| Next changeset 1:6ff67d2860e1 (2024-05-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2 |
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added:
macro.xml test-data/abricate/report.tsv test-data/bakta/bakta.json test-data/bakta/bakta_aminoacid.faa test-data/bakta/bakta_annotation.gff3 test-data/bakta/bakta_annotation.tsv test-data/bakta/bakta_contigs_sequences.fna test-data/bakta/bakta_embl.embl test-data/bakta/bakta_gbff.gbff test-data/bakta/bakta_hypothetical.faa test-data/bakta/bakta_hypothetical.tsv test-data/bakta/bakta_nucleotide_annotation.ffn test-data/bakta/bakta_plot.svg test-data/bakta/bakta_summary.txt test-data/bandage/bandage_info.txt test-data/bandage/bandage_plot.svg test-data/bracken/bracken_kraken_report.tsv test-data/bracken/bracken_report.tsv test-data/fastp/fastp_report.html test-data/fastp/fastp_report.json test-data/fastp/trimmed_R1.fastq.gz test-data/fastp/trimmed_R2.fastq.gz test-data/integronfinder2/results.integrons test-data/integronfinder2/results.summary test-data/isescan/annotation.gff test-data/isescan/is.fna test-data/isescan/orf.faa test-data/isescan/orf.fna test-data/isescan/results.tsv test-data/isescan/summary.tsv test-data/kraken2/taxonomy_report.tsv test-data/kraken2/taxonomy_result.tsv test-data/plasmidfinder/genome_hit.fasta test-data/plasmidfinder/plasmid_hit.fasta test-data/plasmidfinder/plasmidfinder_result.json test-data/quast/quast_report.html test-data/quast/quast_result.tsv test-data/recentrifuge/rcf_data.tsv test-data/recentrifuge/rcf_report.html test-data/recentrifuge/rcf_stat.tsv test-data/refseqmasher/refsesqmasher.tsv test-data/shovill/alignment.bam test-data/shovill/contigs.fa test-data/shovill/contigs.gfa test-data/staramr/mlst.tsv test-data/staramr/plasmidfinder.tsv test-data/staramr/pointfinder.tsv test-data/staramr/resfinder.tsv test-data/staramr/settings.txt test-data/summarize/abricate_output.json test-data/summarize/bakta_all_output.json test-data/summarize/bandage_output.json test-data/summarize/bracken_full_output.json test-data/summarize/fastp_output.json test-data/summarize/integronfinder2_output.json test-data/summarize/isescan_output.json test-data/summarize/kraken2_output.json test-data/summarize/multiqc_output.json test-data/summarize/plasmidfinder_output.json test-data/summarize/quast_output.json test-data/summarize/recentrifuge_output.json test-data/summarize/refseqmasher_output.json test-data/summarize/shovill_output.json test-data/summarize/staramr_output.json test-data/summarize/summarize.json test-data/summarize/tabular_file_output.json test-data/tabular_file/report.tsv tooldistillator_summarize.xml |
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| diff -r 000000000000 -r 05c1bcba20c9 macro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macro.xml Tue Apr 30 08:41:54 2024 +0000 |
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| @@ -0,0 +1,38 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">0.8.4.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <xml name="version_command"> + <version_command><![CDATA[tooldistillator --version]]></version_command> + </xml> + <xml name="analysis_software_version"> + <param argument="--analysis_software_version" type="text" optional="true" label="Analysis software version"/> + </xml> + <xml name="reference_database_version"> + <param argument="--reference_database_version" type="text" optional="true" label="Database software version"/> + </xml> + <xml name="biotools"> + <xrefs> + <xref type="bio.tools">tooldistillator</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">tooldistillator</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.5281/zenodo.8282656</citation> + </citations> + </xml> + <xml name="element_assert" token_name="" token_text=""> + <element name="@NAME@"> + <assert_contents> + <has_text text="@TEXT@"/> + <yield/> + </assert_contents> + </element> + </xml> +</macros> |
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| diff -r 000000000000 -r 05c1bcba20c9 test-data/abricate/report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abricate/report.tsv Tue Apr 30 08:41:54 2024 +0000 |
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| @@ -0,0 +1,25 @@ +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00002 142975 143985 + bopD 1-1011/1011 =============== 0/0 100.00 98.91 vfdb NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00003 7884 11111 - fss3 1-3228/3228 =============== 0/0 100.00 99.38 vfdb NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00003 162314 163240 + efaA 1-927/927 =============== 0/0 100.00 99.89 vfdb NP_815739 (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00006 33703 37014 + ebpA 1-3312/3312 =============== 0/0 100.00 99.49 vfdb NP_814821 (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00006 37018 38448 + ebpB 1-1431/1431 =============== 0/0 100.00 99.30 vfdb NP_814822 (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00006 38445 40328 + ebpC 1-1878/1878 ========/====== 1/6 100.00 98.99 vfdb NP_814823 (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00006 40422 41276 + srtC 1-855/855 =============== 0/0 100.00 99.30 vfdb NP_814824 (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00006 44356 46374 + ace 1-2025/2025 ========/====== 2/6 99.70 96.74 vfdb NP_814829 (ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00010 49447 50301 - sprE 1-855/855 =============== 0/0 100.00 98.36 vfdb NP_815515 (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00010 50350 51882 - gelE 1-1533/1533 =============== 0/0 100.00 98.96 vfdb NP_815516 (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00010 52117 53200 - fsrC 261-1344/1344 ..============= 0/0 80.65 99.26 vfdb NP_815517 (fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00018 14420 15232 - cpsK 1-813/813 =============== 0/0 100.00 99.88 vfdb NP_816131 (cpsK) ABC transporter permease protein [Capsule (VF0361)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00018 15232 16575 - cpsJ 1-1344/1344 =============== 0/0 100.00 98.96 vfdb NP_816132 (cpsJ) ABC transporter ATP-binding protein [Capsule (VF0361)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00018 16601 17739 - cpsI 1-1140/1140 ========/====== 1/1 99.91 98.33 vfdb NP_816133 (cpsI) UDP-galactopyranose mutase [Capsule (VF0361)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00018 17798 18196 - cpsH 1-399/399 =============== 0/0 100.00 97.49 vfdb NP_816134 (cpsH) lipoprotein [Capsule (VF0361)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00018 18214 20666 - cpsG 1-2454/2454 ========/====== 1/1 99.96 99.51 vfdb NP_816135 (cpsG) MurB family protein [Capsule (VF0361)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00018 20736 23245 - cpsE 1-2510/2511 =============== 0/0 99.96 99.40 vfdb NP_816137 (cpsE) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00018 23315 24781 - cpsD 1-1467/1467 =============== 0/0 100.00 98.91 vfdb NP_816138 (cpsD) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00018 24800 25969 - cpsC 1-1170/1170 =============== 0/0 100.00 99.57 vfdb NP_816139 (cpsC) teichoic acid biosynthesis protein putative [Capsule (VF0361)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00018 26443 27243 - cpsB 1-801/801 =============== 0/0 100.00 99.50 vfdb NP_816140 (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00018 27240 28055 - cpsA 1-816/816 =============== 0/0 100.00 99.51 vfdb NP_816141 (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00018 36270 40580 - fss2 1-4305/4956 ========/=====. 11/22 86.70 92.92 vfdb NP_816151 (fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00023 14087 18004 + prgB/asc10 1-3918/3918 ========/====== 2/4 99.95 94.26 vfdb NP_817031 (prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00042 2539 8502 - fss1 1-5964/5964 =============== 0/0 100.00 98.31 vfdb NP_813892 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583] |
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| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta.json Tue Apr 30 08:41:54 2024 +0000 |
