGCGCCGTATTCCACGACCTGGGCAATTTAAATTTTACCTTCATCACAAGAAAAG\n+ATAACTACGATGTCACAAAACAGACGGAGGTTATCCTAAGGGCGGTCAAAAAGCTGGGTG\n+TAAATGCAGAACGGACCGGCCGCAATGATATCACAGTGGATGGCCGCAAGTTTTCCGGCA\n+ACGCGTACTACGAGACCGGGGACTTCTGCTATCATCACGGGACCATTCTGCTCTCCGTGG\n+ACAAAGAAGAGATGGCCCGCTATCTAAACGTTTCCAGGGAAAAACTGAGATCCAAAAGCG\n+TGGATTCCGTCAAAAGCCGTGTGGCCAATTTAATCGAATTCGTACCGGATCTGACGGTTA\n+GACGCATGAGAGACAGTCTGGAGGAAAGCTTCGGCGAGGTCTACGGCCTTCCCGCAGGCC\n+CATTTCCTCCGGAACGGCTTTGCGAAGACGAGGTAAGGGAGCGGACGGAGCGGTTTGCCT\n+CCTGGGAGTGGAAATACGGCAGGAAGATCCCGTTCAGCGATGAAGCCGCCGCCCGTTTTA\n+CCTGGGGGGAGGCCCAGGTGCTGGTCCATGTGGAAGAGGGGCGTGTCCGGGAAGGAAAGA\n+TCTGGTCCGACGCCCTGGATACGGATTTTATCAAAGCTACGGAAGACATTCTGACCGGCA\n+TGATCTGGAACAGAAAGGCAGCGGCAGACCGTTTTGCAGCCCTGTCCTGCGGCACTCCGG\n+TTCAGGAGGCGATGCGGCAGGATTTACAGGATCTGGTCTGCGATATGATGTAGTGCTGTG\n+CCGTCGATTCACAGACGCGCCTGAGAGAACAGGAGGATTGGATGGAAAAACATTATGATC\n+TCGTCGTAATCGGCGCGGGGCCGGGCGGCTATATGACGGCCCTGTACGCGTCGAAGGCGG\n+GAAAAAGAACGGCCGTGATCGAACGGTCCCATGTGGGGGGCACCTGTTTAAACTGCGGAT\n+GCATTCCTACGAAAACGTATCTCCACACCACCGGCCTTTACCGGGAGGTGAAGAAGACAG\n+AGGCCGCCGGCCTCCATACGGAAGGCCTGCGCGTATCCATGGAGGAACTGAAGAAACGCA\n+AAGACGCCGTGGTGGAAGAATTGCGCGCCGGCATCGAGAAGCAGCTGGCCGCCGC\n' |