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| @@ -0,0 +1,95 @@ +{ + "genome": { + "genus": null, + "species": null, + "strain": null, + "complete": true, + "gram": "?", + "translation_table": 11 + }, + "stats": { + "no_sequences": 1, + "size": 1330, + "gc": 0.4518796992481203, + "n_ratio": 0.0, + "n50": 1330, + "coding_ratio": 0.6203007518796992 + }, + "features": [ + { + "type": "cds", + "contig": "contig_1", + "start": 413, + "stop": 736, + "strand": "+", + "frame": 2, + "gene": null, + "product": "hypothetical protein", + "db_xrefs": [], + "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG", + "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD", + "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", + "start_type": "ATG", + "rbs_motif": "GGAG/GAGG", + "hypothetical": true, + "genes": [], + "seq_stats": { + "molecular_weight": 12072.90819999999, + "isoelectric_point": 10.367886161804197 + }, + "id": "IHHALPPJCH_1", + "locus": "IHHALP_00005" + }, + { + "type": "cds", + "contig": "contig_1", + "start": 971, + "stop": 141, + "strand": "-", + "frame": 1, + "gene": null, + "product": "hypothetical protein", + "db_xrefs": [], + "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA", + "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI", + "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584", + "start_type": "ATG", + "rbs_motif": "AGGA/GGAG/GAGG", + "edge": true, + "hypothetical": true, + "genes": [], + "seq_stats": { + "molecular_weight": 18866.325799999995, + "isoelectric_point": 7.696590614318848 + }, + "id": "IHHALPPJCH_2", + "locus": "IHHALP_00010" + } + ], + "sequences": [ + { + "id": "contig_1", + "description": "[gcode=11] [completeness=complete] [topology=circular] [plasmid-name=unnamed1]", + "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG", + "length": 1330, + "complete": true, + "type": "plasmid", + "topology": "circular", + "simple_id": "contig_1", + "orig_id": "NC_002127.1", + "orig_description": "Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence", + "name": "unnamed1" + } + ], + "run": { + "start": "2024-02-11 00:24:53", + "end": "2024-02-11 00:25:06" + }, + "version": { + "bakta": "1.9.2", + "db": { + "version": "5.0", + "type": "full" + } + } +} \ No newline at end of file |
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| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta_aminoacid.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta_aminoacid.faa Tue Apr 30 08:41:54 2024 +0000 |
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| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
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| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta_annotation.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta_annotation.gff3 Tue Apr 30 08:41:54 2024 +0000 |
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| @@ -0,0 +1,36 @@ +##gff-version 3 +##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo +# Annotated with Bakta +# Software: v1.9.2 +# Database: v5.0, full +# DOI: 10.1099/mgen.0.000685 +# URL: github.com/oschwengers/bakta +##sequence-region contig_1 1 1330 +contig_1 Bakta region 1 1330 . + . ID=contig_1;Name=contig_1;Is_circular=true +contig_1 Prodigal CDS 413 736 . + 0 ID=IHHALP_00005;Name=hypothetical protein;locus_tag=IHHALP_00005;product=hypothetical protein +contig_1 Prodigal CDS 971 1471 . - 0 ID=IHHALP_00010;Name=hypothetical protein;locus_tag=IHHALP_00010;product=hypothetical protein +##FASTA +>contig_1 +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
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| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta_annotation.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta_annotation.tsv Tue Apr 30 08:41:54 2024 +0000 |
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| @@ -0,0 +1,8 @@ +# Annotated with Bakta +# Software: v1.9.2 +# Database: v5.0, full +# DOI: 10.1099/mgen.0.000685 +# URL: github.com/oschwengers/bakta +#Sequence Id Type Start Stop Strand Locus Tag Gene Product DbXrefs +contig_1 cds 413 736 + IHHALP_00005 hypothetical protein +contig_1 cds 971 141 - IHHALP_00010 hypothetical protein |
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| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta_contigs_sequences.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta_contigs_sequences.fna Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,24 @@ +>contig_1 [gcode=11] [completeness=complete] [topology=circular] [plasmid-name=unnamed1] +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta_embl.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta_embl.embl Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,85 @@ +ID contig_1; ; circular; DNA; ; PRO; 1330 BP. +XX +AC contig_1; +XX +DE plasmid unnamed1, complete sequence +XX +OS . +OC . +XX +CC Annotated with Bakta +CC Software: v1.9.2 +CC Database: v5.0, full +CC DOI: 10.1099/mgen.0.000685 +CC URL: github.com/oschwengers/bakta +CC +CC ##Genome Annotation Summary:## +CC Annotation Date :: 02/11/2024, 00:24:56 +CC CDSs :: 2 +CC tRNAs :: 0 +CC tmRNAs :: 0 +CC rRNAs :: 0 +CC ncRNAs :: 0 +CC regulatory ncRNAs :: 0 +CC CRISPR Arrays :: 0 +CC oriCs/oriVs :: 0 +CC oriTs :: 0 +CC gaps :: 0 +CC pseudogenes :: 0 +XX +FH Key Location/Qualifiers +FH +FT source 1..1330 +FT /mol_type="genomic DNA" +FT /plasmid="unnamed1" +FT gene 413..736 +FT /locus_tag="IHHALP_00005" +FT CDS 413..736 +FT /product="hypothetical protein" +FT /locus_tag="IHHALP_00005" +FT /protein_id="gnl|Bakta|IHHALP_00005" +FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA +FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL +FT MAD" +FT /codon_start=1 +FT /transl_table=11 +FT /inference="ab initio prediction:Prodigal:2.6" +FT gene complement(join(971..1330,1..141)) +FT /locus_tag="IHHALP_00010" +FT CDS complement(join(971..1330,1..141)) +FT /product="hypothetical protein" +FT /locus_tag="IHHALP_00010" +FT /protein_id="gnl|Bakta|IHHALP_00010" +FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA +FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR +FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG +FT IPI" +FT /codon_start=1 +FT /transl_table=11 +FT /inference="ab initio prediction:Prodigal:2.6" +XX +SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; + ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc 60 + gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc 120 + agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg 180 + tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt 240 + tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt 300 + gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac 360 + cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa 420 + acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga 480 + agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt 540 + acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga 600 + agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga 660 + cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag 720 + gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt 780 + aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga 840 + tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc 900 + agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc 960 + tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa 1020 + ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat 1080 + cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat 1140 + taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa 1200 + aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc 1260 + tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg 1320 + cttctatttg 1330 +// |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta_gbff.gbff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta_gbff.gbff Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,81 @@ +LOCUS contig_1 1330 bp DNA circular BCT 11-FEB-2024 +DEFINITION plasmid unnamed1, complete sequence. +ACCESSION contig_1 +VERSION contig_1 +KEYWORDS . +SOURCE None + ORGANISM . + . +COMMENT Annotated with Bakta + Software: v1.9.2 + Database: v5.0, full + DOI: 10.1099/mgen.0.000685 + URL: github.com/oschwengers/bakta + + ##Genome Annotation Summary:## + Annotation Date :: 02/11/2024, 00:24:56 + CDSs :: 2 + tRNAs :: 0 + tmRNAs :: 0 + rRNAs :: 0 + ncRNAs :: 0 + regulatory ncRNAs :: 0 + CRISPR Arrays :: 0 + oriCs/oriVs :: 0 + oriTs :: 0 + gaps :: 0 + pseudogenes :: 0 +FEATURES Location/Qualifiers + source 1..1330 + /mol_type="genomic DNA" + /plasmid="unnamed1" + gene 413..736 + /locus_tag="IHHALP_00005" + CDS 413..736 + /product="hypothetical protein" + /locus_tag="IHHALP_00005" + /protein_id="gnl|Bakta|IHHALP_00005" + /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA + AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL + MAD" + /codon_start=1 + /transl_table=11 + /inference="ab initio prediction:Prodigal:2.6" + gene complement(join(971..1330,1..141)) + /locus_tag="IHHALP_00010" + CDS complement(join(971..1330,1..141)) + /product="hypothetical protein" + /locus_tag="IHHALP_00010" + /protein_id="gnl|Bakta|IHHALP_00010" + /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA + EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR + YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG + IPI" + /codon_start=1 + /transl_table=11 + /inference="ab initio prediction:Prodigal:2.6" +ORIGIN + 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc + 61 gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc + 121 agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg + 181 tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt + 241 tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt + 301 gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac + 361 cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa + 421 acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga + 481 agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt + 541 acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga + 601 agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga + 661 cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag + 721 gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt + 781 aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga + 841 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc + 901 agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc + 961 tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa + 1021 ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat + 1081 cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat + 1141 taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa + 1201 aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc + 1261 tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg + 1321 cttctatttg +// |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta_hypothetical.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta_hypothetical.faa Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta_hypothetical.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta_hypothetical.tsv Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,5 @@ +#Annotated with Bakta v1.9.2, https://github.com/oschwengers/bakta +#Database v5.0, https://doi.org/10.5281/zenodo.4247252 +#Sequence Id Start Stop Strand Locus Tag Mol Weight [kDa] Iso El. Point Pfam hits Dbxrefs +contig_1 413 736 + IHHALP_00005 12.1 10.4 +contig_1 971 141 - IHHALP_00010 18.9 7.7 |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta_nucleotide_annotation.ffn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta_nucleotide_annotation.ffn Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG +>IHHALP_00010 hypothetical protein +ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta_plot.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta_plot.svg Tue Apr 30 08:41:54 2024 +0000 |
| b |
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| diff -r 000000000000 -r 05c1bcba20c9 test-data/bakta/bakta_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bakta/bakta_summary.txt Tue Apr 30 08:41:54 2024 +0000 |
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| @@ -0,0 +1,30 @@ +Sequence(s): +Length: 1330 +Count: 1 +GC: 45.2 +N50: 1330 +N ratio: 0.0 +coding density: 62.0 + +Annotation: +tRNAs: 0 +tmRNAs: 0 +rRNAs: 0 +ncRNAs: 0 +ncRNA regions: 0 +CRISPR arrays: 0 +CDSs: 2 +pseudogenes: 0 +hypotheticals: 2 +signal peptides: 0 +sORFs: 0 +gaps: 0 +oriCs: 0 +oriVs: 0 +oriTs: 0 + +Bakta: +Software: v1.9.2 +Database: v5.0, full +DOI: 10.1099/mgen.0.000685 +URL: github.com/oschwengers/bakta |
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| diff -r 000000000000 -r 05c1bcba20c9 test-data/bandage/bandage_info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bandage/bandage_info.txt Tue Apr 30 08:41:54 2024 +0000 |
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| @@ -0,0 +1,19 @@ +Node count: 222 +Edge count: 299 +Smallest edge overlap (bp): 127 +Largest edge overlap (bp): 127 +Total length (bp): 3042326 +Total length no overlaps (bp): 3014132 +Dead ends: 0 +Percentage dead ends: 0% +Connected components: 2 +Largest component (bp): 3042198 +Total length orphaned nodes (bp): 3042198 +N50 (bp): 79920 +Shortest node (bp): 128 +Lower quartile node (bp): 151 +Median node (bp): 256 +Upper quartile node (bp): 7566 +Longest node (bp): 239204 +Median depth: 22.997 +Estimated sequence length (bp): 3234717 |
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| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/bracken/bracken_kraken_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bracken/bracken_kraken_report.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,24 @@ +100.00 95 0 R 1 root +100.00 95 0 R1 131567 cellular organisms +100.00 95 0 D 2 Bacteria +100.00 95 0 D1 1783272 Terrabacteria group +100.00 95 0 P 1239 Firmicutes +100.00 95 0 C 91061 Bacilli +97.87 92 0 O 186826 Lactobacillales +95.16 90 0 F 81852 Enterococcaceae +95.16 90 0 G 1350 Enterococcus +89.01 84 84 S 1351 Enterococcus faecalis +4.89 4 4 S 1352 Enterococcus faecium +1.25 1 1 S 37734 Enterococcus casseliflavus +2.71 2 0 F 1300 Streptococcaceae +1.63 1 0 G 1301 Streptococcus +1.63 1 1 S 45634 Streptococcus cristatus +1.08 1 0 G 1357 Lactococcus +1.08 1 1 S 1363 Lactococcus garvieae +2.13 2 0 O 1385 Bacillales +1.08 1 0 F 90964 Staphylococcaceae +1.08 1 0 G 1279 Staphylococcus +1.08 1 1 S 1280 Staphylococcus aureus +1.05 1 0 F 186817 Bacillaceae +1.05 1 0 G 1386 Bacillus +1.05 1 1 S 38875 Bacillus oleronius |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/bracken/bracken_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bracken/bracken_report.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,8 @@ +name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads +Enterococcus faecalis 1351 S 63 21 84 0.88421 +Enterococcus faecium 1352 S 4 0 4 0.04211 +Enterococcus casseliflavus 37734 S 1 0 1 0.01053 +Streptococcus cristatus 45634 S 1 0 1 0.01053 +Lactococcus garvieae 1363 S 1 0 1 0.01053 +Staphylococcus aureus 1280 S 1 0 1 0.01053 +Bacillus oleronius 38875 S 1 0 1 0.01053 |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/fastp/fastp_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastp/fastp_report.html Tue Apr 30 08:41:54 2024 +0000 |
| b |
| b'@@ -0,0 +1,4650 @@\n+<html><head><meta http-equiv="content-type" content="text/html;charset=utf-8" /><title>fastp report at 2023-06-13 14:25:49 </title><script src=\'http://opengene.org/plotly-1.2.0.min.js\'></script>\n+\n+<script type=\'text/javascript\'>\n+ window.Plotly || document.write(\'<script src="https://cdn.plot.ly/plotly-1.2.0.min.js"><\\/script>\')\n+</script>\n+\n+<script type="text/javascript">\n+ function showOrHide(divname) {\n+ div = document.getElementById(divname);\n+ if(div.style.display == \'none\')\n+ div.style.display = \'block\';\n+ else\n+ div.style.display = \'none\';\n+ }\n+</script>\n+<style type="text/css">\n+td {border:1px solid #dddddd;padding:5px;font-size:12px;}\n+table {border:1px solid #999999;padding:2x;border-collapse:collapse; width:800px}\n+.col1 {width:240px; font-weight:bold;}\n+.adapter_col {width:500px; font-size:10px;}\n+img {padding:30px;}\n+#menu {font-family:Consolas, \'Liberation Mono\', Menlo, Courier, monospace;}\n+#menu a {color:#0366d6; font-size:18px;font-weight:600;line-height:28px;text-decoration:none;font-family:-apple-system, BlinkMacSystemFont, \'Segoe UI\', Helvetica, Arial, sans-serif, \'Apple Color Emoji\', \'Segoe UI Emoji\', \'Segoe UI Symbol\'}\n+a:visited {color: #999999}\n+.alignleft {text-align:left;}\n+.alignright {text-align:right;}\n+.figure {width:800px;height:600px;}\n+.header {color:#ffffff;padding:1px;height:20px;background:#000000;}\n+.section_title {color:#ffffff;font-size:20px;padding:5px;text-align:left;background:#663355; margin-top:10px;}\n+.subsection_title {font-size:16px;padding:5px;margin-top:10px;text-align:left;color:#663355}\n+#container {text-align:center;padding:3px 3px 3px 10px;font-family:Arail,\'Liberation Mono\', Menlo, Courier, monospace;}\n+.menu_item {text-align:left;padding-top:5px;font-size:18px;}\n+.highlight {text-align:left;padding-top:30px;padding-bottom:30px;font-size:20px;line-height:35px;}\n+#helper {text-align:left;border:1px dotted #fafafa;color:#777777;font-size:12px;}\n+#footer {text-align:left;padding:15px;color:#ffffff;font-size:10px;background:#663355;font-family:Arail,\'Liberation Mono\', Menlo, Courier, monospace;}\n+.kmer_table {text-align:center;font-size:8px;padding:2px;}\n+.kmer_table td{text-align:center;font-size:8px;padding:0px;color:#ffffff}\n+.sub_section_tips {color:#999999;font-size:10px;padding-left:5px;padding-bottom:3px;}\n+</style>\n+</head><body><div id=\'container\'>\n+<h1 style=\'text-align:left;\'><a href=\'https://github.com/OpenGene/fastp\' target=\'_blank\' style=\'color:#663355;text-decoration:none;\'>fastp report for 9_Enterococcus_faecium_S20_L001_R1_fastq_gz.fastq.gz</a>\n+<div class=\'section_div\'>\n+<div class=\'section_title\' onclick=showOrHide(\'summary\')><a name=\'summary\'>Summary</a></div>\n+<div id=\'summary\'>\n+<div class=\'subsection_title\' onclick=showOrHide(\'general\')>General</div>\n+<div id=\'general\'>\n+<table class=\'summary_table\'>\n+<tr><td class=\'col1\'>fastp version:</td><td class=\'col2\'>0.23.2 (<a href=\'https://github.com/OpenGene/fastp\'>https://github.com/OpenGene/fastp</a>)</td></tr>\n+<tr><td class=\'col1\'>sequencing:</td><td class=\'col2\'>paired end (301 cycles + 301 cycles)</td></tr>\n+<tr><td class=\'col1\'>mean length before filtering:</td><td class=\'col2\'>301bp, 301bp</td></tr>\n+<tr><td class=\'col1\'>mean length after filtering:</td><td class=\'col2\'>216bp, 216bp</td></tr>\n+<tr><td class=\'col1\'>duplication rate:</td><td class=\'col2\'>0.013477%</td></tr>\n+<tr><td class=\'col1\'>Insert size peak:</td><td class=\'col2\'>152</td></tr>\n+<tr><td class=\'col1\'>Detected read1 adapter:</td><td class=\'col2\'>AGATCGGAAGAGCACACGTCTGAACTCCAGTCA</td></tr>\n+<tr><td class=\'col1\'>Detected read2 adapter:</td><td class=\'col2\'>AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT</td></tr>\n+</table>\n+</div>\n+<div class=\'subsection_title\' onclick=showOrHide(\'before_filtering_summary\')>Before filtering</div>\n+<div id=\'before_filtering_summary\'>\n+<table class=\'summary_table\'>\n+<tr><td class=\'col1\'>total reads:</td><td class=\'col2\'>74.198000 K</td></tr>\n+<'..b"</td><td style='background:#8b8b8b' title='GGTCC: 1761\n+0.45242 times as mean value'>GGTCC</td><td style='background:#7f7f7f' title='GGTCG: 2656\n+0.682355 times as mean value'>GGTCG</td><td style='background:#7f7f7f' title='GGTGA: 4840\n+1.24345 times as mean value'>GGTGA</td><td style='background:#7f7f7f' title='GGTGT: 4847\n+1.24525 times as mean value'>GGTGT</td><td style='background:#7f7f7f' title='GGTGC: 3521\n+0.904583 times as mean value'>GGTGC</td><td style='background:#7f7f7f' title='GGTGG: 3522\n+0.90484 times as mean value'>GGTGG</td></tr>\n+<tr><td style='color:#333333'>GGC</td><td style='background:#7f7f7f' title='GGCAA: 7004\n+1.7994 times as mean value'>GGCAA</td><td style='background:#7f7f7f' title='GGCAT: 5116\n+1.31436 times as mean value'>GGCAT</td><td style='background:#7f7f7f' title='GGCAC: 2771\n+0.7119 times as mean value'>GGCAC</td><td style='background:#7f7f7f' title='GGCAG: 4419\n+1.13529 times as mean value'>GGCAG</td><td style='background:#7f7f7f' title='GGCTA: 3886\n+0.998356 times as mean value'>GGCTA</td><td style='background:#7f7f7f' title='GGCTT: 5984\n+1.53735 times as mean value'>GGCTT</td><td style='background:#7f7f7f' title='GGCTC: 2608\n+0.670024 times as mean value'>GGCTC</td><td style='background:#7f7f7f' title='GGCTG: 4310\n+1.10729 times as mean value'>GGCTG</td><td style='background:#7f7f7f' title='GGCCA: 2077\n+0.533604 times as mean value'>GGCCA</td><td style='background:#a8a8a8' title='GGCCT: 1320\n+0.339122 times as mean value'>GGCCT</td><td style='background:#cfcfcf' title='GGCCC: 724\n+0.186003 times as mean value'>GGCCC</td><td style='background:#b2b2b2' title='GGCCG: 1162\n+0.29853 times as mean value'>GGCCG</td><td style='background:#7f7f7f' title='GGCGA: 3500\n+0.899188 times as mean value'>GGCGA</td><td style='background:#7f7f7f' title='GGCGT: 3055\n+0.784863 times as mean value'>GGCGT</td><td style='background:#7f7f7f' title='GGCGC: 2148\n+0.551845 times as mean value'>GGCGC</td><td style='background:#7f7f7f' title='GGCGG: 2935\n+0.754034 times as mean value'>GGCGG</td></tr>\n+<tr><td style='color:#333333'>GGG</td><td style='background:#7f7f7f' title='GGGAA: 6178\n+1.5872 times as mean value'>GGGAA</td><td style='background:#7f7f7f' title='GGGAT: 5398\n+1.38681 times as mean value'>GGGAT</td><td style='background:#7f7f7f' title='GGGAC: 2202\n+0.565718 times as mean value'>GGGAC</td><td style='background:#7f7f7f' title='GGGAG: 2251\n+0.578306 times as mean value'>GGGAG</td><td style='background:#7f7f7f' title='GGGTA: 2773\n+0.712414 times as mean value'>GGGTA</td><td style='background:#7f7f7f' title='GGGTT: 3375\n+0.867074 times as mean value'>GGGTT</td><td style='background:#959595' title='GGGTC: 1615\n+0.414911 times as mean value'>GGGTC</td><td style='background:#7f7f7f' title='GGGTG: 1968\n+0.505601 times as mean value'>GGGTG</td><td style='background:#7f7f7f' title='GGGCA: 2564\n+0.65872 times as mean value'>GGGCA</td><td style='background:#7f7f7f' title='GGGCT: 2243\n+0.576251 times as mean value'>GGGCT</td><td style='background:#d3d3d3' title='GGGCC: 662\n+0.170075 times as mean value'>GGGCC</td><td style='background:#949494' title='GGGCG: 1627\n+0.417994 times as mean value'>GGGCG</td><td style='background:#7f7f7f' title='GGGGA: 2907\n+0.74684 times as mean value'>GGGGA</td><td style='background:#898989' title='GGGGT: 1797\n+0.461669 times as mean value'>GGGGT</td><td style='background:#969696' title='GGGGC: 1592\n+0.409002 times as mean value'>GGGGC</td><td style='background:#aeaeae' title='GGGGG: 1232\n+0.316514 times as mean value'>GGGGG</td></tr>\n+</table>\n+</div>\n+</div>\n+</div>\n+\n+</div>\n+<div id='footer'> <p>fastp --thread 1 --report_title fastp report for 9_Enterococcus_faecium_S20_L001_R1_fastq_gz.fastq.gz -i 9_Enterococcus_faecium_S20_L001_R1_fastq_gz.fastq.gz -o first.fastq.gz -I 9_Enterococcus_faecium_S20_L001_R2_fastq_gz_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe -q 15 -l 15 -Y 30 -c </p>fastp 0.23.2, at 2023-06-13 14:25:49 </div></body></html>\n\\ No newline at end of file\n" |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/fastp/fastp_report.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastp/fastp_report.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| b'@@ -0,0 +1,414 @@\n+{\n+\t"summary": {\n+\t\t"fastp_version": "0.23.2",\n+\t\t"sequencing": "paired end (301 cycles + 301 cycles)",\n+\t\t"before_filtering": {\n+\t\t\t"total_reads":3489582,\n+\t\t\t"total_bases":705053822,\n+\t\t\t"q20_bases":672633294,\n+\t\t\t"q30_bases":625189177,\n+\t\t\t"q20_rate":0.954017,\n+\t\t\t"q30_rate":0.886725,\n+\t\t\t"read1_mean_length":201,\n+\t\t\t"read2_mean_length":202,\n+\t\t\t"gc_content":0.374995\n+\t\t},\n+\t\t"after_filtering": {\n+\t\t\t"total_reads":3440258,\n+\t\t\t"total_bases":690189367,\n+\t\t\t"q20_bases":665469579,\n+\t\t\t"q30_bases":620744461,\n+\t\t\t"q20_rate":0.964184,\n+\t\t\t"q30_rate":0.899383,\n+\t\t\t"read1_mean_length":200,\n+\t\t\t"read2_mean_length":200,\n+\t\t\t"gc_content":0.374878\n+\t\t}\n+\t},\n+\t"filtering_result": {\n+\t\t"passed_filter_reads": 3440258,\n+\t\t"corrected_reads": 464332,\n+\t\t"corrected_bases": 996846,\n+\t\t"low_quality_reads": 49324,\n+\t\t"too_many_N_reads": 0,\n+\t\t"too_short_reads": 0,\n+\t\t"too_long_reads": 0\n+\t},\n+\t"duplication": {\n+\t\t"rate": 0.0185954\n+\t},\n+\t"insert_size": {\n+\t\t"peak": 147,\n+\t\t"unknown": 18596,\n+\t\t"histogram": [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,528,88,57,60,72,95,143,159,219,267,229,179,112,111,111,178,221,273,276,358,350,296,199,163,192,231,347,432,475,491,524,385,336,252,243,325,382,502,628,650,631,582,541,420,386,377,523,624,753,847,852,804,641,555,490,473,624,763,923,961,1057,972,858,740,657,609,670,847,1038,1182,1254,1208,1139,995,831,783,782,991,1065,1327,1443,1450,1258,1115,1013,901,901,1046,1190,1299,1488,1510,1511,1321,1132,1065,1060,1098,1242,1355,1454,1609,1527,1472,1305,1184,1055,1113,1203,1312,1498,1496,1628,1481,1364,1273,1142,1166,1209,1299,1455,1513,1533,1457,1435,1340,1168,1155,1160,1324,1341,1438,1506,1554,1357,1306,1241,1147,1112,1257,1308,1353,1394,1327,1303,1263,1123,1112,1075,1072,1163,1177,1250,1252,1284,1160,1141,1007,1065,1009,1064,1105,1151,1080,1136,1133,1046,992,985,949,1044,1098,1038,1043,1082,1021,1026,905,881,853,868,946,954,937,985,898,986,877,856,814,807,823,812,831,897,842,826,781,828,767,773,775,806,820,790,783,738,748,688,727,715,704,701,739,702,667,716,687,669,673,663,611,679,666,663,650,622,611,624,596,599,546,588,613,639,588,627,589,572,568,541,553,583,525,500,548,563,548,542,570,566,502,500,502,530,547,543,480,477,487,459,494,484,476,497,554,401,463,459,436,417,453,454,472,448,444,487,452,442,453,361,418,391,432,432,417,367,432,350,382,390,390,371,403,382,379,372,397,391,345,352,358,351,351,355,339,391,340,330,358,336,312,325,317,329,337,329,335,302,308,298,304,295,292,263,326,314,310,326,300,270,270,292,255,296,298,284,278,272,275,253,230,249,241,249,257,282,264,257,243,238,248,262,227,215,261,260,240,221,246,253,227,223,194,246,245,227,235,207,228,209,197,239,205,189,189,217,185,197,211,179,190,212,180,178,182,171,190,196,192,174,202,162,167,169,170,162,162,169,162,145,160,141,175,165,160,151,161,151,166,148,151,124,169,148,144,138,137,143,156,153,130,140,165,149,130,170,150,114,130,129,129,134,121,117,127,125,124,115,117,134,127,128,107,129,115,135,106,112,100,117,121,113,104,106,112,101,96,112,102,96,126,90,111,106,97,109,121,99,89,111,81,104,95,96,97,93]\n+\t},\n+\t"adapter_cutting": {\n+\t\t"adapter_trimmed_reads": 75904,\n+\t\t"adapter_trimmed_bases": 2561055,\n+\t\t"read1_adapter_sequence": "unspecified",\n+\t\t"read2_adapter_sequence": "unspecified",\n+\t\t"read1_adapter_counts": {"C":292, "CTG":108, "CTT":147, "CTGG":56, "CTGTC":815, "CTGTCTC":118, "others":3652},\n+\t\t"read2_adapter_counts": {"C":2063, "CT":916, "CTG":1466, "CTGTC":2405, "CTGTCTC":1782, "CTGTCTCT":427, "others":28893}\n+\t},\n+\t"read1_before_filtering": {\n+\t\t"total_reads": 1744791,\n+\t\t"total_bases": 351848724,\n+\t\t"q20_bases": 342040599,\n+\t\t"q30_bases": 323015923,\n+\t\t"total_cycles": 301,\n+\t\t"quality_curves": {\n+\t\t\t"A":[33.5141,33.4002,33.5409,33.4475,33.6268,37.3955,37.3028,37.259,36.9535,36.9595,37.0138,36.9114,36.9389,36.8512,37.0206,37.0099,36.9835,36.9291,36.9474,36.9193,36.9612,36.8893,36.9089,36.9015,36.929,36.8349,36.7791,36.7675,36.7737,36.7637,36.8469,36.7628,36.8111,36.7922,36.7857,36.6576,36'..b',\t\t\t"GAGCG":117905,\t\t\t"GAGGA":192195,\t\t\t"GAGGT":116922,\t\t\t"GAGGC":92674,\t\t\t"GAGGG":69800,\n+\t\t\t"GTAAA":637139,\t\t\t"GTAAT":490020,\t\t\t"GTAAC":279558,\t\t\t"GTAAG":196905,\t\t\t"GTATA":259328,\t\t\t"GTATT":464019,\t\t\t"GTATC":274028,\t\t\t"GTATG":217409,\t\t\t"GTACA":206154,\t\t\t"GTACT":181575,\t\t\t"GTACC":166140,\t\t\t"GTACG":115022,\t\t\t"GTAGA":210678,\t\t\t"GTAGT":210168,\t\t\t"GTAGC":209477,\t\t\t"GTAGG":127713,\n+\t\t\t"GTTAA":532759,\t\t\t"GTTAT":425576,\t\t\t"GTTAC":280577,\t\t\t"GTTAG":265620,\t\t\t"GTTTA":537425,\t\t\t"GTTTT":937942,\t\t\t"GTTTC":534060,\t\t\t"GTTTG":484945,\t\t\t"GTTCA":414554,\t\t\t"GTTCT":360266,\t\t\t"GTTCC":288409,\t\t\t"GTTCG":194937,\t\t\t"GTTGA":443793,\t\t\t"GTTGT":437840,\t\t\t"GTTGC":352748,\t\t\t"GTTGG":371411,\n+\t\t\t"GTCAA":410133,\t\t\t"GTCAT":319626,\t\t\t"GTCAC":194565,\t\t\t"GTCAG":146749,\t\t\t"GTCTA":173544,\t\t\t"GTCTT":331328,\t\t\t"GTCTC":107874,\t\t\t"GTCTG":152085,\t\t\t"GTCCA":218236,\t\t\t"GTCCT":163341,\t\t\t"GTCCC":109074,\t\t\t"GTCCG":97788,\t\t\t"GTCGA":152754,\t\t\t"GTCGT":208474,\t\t\t"GTCGC":158790,\t\t\t"GTCGG":126162,\n+\t\t\t"GTGAA":412566,\t\t\t"GTGAT":336321,\t\t\t"GTGAC":194240,\t\t\t"GTGAG":105830,\t\t\t"GTGTA":204914,\t\t\t"GTGTT":332135,\t\t\t"GTGTC":178535,\t\t\t"GTGTG":141219,\t\t\t"GTGCA":180824,\t\t\t"GTGCT":203123,\t\t\t"GTGCC":169833,\t\t\t"GTGCG":106833,\t\t\t"GTGGA":222611,\t\t\t"GTGGT":256316,\t\t\t"GTGGC":220378,\t\t\t"GTGGG":124773,\n+\t\t\t"GCAAA":557213,\t\t\t"GCAAT":531089,\t\t\t"GCAAC":350546,\t\t\t"GCAAG":270365,\t\t\t"GCATA":232649,\t\t\t"GCATT":411957,\t\t\t"GCATC":256817,\t\t\t"GCATG":173370,\t\t\t"GCACA":189030,\t\t\t"GCACT":156517,\t\t\t"GCACC":183598,\t\t\t"GCACG":121774,\t\t\t"GCAGA":285296,\t\t\t"GCAGT":216387,\t\t\t"GCAGC":231051,\t\t\t"GCAGG":162360,\n+\t\t\t"GCTAA":433526,\t\t\t"GCTAT":274746,\t\t\t"GCTAC":209397,\t\t\t"GCTAG":168148,\t\t\t"GCTTA":275424,\t\t\t"GCTTT":620080,\t\t\t"GCTTC":421016,\t\t\t"GCTTG":366857,\t\t\t"GCTCA":169397,\t\t\t"GCTCT":168970,\t\t\t"GCTCC":122995,\t\t\t"GCTCG":109385,\t\t\t"GCTGA":297527,\t\t\t"GCTGT":299400,\t\t\t"GCTGC":233353,\t\t\t"GCTGG":252928,\n+\t\t\t"GCCAA":474431,\t\t\t"GCCAT":363930,\t\t\t"GCCAC":219705,\t\t\t"GCCAG":198571,\t\t\t"GCCTA":158591,\t\t\t"GCCTT":316973,\t\t\t"GCCTC":95179,\t\t\t"GCCTG":141154,\t\t\t"GCCCA":163914,\t\t\t"GCCCT":83859,\t\t\t"GCCCC":91276,\t\t\t"GCCCG":64505,\t\t\t"GCCGA":162690,\t\t\t"GCCGT":176702,\t\t\t"GCCGC":159966,\t\t\t"GCCGG":61258,\n+\t\t\t"GCGAA":269264,\t\t\t"GCGAT":262751,\t\t\t"GCGAC":156469,\t\t\t"GCGAG":81117,\t\t\t"GCGTA":159274,\t\t\t"GCGTT":289037,\t\t\t"GCGTC":91245,\t\t\t"GCGTG":119627,\t\t\t"GCGCA":169338,\t\t\t"GCGCT":162862,\t\t\t"GCGCC":153405,\t\t\t"GCGCG":63212,\t\t\t"GCGGA":169615,\t\t\t"GCGGT":174750,\t\t\t"GCGGC":159727,\t\t\t"GCGGG":91200,\n+\t\t\t"GGAAA":572492,\t\t\t"GGAAT":411350,\t\t\t"GGAAC":282731,\t\t\t"GGAAG":262988,\t\t\t"GGATA":268641,\t\t\t"GGATT":429098,\t\t\t"GGATC":154559,\t\t\t"GGATG":202465,\t\t\t"GGACA":203164,\t\t\t"GGACT":146635,\t\t\t"GGACC":100589,\t\t\t"GGACG":125871,\t\t\t"GGAGA":175926,\t\t\t"GGAGT":118343,\t\t\t"GGAGC":121295,\t\t\t"GGAGG":112157,\n+\t\t\t"GGTAA":346420,\t\t\t"GGTAT":231611,\t\t\t"GGTAC":164801,\t\t\t"GGTAG":147299,\t\t\t"GGTTA":269807,\t\t\t"GGTTT":463440,\t\t\t"GGTTC":253317,\t\t\t"GGTTG":272685,\t\t\t"GGTCA":201814,\t\t\t"GGTCT":130918,\t\t\t"GGTCC":101230,\t\t\t"GGTCG":125540,\t\t\t"GGTGA":241660,\t\t\t"GGTGT":231666,\t\t\t"GGTGC":183585,\t\t\t"GGTGG":211260,\n+\t\t\t"GGCAA":380065,\t\t\t"GGCAT":253024,\t\t\t"GGCAC":167326,\t\t\t"GGCAG":159044,\t\t\t"GGCTA":213608,\t\t\t"GGCTT":360565,\t\t\t"GGCTC":117871,\t\t\t"GGCTG":187686,\t\t\t"GGCCA":155497,\t\t\t"GGCCT":88425,\t\t\t"GGCCC":58580,\t\t\t"GGCCG":81779,\t\t\t"GGCGA":199113,\t\t\t"GGCGT":188685,\t\t\t"GGCGC":152509,\t\t\t"GGCGG":151043,\n+\t\t\t"GGGAA":269835,\t\t\t"GGGAT":217695,\t\t\t"GGGAC":106953,\t\t\t"GGGAG":73751,\t\t\t"GGGTA":107585,\t\t\t"GGGTT":169248,\t\t\t"GGGTC":77547,\t\t\t"GGGTG":90238,\t\t\t"GGGCA":134473,\t\t\t"GGGCT":112465,\t\t\t"GGGCC":58310,\t\t\t"GGGCG":93397,\t\t\t"GGGGA":135255,\t\t\t"GGGGT":85222,\t\t\t"GGGGC":89825,\t\t\t"GGGGG":54021\n+\t\t},\n+\t\t"overrepresented_sequences": {\n+\t\t}\n+\t},\n+\t"command": "fastp --thread 6 --report_title fastp_report --compression 4 --html ./report.html --json ./report.json -i /home/pierre/Seafile/ABROMICS_IFB/genome_test_CNR/fastq/10_Enterococcus_faecalis_S17_L001_R1_001.fastq.gz -I /home/pierre/Seafile/ABROMICS_IFB/genome_test_CNR/fastq/10_Enterococcus_faecalis_S17_L001_R2_001.fastq.gz --detect_adapter_for_pe -q 15 -c "\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/fastp/trimmed_R1.fastq.gz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastp/trimmed_R1.fastq.gz Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,3 @@ +@M00536:853:000000000-C843B:1:1101:13480:1462 1:N:0:20 +AAATAGATTGGTACCTTTATTTTTAGCCAATAAAGCACGCCTAGACAATTTGCGTTTTTCACGCTTTAGTTTCTTTTCCATTTTGGAGATCGGAAGTGCACACGTCTTAACTCCAGTCACTACATCTTTTCTCGTATGCCGTCTTCTTCTTTATAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ++ |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/fastp/trimmed_R2.fastq.gz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastp/trimmed_R2.fastq.gz Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,5 @@ + + +@M00536:853:000000000-C843B:1:1101:13480:1462 1:N:0:20 +AAATAGATTGGTACCTTTATTTTTAGCCAATAAAGCACGCCTAGACAATTTGCGTTTTTCACGCTTTAGTTTCTTTTCCATTTTGGAGATCGGAAGTGCACACGTCTTAACTCCAGTCACTACATCTTTTCTCGTATGCCGTCTTCTTCTTTATAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ++ |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/integronfinder2/results.integrons --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/integronfinder2/results.integrons Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,8 @@ +# cmd: integron_finder --cpu 4 --local-max --eagle-eyes --promoter-attI --pdf --gbk --keep-tmp --outdir /storage/scratch/piemari/60579123/integronfinder/integronfinder_10_Enterococcus_faecalis_S17_L001 /storage/scratch/piemari/60579123/integronfinder/10_Enterococcus_faecalis_S17_L001.fasta +ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology +integron_01 contig00017 contig00017_42 41235 41546 -1 NA protein protein NA CALIN No NA lin +integron_01 contig00017 contig00017_43 41543 42391 -1 NA protein protein NA CALIN No NA lin +integron_01 contig00017 attc_001 41600 41701 -1 0.15 attC attC attc_4 CALIN No NA lin +integron_01 contig00017 contig00017_44 42419 43705 -1 NA protein protein NA CALIN No NA lin +integron_01 contig00017 contig00017_45 43702 45213 -1 NA protein protein NA CALIN No NA lin +integron_01 contig00017 attc_002 44054 44100 -1 0.095 attC attC attc_4 CALIN No 2353.0 lin |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/integronfinder2/results.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/integronfinder2/results.summary Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,93 @@ +# cmd: integron_finder --cpu 4 --local-max --eagle-eyes --promoter-attI --pdf --gbk --keep-tmp --outdir /storage/scratch/piemari/60579123/integronfinder/integronfinder_10_Enterococcus_faecalis_S17_L001 /storage/scratch/piemari/60579123/integronfinder/10_Enterococcus_faecalis_S17_L001.fasta +ID_replicon CALIN complete In0 topology size +contig00001 0 0 0 lin 436224 +contig00002 0 0 0 lin 252900 +contig00003 0 0 0 lin 206370 +contig00004 0 0 0 lin 168397 +contig00005 0 0 0 lin 132811 +contig00006 0 0 0 lin 115359 +contig00007 0 0 0 lin 113419 +contig00008 0 0 0 lin 99915 +contig00009 0 0 0 lin 97190 +contig00010 0 0 0 lin 92075 +contig00011 0 0 0 lin 86662 +contig00012 0 0 0 lin 82418 +contig00013 0 0 0 lin 81741 +contig00014 0 0 0 lin 81694 +contig00015 0 0 0 lin 71911 +contig00016 0 0 0 lin 66886 +contig00017 1 0 0 lin 64537 +contig00018 0 0 0 lin 62649 +contig00019 0 0 0 lin 55461 +contig00020 0 0 0 lin 52826 +contig00021 0 0 0 lin 48115 +contig00022 0 0 0 lin 47790 +contig00023 0 0 0 lin 45935 +contig00024 0 0 0 lin 44497 +contig00025 0 0 0 lin 35306 +contig00026 0 0 0 lin 35051 +contig00027 0 0 0 lin 29358 +contig00028 0 0 0 lin 27780 +contig00029 0 0 0 lin 24296 +contig00030 0 0 0 lin 23952 +contig00031 0 0 0 lin 18776 +contig00032 0 0 0 lin 17346 +contig00033 0 0 0 lin 16026 +contig00034 0 0 0 lin 15602 +contig00035 0 0 0 lin 15587 +contig00036 0 0 0 lin 15306 +contig00037 0 0 0 lin 13750 +contig00038 0 0 0 lin 13168 +contig00039 0 0 0 lin 12357 +contig00040 0 0 0 lin 12074 +contig00041 0 0 0 lin 11206 +contig00042 0 0 0 lin 9892 +contig00043 0 0 0 lin 8939 +contig00044 0 0 0 lin 7812 +contig00045 0 0 0 lin 6929 +contig00046 0 0 0 lin 6828 +contig00047 0 0 0 lin 5969 +contig00048 0 0 0 lin 5336 +contig00049 0 0 0 lin 3276 +contig00050 0 0 0 lin 2262 +contig00051 0 0 0 lin 2083 +contig00052 0 0 0 lin 1817 +contig00053 0 0 0 lin 1775 +contig00055 0 0 0 lin 1578 +contig00056 0 0 0 lin 1526 +contig00057 0 0 0 lin 1515 +contig00058 0 0 0 lin 1299 +contig00059 0 0 0 lin 652 +contig00060 0 0 0 lin 607 +contig00061 0 0 0 lin 534 +contig00062 0 0 0 lin 525 +contig00063 0 0 0 lin 442 +contig00065 0 0 0 lin 405 +contig00066 0 0 0 lin 398 +contig00067 0 0 0 lin 378 +contig00068 0 0 0 lin 372 +contig00070 0 0 0 lin 332 +contig00074 0 0 0 lin 256 +contig00075 0 0 0 lin 255 +contig00076 0 0 0 lin 255 +contig00077 0 0 0 lin 255 +contig00078 0 0 0 lin 255 +contig00079 0 0 0 lin 255 +contig00080 0 0 0 lin 255 +contig00081 0 0 0 lin 255 +contig00082 0 0 0 lin 255 +contig00083 0 0 0 lin 255 +contig00084 0 0 0 lin 255 +contig00085 0 0 0 lin 255 +contig00086 0 0 0 lin 254 +contig00088 0 0 0 lin 253 +contig00089 0 0 0 lin 252 +contig00090 0 0 0 lin 250 +contig00091 0 0 0 lin 246 +contig00092 0 0 0 lin 235 +contig00093 0 0 0 lin 231 +contig00094 0 0 0 lin 206 +contig00095 0 0 0 lin 205 +contig00096 0 0 0 lin 161 +contig00097 0 0 0 lin 151 +contig00098 0 0 0 lin 138 |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/isescan/annotation.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isescan/annotation.gff Tue Apr 30 08:41:54 2024 +0000 |
| b |
| b'@@ -0,0 +1,92 @@\n+##gff-version 3\n+contig00001\tISEScan\tinsertion_sequence\t104722\t106001\t.\t+\t.\tID=contig00001_IS_1;family=IS21;cluster=IS21_259\n+contig00001\tISEScan\tterminal_inverted_repeat\t104722\t104735\t.\t+\t.\tID=contig00001_IS_1_TIR;parent=contig00001_IS_1\n+contig00001\tISEScan\tterminal_inverted_repeat\t105988\t106001\t.\t+\t.\tID=contig00001_IS_1_TIR;parent=contig00001_IS_1\n+contig00002\tISEScan\tinsertion_sequence\t179502\t180572\t.\t-\t.\tID=contig00002_IS_1;family=IS200/IS605;cluster=IS200/IS605_96\n+contig00002\tISEScan\tinsertion_sequence\t210210\t214514\t.\t-\t.\tID=contig00002_IS_2;family=IS21;cluster=IS21_288\n+contig00002\tISEScan\tterminal_inverted_repeat\t210210\t210236\t.\t-\t.\tID=contig00002_IS_2_TIR;parent=contig00002_IS_2\n+contig00002\tISEScan\tterminal_inverted_repeat\t214488\t214514\t.\t-\t.\tID=contig00002_IS_2_TIR;parent=contig00002_IS_2\n+contig00002\tISEScan\tinsertion_sequence\t252678\t252900\t.\t+\t.\tID=contig00002_IS_3;family=IS30;cluster=IS30_241\n+contig00005\tISEScan\tinsertion_sequence\t54\t3033\t.\t+\t.\tID=contig00005_IS_1;family=IS30;cluster=IS30_241\n+contig00005\tISEScan\tterminal_inverted_repeat\t54\t67\t.\t+\t.\tID=contig00005_IS_1_TIR;parent=contig00005_IS_1\n+contig00005\tISEScan\tterminal_inverted_repeat\t3020\t3033\t.\t+\t.\tID=contig00005_IS_1_TIR;parent=contig00005_IS_1\n+contig00005\tISEScan\tinsertion_sequence\t84142\t85683\t.\t-\t.\tID=contig00005_IS_2;family=IS21;cluster=IS21_259\n+contig00005\tISEScan\tterminal_inverted_repeat\t84142\t84174\t.\t-\t.\tID=contig00005_IS_2_TIR;parent=contig00005_IS_2\n+contig00005\tISEScan\tterminal_inverted_repeat\t85651\t85683\t.\t-\t.\tID=contig00005_IS_2_TIR;parent=contig00005_IS_2\n+contig00008\tISEScan\tinsertion_sequence\t99798\t99915\t.\t-\t.\tID=contig00008_IS_1;family=IS30;cluster=IS30_241\n+contig00010\tISEScan\tinsertion_sequence\t1\t138\t.\t-\t.\tID=contig00010_IS_1;family=IS6;cluster=IS6_292\n+contig00010\tISEScan\tinsertion_sequence\t63216\t65257\t.\t-\t.\tID=contig00010_IS_2;family=IS256;cluster=IS256_47\n+contig00010\tISEScan\tterminal_inverted_repeat\t63216\t63259\t.\t-\t.\tID=contig00010_IS_2_TIR;parent=contig00010_IS_2\n+contig00010\tISEScan\tterminal_inverted_repeat\t65215\t65257\t.\t-\t.\tID=contig00010_IS_2_TIR;parent=contig00010_IS_2\n+contig00010\tISEScan\tinsertion_sequence\t65906\t67630\t.\t+\t.\tID=contig00010_IS_3;family=IS3;cluster=IS3_176\n+contig00010\tISEScan\tterminal_inverted_repeat\t65906\t65936\t.\t+\t.\tID=contig00010_IS_3_TIR;parent=contig00010_IS_3\n+contig00010\tISEScan\tterminal_inverted_repeat\t67600\t67630\t.\t+\t.\tID=contig00010_IS_3_TIR;parent=contig00010_IS_3\n+contig00010\tISEScan\tinsertion_sequence\t70798\t72118\t.\t+\t.\tID=contig00010_IS_4;family=IS256;cluster=IS256_162\n+contig00010\tISEScan\tterminal_inverted_repeat\t70798\t70826\t.\t+\t.\tID=contig00010_IS_4_TIR;parent=contig00010_IS_4\n+contig00010\tISEScan\tterminal_inverted_repeat\t72090\t72118\t.\t+\t.\tID=contig00010_IS_4_TIR;parent=contig00010_IS_4\n+contig00010\tISEScan\tinsertion_sequence\t74315\t76017\t.\t+\t.\tID=contig00010_IS_5;family=ISL3;cluster=ISL3_126|ISL3||protein:plasmid:139408\n+contig00010\tISEScan\tterminal_inverted_repeat\t74315\t74360\t.\t+\t.\tID=contig00010_IS_5_TIR;parent=contig00010_IS_5\n+contig00010\tISEScan\tterminal_inverted_repeat\t75974\t76017\t.\t+\t.\tID=contig00010_IS_5_TIR;parent=contig00010_IS_5\n+contig00010\tISEScan\tinsertion_sequence\t81227\t82564\t.\t+\t.\tID=contig00010_IS_6;family=IS256;cluster=IS256_162\n+contig00010\tISEScan\tterminal_inverted_repeat\t81227\t81253\t.\t+\t.\tID=contig00010_IS_6_TIR;parent=contig00010_IS_6\n+contig00010\tISEScan\tterminal_inverted_repeat\t82538\t82564\t.\t+\t.\tID=contig00010_IS_6_TIR;parent=contig00010_IS_6\n+contig00017\tISEScan\tinsertion_sequence\t93\t1807\t.\t+\t.\tID=contig00017_IS_1;family=ISL3;cluster=ISL3_126|ISL3||protein:plasmid:139408\n+contig00017\tISEScan\tterminal_inverted_repeat\t93\t102\t.\t+\t.\tID=contig00017_IS_1_TIR;parent=contig00017_IS_1\n+contig00017\tISEScan\tterminal_inverted_repeat\t1798\t1807\t.\t+\t.\tID=contig00017_IS_1_TIR;parent=contig00017_IS_1\n+contig00029\tISEScan\tinsertion_sequence\t15381\t16432\t.\t-\t.\tID=contig00029_IS_1;family=IS30;cluster=IS30_241\n+contig00029\tISEScan\tterminal_inverted_repeat\t15381\t15402\t.\t-'..b'ntig00036\tISEScan\tterminal_inverted_repeat\t15126\t15146\t.\t-\t.\tID=contig00036_IS_5_TIR;parent=contig00036_IS_5\n+contig00043\tISEScan\tinsertion_sequence\t211\t1174\t.\t+\t.\tID=contig00043_IS_1;family=IS256;cluster=IS256_162\n+contig00043\tISEScan\tterminal_inverted_repeat\t211\t230\t.\t+\t.\tID=contig00043_IS_1_TIR;parent=contig00043_IS_1\n+contig00043\tISEScan\tterminal_inverted_repeat\t1155\t1174\t.\t+\t.\tID=contig00043_IS_1_TIR;parent=contig00043_IS_1\n+contig00043\tISEScan\tinsertion_sequence\t5366\t6174\t.\t+\t.\tID=contig00043_IS_2;family=IS6;cluster=IS6_292\n+contig00043\tISEScan\tterminal_inverted_repeat\t5366\t5383\t.\t+\t.\tID=contig00043_IS_2_TIR;parent=contig00043_IS_2\n+contig00043\tISEScan\tterminal_inverted_repeat\t6157\t6174\t.\t+\t.\tID=contig00043_IS_2_TIR;parent=contig00043_IS_2\n+contig00045\tISEScan\tinsertion_sequence\t1\t117\t.\t+\t.\tID=contig00045_IS_1;family=IS30;cluster=IS30_241\n+contig00053\tISEScan\tinsertion_sequence\t261\t1613\t.\t+\t.\tID=contig00053_IS_1;family=IS110;cluster=IS110_139\n+contig00053\tISEScan\tterminal_inverted_repeat\t261\t280\t.\t+\t.\tID=contig00053_IS_1_TIR;parent=contig00053_IS_1\n+contig00053\tISEScan\tterminal_inverted_repeat\t1594\t1613\t.\t+\t.\tID=contig00053_IS_1_TIR;parent=contig00053_IS_1\n+contig00056\tISEScan\tinsertion_sequence\t75\t1478\t.\t-\t.\tID=contig00056_IS_1;family=ISL3;cluster=ISL3_126|ISL3||protein:plasmid:139408\n+contig00056\tISEScan\tterminal_inverted_repeat\t75\t118\t.\t-\t.\tID=contig00056_IS_1_TIR;parent=contig00056_IS_1\n+contig00056\tISEScan\tterminal_inverted_repeat\t1433\t1478\t.\t-\t.\tID=contig00056_IS_1_TIR;parent=contig00056_IS_1\n+contig00057\tISEScan\tinsertion_sequence\t7\t1510\t.\t-\t.\tID=contig00057_IS_1;family=IS3;cluster=IS3_97\n+contig00057\tISEScan\tterminal_inverted_repeat\t7\t25\t.\t-\t.\tID=contig00057_IS_1_TIR;parent=contig00057_IS_1\n+contig00057\tISEScan\tterminal_inverted_repeat\t1492\t1510\t.\t-\t.\tID=contig00057_IS_1_TIR;parent=contig00057_IS_1\n+contig00058\tISEScan\tinsertion_sequence\t1\t1299\t.\t-\t.\tID=contig00058_IS_1;family=IS30;cluster=IS30_241\n+contig00058\tISEScan\tterminal_inverted_repeat\t1\t127\t.\t-\t.\tID=contig00058_IS_1_TIR;parent=contig00058_IS_1\n+contig00058\tISEScan\tterminal_inverted_repeat\t1173\t1299\t.\t-\t.\tID=contig00058_IS_1_TIR;parent=contig00058_IS_1\n+contig00059\tISEScan\tinsertion_sequence\t102\t592\t.\t+\t.\tID=contig00059_IS_1;family=IS30;cluster=IS30_241\n+contig00059\tISEScan\tterminal_inverted_repeat\t102\t114\t.\t+\t.\tID=contig00059_IS_1_TIR;parent=contig00059_IS_1\n+contig00059\tISEScan\tterminal_inverted_repeat\t580\t592\t.\t+\t.\tID=contig00059_IS_1_TIR;parent=contig00059_IS_1\n+contig00062\tISEScan\tinsertion_sequence\t140\t474\t.\t-\t.\tID=contig00062_IS_1;family=IS6;cluster=IS6_292\n+contig00062\tISEScan\tterminal_inverted_repeat\t140\t151\t.\t-\t.\tID=contig00062_IS_1_TIR;parent=contig00062_IS_1\n+contig00062\tISEScan\tterminal_inverted_repeat\t463\t474\t.\t-\t.\tID=contig00062_IS_1_TIR;parent=contig00062_IS_1\n+contig00070\tISEScan\tinsertion_sequence\t1\t332\t.\t-\t.\tID=contig00070_IS_1;family=IS6;cluster=IS6_292\n+contig00076\tISEScan\tinsertion_sequence\t1\t223\t.\t-\t.\tID=contig00076_IS_1;family=IS30;cluster=IS30_241\n+contig00079\tISEScan\tinsertion_sequence\t1\t255\t.\t-\t.\tID=contig00079_IS_1;family=IS30;cluster=IS30_241\n+contig00083\tISEScan\tinsertion_sequence\t1\t128\t.\t+\t.\tID=contig00083_IS_1;family=IS6;cluster=IS6_292\n+contig00083\tISEScan\tinsertion_sequence\t135\t255\t.\t+\t.\tID=contig00083_IS_2;family=IS6;cluster=IS6_292\n+contig00085\tISEScan\tinsertion_sequence\t1\t255\t.\t+\t.\tID=contig00085_IS_1;family=IS30;cluster=IS30_241\n+contig00090\tISEScan\tinsertion_sequence\t1\t250\t.\t-\t.\tID=contig00090_IS_1;family=IS6;cluster=IS6_292\n+contig00093\tISEScan\tinsertion_sequence\t1\t231\t.\t-\t.\tID=contig00093_IS_1;family=IS6;cluster=IS6_292\n+contig00094\tISEScan\tinsertion_sequence\t69\t206\t.\t+\t.\tID=contig00094_IS_1;family=IS6;cluster=IS6_292\n+contig00096\tISEScan\tinsertion_sequence\t1\t161\t.\t-\t.\tID=contig00096_IS_1;family=IS30;cluster=IS30_241\n+contig00097\tISEScan\tinsertion_sequence\t1\t151\t.\t-\t.\tID=contig00097_IS_1;family=IS6;cluster=IS6_292\n+contig00098\tISEScan\tinsertion_sequence\t1\t138\t.\t+\t.\tID=contig00098_IS_1;family=IS30;cluster=IS30_241\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/isescan/is.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isescan/is.fna Tue Apr 30 08:41:54 2024 +0000 |
| b |
| b'@@ -0,0 +1,728 @@\n+>contig00001_104722_106001_+ IS21_259\n+TTGAAAAAAATAGCAAAGCTTATACGTTTAAAGCAGAATCGTCTGTCAGTGGTCAACCAG\n+CTGACTACCAACGGTTACCACAGGAAAGCATAGTCCAGTCTAAGTTAGGTCAGAGTCAAG\n+GTAGTAGTTCAGAAAACGATTGTTTAAAGATGATTTATCATTTTTATGAGGAAAACGGCT\n+TTGGTACACTGGCCTCAAAAACAAGCCAAGATTTTAAGTATTGGTTGCAAGATTTTATGC\n+AAAAAGGGGCTAGCCAAGAGGAAGCATGCCAATTAATCTTGCATGCTTTAGGAATTGCCA\n+TCGATCGAAATAAACGGAATTATGGCTATGTAAATGCTATTTTGAAAAGTTGGGAGCAAC\n+AAAATTATTTATCCGTACATGAAGTTCTGGTAAATGATAAAAAACAAGTGTCGGAGCATG\n+CGCCGCAAATGACAGAAGAATATCAAGAGTTAGGTTTTTAAAGAAAGGAGGAAATCAGTA\n+TGCATGCGACAGATCAAACTTTTCAAATACTATTGAGTCAATTGTTAGAAAAAGTTGAAG\n+ACCGTTGTCCTGAATGTGGCAGTGAACAATATGTTTGGCAACAAAAAAATAAAGATGGCA\n+CAGAACGTTGTGCCCCAACTTGTTGGTCGTGTGGGTATAAAATGCTAAAAAAACATGAAC\n+AAGAAGCCACTCAACAACGTTCTCAAGAGAGTTTTATGGCACGTACACAAAAATTTTTTC\n+ATCAAGGGTCCTTAATTGCTGATGATGCGCTACGGCAATGTCGCTTAACCAATTACCAAA\n+CCACTGAATTAGAAACAAGACAAGCAAAAGAACGGGCCTTAGCAGCAGTTTCAGCGATTG\n+TTGAAGGAAAGCCAATCCACGTTATTTTTTCAGGGAAACCTGGTGTTGGTAAAAGTCATT\n+TGGCTATCAGTATTTTAGTTGAAGTCTTAGAACGCTCTGCATATCAAAAGTATTGTTTAT\n+TTGTCAGCTACTCTGAGTTATTAGAAAAACTAAAAATGTCCATGAATGAATCGGCCAAAA\n+GCCAAGCAAAGGCTCAAGCGTATATTACTAGAATGAAAAAAGCAGACGTTTTGGTTTTAG\n+ATGATTTAGGTGCTGAATTAGGAATTAAAAATAAAGTTAGTACGGATTTTAATAATGACA\n+TCTTAAACCGAATTTTAGAAGGTAGACAGAATAAAGCAACTATTTTTACTACTAATTTTT\n+CTGGAAAACAACTGGTGGAGGCCTATGGAACACGCATTATTTCTCGTCTAATGAAGCACG\n+CCAGTGGCTATGTTTTCCAA\n+>contig00002_179502_180572_- IS200/IS605_96\n+ATGAAGGCTCTGAAAGCTTATAAATACAGACTTTATCCAACCTCAAAACAAGAAGAGTTT\n+ATTCAAAAAACATTTTCTTGTGTTCGCTTGGTGTATAATTTAATGTTACAAGACCGGATT\n+GATATCTACAAAGAGATGCGAAAAAATCCTCAACAAACGTTTAAAATGCCAACGCCAGCT\n+AAATATAAGAAACAATACCCTGTCCTCAGAGAAGTTGATAGTTTAGCTTTGGCAAATGCA\n+CAAGTTTATTTGGATCGAGCCTTTAAAAATTTTTATCGGGAAAAAGGGATGGGCTTTCCA\n+AAAAAGAAAAAGAAAGAAACGGTGCATTCCTACACTACGAACAATCAACATGGCACGGTC\n+AAAATTTTGGATAATCGTTATTTGAAAGTACCTAAATTGAAATCTTTAATTAAAATGAAG\n+GTACACCGCCAACCGCTGGGGGAGATAAAATCTGTAACTATTTCTATGAGTGCGAGTCAC\n+AATTATTATGTTTCCATTTTGTGTGAAGCGCCGATTGAAACGAAAACAAAGCAACAAAAA\n+ATGGTGGGAATTTGTAGCAGTAGGGAAAAATTTGCGCTGCTTTCGAATGGTGAAAGCTTC\n+GAAAAAAGCTATTGTTCAAAGCATTTAAAGCAAAAACTATGTCAAGAAGAACGAAAATTA\n+AACAAGCGTAAAATGATTGCTTTAGAAAAAGGTGTCGATCTTTCACAAGCAAAAAATTAT\n+CAAAAACAAAAAATAAAAGTCGCAAAAATTCGCGAAAAAATAGCCAACCAACGAACGGAT\n+ATTTTAAACAAAATTACAACGGAATTGGTTTCAAGTTACGATGTTATTTGTATTGAAAAA\n+GCCCATCACAGTAATGAGCGGCCGCCAAAACATGATCGTTCTGAACTGGCTTGGTCTTTA\n+TTTTTAGCTAAACTGTTGTATAAAGCACAATGGTATGGCAAAGAACTCATTTGTATTGAG\n+TCAGAGGAGATCGAAACAGAGTTGTCTTTTTCTGAAAGTACAGAAAATTCAGAGTATCTT\n+AGAAGCCAAAAAATCTTAGAACGTGGCTTGTCTAAACGAGAAACCTTATAA\n+>contig00002_210210_214514_- IS21_288\n+ATCAAGAAAAATGGGGATCGTGAAGAATTTAATCGTGATAAAATTTTGCGTGGGCTCATT\n+CGCTCTGCGGAAAAAAGACCCGTTGCTATGGAACAAATGGTTCAAATTGTCGATAATGTT\n+GAAAATCGAGTGCGTAGTTTAGGGGAAAATGAAGTCTCTACAACGCTTATCGGTGAATAT\n+GTGATGGAAGATTTAGTCAATCTAGATGAAATTGCCTACATCCGCTTTGCGAGTGTTTAT\n+CGACAATTCAAAGATATGAGCGTGTTTTTGAAAGAGTTACAGGACATTGTCGACAAAGCA\n+AAATCTTCTTCTCCTGACTCAGAAAATTAAAAAGGAGGTCTTTCTTTGAAAGGAAATCGG\n+CAAAGAATCCAACCAAAAAATATTTTTCAAGCGGTTATTGATTCACCGCTTTCTGATCAA\n+GAGAAAGAGGTTTTAACCTTTTTATATCAACCAATTGTCGGCGCCAATGCGTTTAGTTTA\n+TATTGGCTTTTGTTATCTGAAACAACAGACTCAGAGGAGAATGGCTCGCTGTTTCATGCA\n+GATTTAATTAGTTTGCTGGACTTGAGTTGTCAACAATTAGAAGAAGCTTGCTACAAATTA\n+GAAGGCATTGGGTTGCTAGAAACGTATAAAAAAACAGATCGGGAATTAGGAGATTGTTAT\n+TTATATTATTTAAAAGCACCTGAAACAGCCGCTCGTTTTTTTAAAGATGAAGTGTTAGCT\n+TTAGTGTTATTTAATCGGGTTGGACAACGGAAATTTGATCAATTAGTGCAAAAGTTTCAA\n+CCGCATCCTACCAAAACAGAGGGCTATCAAAATGTTTCCGCTAGCTTTCAAGAGGTTTAT\n+GCCTTTAAAGAAGAACAAATTGTTTCCGAAGCGAACCGATTGACAACGATTCAAGAAACT\n+TTTTCTCAAAAAGAAAAATCGAAGAAAATTTCTGTATCAACGGATTCTTTTGATTGGCAC\n+TATTTTGTGGAAGGTTTGCACCGTTTAGGTTTACAACTGCCTGAAGATGAGGCTAGTTTT\n+CAAGAAGAAGTCTATGTTTTTCATCAATTATATGGCATCAATGAGTTAGATATGGTAGAC\n+TTTGCTTCGAAATCATTTGACTATTATACAAGTCGAATTTTGCCTAAGGAATTAGTGCGA\n+ACGATTCATCAAGCGTTTGATCCTGATAAAAAACCACAATCAACAAACGTAGTGACAAAC\n+AAGCAAGCACAATTGACGGTGGAAGAGCAACAAACGTATCGATATAACGCATTAAAAATG\n+AATGGTTTTTCTGAACTGGATATTCAAATGATTATGGATAGTGAAAAGAATCCGCCTATT\n+CAATATTTAGAAGCTTTAAAAAATAGTCGAGGCGGCTATACGACACCACAAGAACGTTCA\n+'..b'GATGA\n+TTTGTCTAACTTAACTTGACAATTAAGAGTAAATAAAAACTACTACTGGATATACTTCTT\n+CCTTTTTCTTAACTCGTTAGCTATTTTATACTCGGTTCTGTTGCAAAGTTTTAAATCTAC\n+TATCAAATAAGGTAGAATAATAGAAAAAGATAGCAGGAGGAATGACGATGAATCATTTTA\n+AAGGAAAGCAATTTCAGCAGGATGTGATTATTGTAGCCG\n+>contig00059_102_592_+ IS30_241\n+TAGAAAAGTCATTCAATTACCTGCTCATGAAGTAGATTACATTAAAGAGAAAGTCACTCT\n+TGGTTGGACGCCTGACGTCATTATCGGGCGAAAAGAAAGGCCTGTTTCATGCGGTATGAG\n+AACACTTTATCGTTTATTTTCTAAAGGGATATTTGATATTGACACACTACCGATGAAAGG\n+TAAAAGAAAACCCAATGGCCATCAGGAAAAACGGGGAAAACAACAATATCAGCGCTCAAT\n+CCATGATCGACCTGATAATTATCCTGATTTCAATTCTGAGTTTGGTCACCTTGAAGGTGA\n+TACGATCGTTGGCATTCATCATAAAAGTGCCGTCATTACTTTAGTTGAAAGATTATCTAA\n+AGTCATTATCACGATTAAACCCAACGGCCGTAAGGCATTAGATATTGAAACCGCCCTTAA\n+TCAATGGTTTTCTCGCTTCCCTAAAAACTTCTTTAAATCTATTACGTTTGACTGTGGAAA\n+AGAATTTTCTA\n+>contig00062_140_474_- IS6_292\n+CTACTATCTTCGTTATAACCTTAGCTATCGTGAAGTTCAAGAAATCTTATATGATCGTGG\n+CATTAACGTTTCTCATACGACGATTTATCGTTGGGTGCAAGAATATGGCAAACTACTCTA\n+TCAAATTTGGAAAAAGAAAAATAAAAAATCCTTTTATTCATGGAAAATGGATGAAACATA\n+CATCAAAATTAAAGGAAAATGGCATTATTTGTATCGAGCCATCGATGCAGATGGTTTAAC\n+CTTGGATATTTGGTTACGTAAAAAACGGGACACACAAGCAGCCTATGCTTTTCTTAAGCG\n+GTTAGTGAAGCAGTTTGATGAACCGAAGGTTGTAG\n+>contig00070_1_332_- IS6_292\n+CCCCCTCTATTACAAGTGCCTTTAAGAAACTAAAAGAATACGGCTTTTATCAAGGGACAG\n+AACATCGTACCATTAAATACCTGAATAATTTGATTGAACAAGACCATCGTCCAGTAAAGA\n+GACGCAATAAATTCTATCGAAGTTTACGCACTGCCTCTACCACGATTAAAGGCATGGAAG\n+CCATTCGAGGATTATATAAGAAAACCCGAAAAGAAGGCACTCTCTTCGGGTTTTCGGTCT\n+GTACTGAAATCAAGGTATTATTGGGAATCCCAGCTTAAATCATAGATACCGTAAGGGATT\n+TTATTCTTTATTTAAAACTTTGCAACAGAACC\n+>contig00076_1_223_- IS30_241\n+ATGACCTACAAACATCTTACCATAGACGAACTGACAATGATAGAATCATATTATCTTCAA\n+CATAATAAACCGGTTGAAATCGCTAACCGAATGGGACGTGCTATACAAACTATTTATAAT\n+GTAGTCAATAAGTTCAAGCAAGGCAAGACTGCTCTTGATTATTGGCACCAGTATAAAGAA\n+AATAAGAAAAAATGTGGTAGAAAAGTCATTCAATTACCTGCTC\n+>contig00079_1_255_- IS30_241\n+CTATTACGTTTGACTGTGGAAAAGAATTTTCTAACTGGAAAGCCATTAGTAACCAACACG\n+ATATTGATATATATTTTGCGGACCCTGGAACACTTTCTCAACGCCCATTAAACGAGAATT\n+CTAACGGGATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATC\n+AGACATTTATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATT\n+ACAGAACACCAATTG\n+>contig00083_1_128_+ IS6_292\n+ATACGACGATTTATCGTTGGGTGCAAGAATATGGCAAACTACTCTATCAAATTTGGAAAA\n+AGAAAAATAAAAAATCCTTTTATTCATGGAAAATGGATGAAACGTACATCAAAATTAAAG\n+GAAAATGA\n+>contig00083_135_255_+ IS6_292\n+TTGTATCGAGCCATCGATGCAGATGGTTTAACCTTGGATATTTGGTTACGTAAAAAACGG\n+GACACACAAGCAGCCTATGCTTTTCTTAAGCGGTTAGTGAAGCAGTTTGATGAACCGAAG\n+G\n+>contig00085_1_255_+ IS30_241\n+CTATTACGTTTGACTGTGGAAAAGAATTTTCTAACTGGAAAGCCATTAGTAACCAACACG\n+ATATTGATATATATTTTGCGGACCCTGGAACACTTTCTCAACGCCCATTAAACGAGAATT\n+CTAACGGTATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATC\n+AGACATTTATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATT\n+ACAGAACACCAATTG\n+>contig00090_1_250_- IS6_292\n+TGCAGATGGTTTAACCTTGGATATTTGGTTACGTAAAAAACGGGACACACAAGCAGCCTA\n+TGCTTTTCTTAAGCGGTTAGTGAAGCAGTTTGATGAACCGAAGGTTGTAGTCACAGATAA\n+AGCCCCCCTCTATTACAAGTGCCTTTAAGAAACTAAAAGAATACGGCTTTTATCAAGGGA\n+CAGAACATCGTACCATTAAATACCTGAATAATTTGATTGAACAAGACCATCGTCCAGTAA\n+AGAGACGCAA\n+>contig00093_1_231_- IS6_292\n+ATACGACGATTTATCGTTGGGTGCAAGAATATGGCAAACTACTCTATCAAATTTGGAAAA\n+AGAAAAATAAAAAATCCTTTTATTCATGGAAAATGGATGAAACGTACATCAAAATTAAAG\n+GAAAATGGCATTATTTGTATCGAGCCATCGATGCAGATGGTTTAACCTTGGATATTTGGT\n+TACGTAAAAAACGGGACACACAAGCAGCCTATGCTTTTCTTAAGCGGTTAG\n+>contig00094_69_206_+ IS6_292\n+ATGACGATGAGTCATTTTAAAGGAAAGCAATTTCAGCAGGATGTGATTATTGTAGCCGTG\n+GGCTACTATCTTCGTTATAACCTTAGCTATCGTGAAGTTCAAGAAATCTTATATGATCGT\n+GGCATTAACGTTTCTCAT\n+>contig00096_1_161_- IS30_241\n+TGGTTTTCTCGCTTCCCTAAAAACTTCTTTAAATCTATTACGTTTGACTGTGGAAAAGAA\n+TTTTCTAACTGGAAAGCCATTAGTAACCAACACGATATTGATATATATTTTGCGGACCCT\n+GGAACACTTTCTCAACGCCCATTAAACGAGAATTCTAACGG\n+>contig00097_1_151_- IS6_292\n+ATGATCGTGGCATTAACGTTTCTCATACGACGATTTATCGTTGGGTGCAAGAATATGGCA\n+AACTACTCTATCAAATTTGGAAAAAGAAAAATAAAAAATCCTTTTATTCATGGAAAATGG\n+ATGAAACGTACATCAAAATTAAAGGAAAATG\n+>contig00098_1_138_+ IS30_241\n+ATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATCAGACATTT\n+ATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATTACAGAACA\n+CCAATTGAGATATTTTTG\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/isescan/orf.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isescan/orf.faa Tue Apr 30 08:41:54 2024 +0000 |
| b |
| b'@@ -0,0 +1,254 @@\n+>contig00001_105201_106043_+\n+MHATDQTFQILLSQLLEKVEDRCPECGSEQYVWQQKNKDGTERCAPTCWSCGYKMLKKHE\n+QEATQQRSQESFMARTQKFFHQGSLIADDALRQCRLTNYQTTELETRQAKERALAAVSAI\n+VEGKPIHVIFSGKPGVGKSHLAISILVEVLERSAYQKYCLFVSYSELLEKLKMSMNESAK\n+SQAKAQAYITRMKKADVLVLDDLGAELGIKNKVSTDFNNDILNRILEGRQNKATIFTTNF\n+SGKQLVEAYGTRIISRLMKHASGYVFQYKDTTDKRMRSVK\n+>contig00002_179502_180572_-\n+MKALKAYKYRLYPTSKQEEFIQKTFSCVRLVYNLMLQDRIDIYKEMRKNPQQTFKMPTPA\n+KYKKQYPVLREVDSLALANAQVYLDRAFKNFYREKGMGFPKKKKKETVHSYTTNNQHGTV\n+KILDNRYLKVPKLKSLIKMKVHRQPLGEIKSVTISMSASHNYYVSILCEAPIETKTKQQK\n+MVGICSSREKFALLSNGESFEKSYCSKHLKQKLCQEERKLNKRKMIALEKGVDLSQAKNY\n+QKQKIKVAKIREKIANQRTDILNKITTELVSSYDVICIEKAHHSNERPPKHDRSELAWSL\n+FLAKLLYKAQWYGKELICIESEEIETELSFSESTENSEYLRSQKILERGLSKRETL\n+>contig00002_210541_214169_-\n+KGNRQRIQPKNIFQAVIDSPLSDQEKEVLTFLYQPIVGANAFSLYWLLLSETTDSEENGS\n+LFHADLISLLDLSCQQLEEACYKLEGIGLLETYKKTDRELGDCYLYYLKAPETAARFFKD\n+EVLALVLFNRVGQRKFDQLVQKFQPHPTKTEGYQNVSASFQEVYAFKEEQIVSEANRLTT\n+IQETFSQKEKSKKISVSTDSFDWHYFVEGLHRLGLQLPEDEASFQEEVYVFHQLYGINEL\n+DMVDFASKSFDYYTSRILPKELVRTIHQAFDPDKKPQSTNVVTNKQAQLTVEEQQTYRYN\n+ALKMNGFSELDIQMIMDSEKNPPIQYLEALKNSRGGYTTPQERSLVKYLVAKSGLPTSVI\n+NILINYVYNIQQQPTLKAEYVNRIANEWGQSGIHSPEKAIEHVRELAKQSQTKQKQRQQN\n+YSGKRQTVRQERLPEWADQPNDETKLSPAEQAELDRQIQEFLNQGGXPMMEDVGKEMSKI\n+IQKRDINERYEELVNEVLKDQDVQAFIQANRERLTDEDIRKSYAKLYEFVQEKKKFQVND\n+PAMIAPGYEPRLMLNFHYIDVTYVPTADLIARQKEEEIRNRVRAMDIPKDVREANLRDFD\n+PSSQGRAKALAEAMQFLREYPATPKEFHKGLYLQGPFGVGKSFLLGAMANALAERGFTTT\n+IVHFPTFTVEMKQAIGRDQVGEKLDAVKKSPILMIDDIGAESMTSWIRDDVLSVILQYRM\n+QEQLVTFFSSNLDLKALEEHLTVTQRGEQEPLKARRIMERVRYLSKEITMTGNDHETVKA\n+ILLFLWIAFFLAFEXGSVSFAKTSTFVYTDNKEVRKRGVTMKRKLWIFIGVFVVLLGGYF\n+LLFREKSYKVEVEKVNPKIQRLMSTDKQHFLTKHEFHTKETAERKDLLKFFIETRLKTDG\n+GFLTNYLPDAERKDVATGHELLSESSGLYLRNLAFDTQGRFDNFYKQTKDTFYDGVQFSY\n+RIDEQGNKYNVNASIDDLRIIRSLIEAGGHFKTDQYDQEIKKLGKSFMKTSMKDNILIDF\n+YDSKSKQQSSETSLFYIDLITLGYLYKEFGISADYLQYHYQLIDDGYISDDLPLYQTKFN\n+HQTNKYENNGTLNIIESLLTIVHLSEVGMAKQTSIDFVRKQVQQGTLFNSYDLNGSPVDK\n+NQSAASYAIAALIGVAENDKELYRAAITVLNNFQIMDSSSPIYGGFGDKVTKQVYSYNNL\n+MALLAYDF\n+>contig00002_252678_252900_+\n+MTYKHLTIDELTMIESYYLQHNKPVEIANRMGRAIQTIYNVVNKFKQGKTALDYWHQYKE\n+NKKKCGRKVIQLPA\n+>contig00005_1_2892_+\n+WFSRFPKNFFKSITFDCGKEFSNWKAISNQHDIDIYFADPGTPSQRPLNENSNGILRRNG\n+LPKSMDFREVNQTFISSVSNQRNHIPRKSLNYRTPIEIFLSYVQEAFYSNLFDKSYYLNL\n+KRREKICGNEKDFRSFFYSLFFISGTSLVPFLSKTNQAQLQNFIEIIKNRYPYFTYTDLR\n+KLKLIMSIGLLRYQSGFTITNYPEVAAINLAFPYSEFQLLVNDCFIDEQKEPDTWQAEIH\n+FYYDFFSTLTMYSLVQMETINFANLAIMGMDNSPHATWIFEKCTQLQLDLSAIEVVFLLV\n+NLSNASERLIHFPVEEELSYEVANVSLYEKQYPNVSRTTNYFLKRLPFDKQHPLDALFKE\n+TIFLIIRSVLLNKQIPVKILLHSSINQIQENWLAKEINNYCDVPLKFVNHIQEVPDLVIT\n+DKNNPLFHASKTFYWHPVPYLDEYYNLKQVVRKIYFAKLRXGKQFGGNRMLTGLLDVPYR\n+KSFALLEELLERREAEEQTLAISTLATQLKMQQNTILQSVALLQTEIEKNGWENLFSLSA\n+NAKEITFWFAPYFQLSFLMPYFVKKSFAYQVLTYAFNHNAIDSKHFEKVLEISSSTFTRK\n+IGQLNQWLQKYQIEINLKRTNVLVGKEKDIRIFFMMLFWNNYSEGDWPLHTITKKEVHSL\n+FRRLKHSVSFNTTQDFTKDLIFSAVILARWKEGFFIKETFVEEEAIVNPFVNLSEFELFF\n+KEEALHQVPTKFIQKEGLFAFFLLTISVSYATQDVLEIPAARMHMVQLLGSPIKEIIYQL\n+TSFYQIKLTFHEYLYLYTSIQNLSVFFKTFVTIANPFVQESFLKEALQKNPSLYKDVKRL\n+TIEMLPTLIGNEKLLVDCLFILFCTLKTKSLPPIRVLVRTNQSNLILDTLYEKLSKAVDK\n+KLIFVASPEKPFDVIITDIFSEVSVKSTVPTYYVDFSASIGELAQSLENLNTQIVTKQSP\n+RHF\n+>contig00005_84182_85525_-\n+MPDVESFWHSLEEAYQAILSAPSFDAWIKTTRPLKLDNNQLWLEVPSAVHRDYWEKNLSA\n+KIVETGFKLTGAEVMPHFVVADEKDAALAQELEEPAEEEVVFSEQSKKAMLNPKYTFDTF\n+VIGKGNQMAHAAALVVAEDPGSIYNPLFFYGGVGLGKTHLMHAIGHQMLVNQPDAKVKYV\n+SSETFTNEFINSIQTKTSEQFRKEYRNVDLLLVDDIQFLAEKEATLEEFFHTFNDLYNEN\n+KQIVLTSDRPPNDIPKLPERLVSRFAWGLSVDITPPDLETRIAILRKKADAERLEIPDDT\n+LSYIAGQIDSNIRELEGALVRVQAFATINGEDITTSLAADALKSLKSVGSKNQLSILQIQ\n+EEVSKYYHVPLKDLKGKKRVKTIVVPRQISMYLAREMTDNSLPKIGAEFGGKDHTTVIHA\n+HEKIQQLLEKDPAIQKEVSEIKNLLNS\n+>contig00008_99798_99915_-\n+ISSVSNQRNHIPRKSLNYRTPIEIFLSYVQEAFYSNLI\n+>contig00010_1_138_-\n+MTMNHFKGKQFQQDVIIVAVGYYLRYNLSYREVQEILYDRGINVSH\n+>contig00010_63507_64842_-\n+ARKKRNPDAEKLAESILNAYQPESVDDMQDALKDVFGPLFEKMLQGELNNHLGYDAHSKE\n+PKEHDNRRNGYGTKTLKTSFGEVAIDVPRDREASFEPELIPKRKRDVSDIEGKVLSMYAR\n+GMSQRDIAATVEAIYGFDISHEMISDITDAVLPELEEWQARPLAKCYAFLFVDCMYVTLR\n+ENYEAKEYAVY'..b'NLINKVRVKDRKAVINDFKQVHRATNRQEAELKLNDFANNWHQTYP\n+KLIKNLLKMPNLLTFLDFPPAIRGSLYSTNLIENFNKHLKRNTNHKEQFPTENSLDRFLV\n+SQFNVYNDKSMKRIHRGFKGLQDTWNHPLFKLTTYYMYGGISFTQDS\n+>contig00043_591_1213_+\n+MVVRFTTQNIXAFDEVELLHKIVDLTDLPKAKYQHCCVHVSRNIAHKVRVKDRKEICDDF\n+KAVYQASSKEEANTFLGSMIEKWQKTYPKVTQSLIKNQDLLTFYEFPPGIRRSIYSTNLI\n+ESFNKQIKKYSRRKEQFQNEESLERFLVSIFDTYNQKFLNRSHKGFQQVTDTLASMFTXV\n+THYFAEGRVIYTKLLTLPVGTTRIAVA\n+>contig00043_5661_6221_+\n+MDETYIKIKGRWHYLYRAIDADGLTLDIWLRKKWDTQAAYAFLKRLHKQFGEPKAIVTDK\n+APSLGSALRKLQSVGLYTKTEHRTVKYLNNLIEQDHRPIKRRNKFYQSLRTASSTIKGME\n+TPSGIYKKNRRNGTLFGFSVSTEXQGINGNTSLRYLEFRAGAFDFQTSQQNHDYHICYRF\n+GQQWSG\n+>contig00045_1_117_+\n+ISSVSNQRNHIPRKSLNYRTPIEIFLSYVQEAFYSNLI\n+>contig00053_385_1635_+\n+MKLFVGLDVSSEKLDACFMTDDSTCSVLKEASYGNSQLGASQIKEYILEFSQKFEIESLV\n+IGMEATSLYSFHPAMFFKEDLELNQLNLMVSVEQPNKIKKYRDIFEENKNDQIDAFYIAD\n+YFRIQRQVNSIIKEEEYLALQHLTRTRYQLIKQLVRTKQHFIENIYYKCNTLSKELKAEG\n+GSVLSATLVTLMTEDYTMDQLAELSLEEFANLIQKLGKYRFKNPEGIAKAISKAIRSSYR\n+LGKVHQDSVDIVLGVLAKEIRSLEKLIKDLDKAIDDLVVVLPEYQCLTSIPGIGPVYAAG\n+ILAEIGPINRFSDESKLAKYAGLYWRQNQSGNSEYENTPMAKRGNRYLRYYLVEATNSVR\n+RYEPEYHAYYKKKYAETPKHKHKRAIVLTARKFTRLVDTLLRNHQLYMPPRSVIDK\n+>contig00056_84_1367_-\n+MLRITDEHLDLTNTEEYKIKGKNTLVIFGVYSPMPSACRNCGSTIVDNEGKSVVVRNGKK\n+EVTIQLDSYQNMPTILKLKKQRFHCKSCSHNWTAQCSIVEKNCHISKFITLKILELLTEK\n+ISMTFIAKQCHVSLTTVLRVLKSVESQLPQQLKPRSFPEVLMVDEFRSHASYEDKMSFIC\n+ADGETGELVDILPSRKLDKIIPYFNRSPLEEREKVKFLVTDMNAAYFQLTKNVFPTAKLI\n+IDRFHIVKHLNTAFNDFRVREMKRLITNKKKSKANKLKSNWKLLLKNQTNISISEFKTWR\n+SFPSPKYHLLTESMVIDRLLSFSSELKEAYDIFHLLMYHFRNKDDRSFFELLKNLPDSLD\n+TQFRDKIENLISYEEGIRNALKYNFSNGKIEAKNTHIKTLKRVSYGFNSFTNMRIRIFLI\n+NGLIKIK\n+>contig00057_58_1460_-\n+AKYSFEFKLKLVHDYLSGQGGLRFLAKKYGFKDSSQISKWINAYKELGEEGLLRSRKNKN\n+YSVQFKLDAIELYLTTELSYQEVANLLKMNNPSLIANWLRTYQKFGIEGLSKQKGRPPTM\n+SKKKRNEPQPLPSERSQVEKLEKENRMLKIENAYLKXIEETAFRGRTKNERIARIIHSLR\n+RRFRLKDILETLRFPKSTYMYWQKRLDRTASTQIIEEEIQAIRKKHQHYGYRRITQELKR\n+RGFQVNKKKVQRLIQKLKLQVKAFTKKSRKYNSYKGIVGKIAKNLIRRRFKTSVPHQKIT\n+TDTTEFKYFEADNAGIFRQKKLYLDPFMDMYNSEILSYSLSTQPNGKTVMKGLKEAISQT\n+NDCPYRRTFHSDQGWAYQMNVYIQTLKDNNIFQSMSRKGTCLDNSPMENFFSILKQEVYY\n+GKIYQSQNELIEAIENYIYYYNHHRIKEKLNWKSPVEFRQFNQKTA\n+>contig00058_201_1160_-\n+MTYTHLTTDELVMIESYFKINQSVAKTAHCLNRSRQTIHKVYLFFKQGKSALEYYQQYKK\n+NKSNCGRRPLVLPEEQSEYIQRKVVQGWTPDVIVGRAAFPIRCSARTIYRMFKKGLFNPS\n+DLPMKGKRKPNGHQERRGKQAFRRSIHEREKDYSQFSNEFGHLEGDTIVGLKHKSAVITL\n+VERLSKVIITLKPCGRQAIDIENKLNHWFESVPKNLFKSITFDCGKEFSNWKQISNANDI\n+AIYFADPGTPSQRGLNENSNGLLRRDGLLKSMDFNSVDESFIQSVASKRNNIPRKSLNYR\n+TPLEVFLSYVSIDDLSNLT\n+>contig00059_1_652_+\n+RAIQTIYNVVNKFKQGKTALDYWHQYKENKKKCGRKVIQLPAHEVDYIKEKVTLGWTPDV\n+IIGRKERPVSCGMRTLYRLFSKGIFDIDTLPMKGKRKPNGHQEKRGKQQYQRSIHDRPDN\n+YPDFNSEFGHLEGDTIVGIHHKSAVITLVERLSKVIITIKPNGRKALDIETALNQWFSRF\n+PKNFFKSITFDCGKEFSNWKAISNQHDIDIYFADPGT\n+>contig00062_1_525_-\n+HFKGKQFQQDVIIVAVGYYLRYNLSYREVQEILYDRGINVSHTTIYRWVQEYGKLLYQIW\n+KKKNKKSFYSWKMDETYIKIKGKWHYLYRAIDADGLTLDIWLRKKRDTQAAYAFLKRLVK\n+QFDEPKVVVTDKAPSITSAFKKLKEYGFYQGTEHRTIKYLNNLIEQDHRPVKRR\n+>contig00070_1_332_-\n+PSITSAFKKLKEYGFYQGTEHRTIKYLNNLIEQDHRPVKRRNKFYRSLRTASTTIKGMEA\n+IRGLYKKTRKEGTLFGFSVCTEXQGIIGNPSLNHRYRKGFYSLFKTLQQN\n+>contig00076_1_223_-\n+MTYKHLTIDELTMIESYYLQHNKPVEIANRMGRAIQTIYNVVNKFKQGKTALDYWHQYKE\n+NKKKCGRKVIQLPA\n+>contig00079_1_255_-\n+ITFDCGKEFSNWKAISNQHDIDIYFADPGTLSQRPLNENSNGILRHNGLPKSMDFREVNQ\n+TFISSVSNQRNHIPRKSLNYRTPI\n+>contig00083_1_128_+\n+TTIYRWVQEYGKLLYQIWKKKNKKSFYSWKMDETYIKIKGK\n+>contig00083_135_255_+\n+LYRAIDADGLTLDIWLRKKRDTQAAYAFLKRLVKQFDEPK\n+>contig00085_1_255_+\n+ITFDCGKEFSNWKAISNQHDIDIYFADPGTLSQRPLNENSNGILRHNGLPKSMDFREVNQ\n+TFISSVSNQRNHIPRKSLNYRTPI\n+>contig00090_1_250_-\n+ADGLTLDIWLRKKRDTQAAYAFLKRLVKQFDEPKVVVTDKAPSITSAFKKLKEYGFYQGT\n+EHRTIKYLNNLIEQDHRPVKRR\n+>contig00093_1_231_-\n+TTIYRWVQEYGKLLYQIWKKKNKKSFYSWKMDETYIKIKGKWHYLYRAIDADGLTLDIWL\n+RKKRDTQAAYAFLKRL\n+>contig00094_69_206_+\n+MTMSHFKGKQFQQDVIIVAVGYYLRYNLSYREVQEILYDRGINVS\n+>contig00096_1_161_-\n+WFSRFPKNFFKSITFDCGKEFSNWKAISNQHDIDIYFADPGTLSQRPLNENSN\n+>contig00097_1_151_-\n+DRGINVSHTTIYRWVQEYGKLLYQIWKKKNKKSFYSWKMDETYIKIKGK\n+>contig00098_1_138_+\n+ILRHNGLPKSMDFREVNQTFISSVSNQRNHIPRKSLNYRTPIEIF\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/isescan/orf.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isescan/orf.fna Tue Apr 30 08:41:54 2024 +0000 |
| b |
| b'@@ -0,0 +1,641 @@\n+>contig00001_105201_106043_+\n+ATGCATGCGACAGATCAAACTTTTCAAATACTATTGAGTCAATTGTTAGAAAAAGTTGAA\n+GACCGTTGTCCTGAATGTGGCAGTGAACAATATGTTTGGCAACAAAAAAATAAAGATGGC\n+ACAGAACGTTGTGCCCCAACTTGTTGGTCGTGTGGGTATAAAATGCTAAAAAAACATGAA\n+CAAGAAGCCACTCAACAACGTTCTCAAGAGAGTTTTATGGCACGTACACAAAAATTTTTT\n+CATCAAGGGTCCTTAATTGCTGATGATGCGCTACGGCAATGTCGCTTAACCAATTACCAA\n+ACCACTGAATTAGAAACAAGACAAGCAAAAGAACGGGCCTTAGCAGCAGTTTCAGCGATT\n+GTTGAAGGAAAGCCAATCCACGTTATTTTTTCAGGGAAACCTGGTGTTGGTAAAAGTCAT\n+TTGGCTATCAGTATTTTAGTTGAAGTCTTAGAACGCTCTGCATATCAAAAGTATTGTTTA\n+TTTGTCAGCTACTCTGAGTTATTAGAAAAACTAAAAATGTCCATGAATGAATCGGCCAAA\n+AGCCAAGCAAAGGCTCAAGCGTATATTACTAGAATGAAAAAAGCAGACGTTTTGGTTTTA\n+GATGATTTAGGTGCTGAATTAGGAATTAAAAATAAAGTTAGTACGGATTTTAATAATGAC\n+ATCTTAAACCGAATTTTAGAAGGTAGACAGAATAAAGCAACTATTTTTACTACTAATTTT\n+TCTGGAAAACAACTGGTGGAGGCCTATGGAACACGCATTATTTCTCGTCTAATGAAGCAC\n+GCCAGTGGCTATGTTTTCCAATACAAAGACACAACAGACAAACGAATGAGGAGTGTGAAA\n+TAA\n+>contig00002_179502_180572_-\n+ATGAAGGCTCTGAAAGCTTATAAATACAGACTTTATCCAACCTCAAAACAAGAAGAGTTT\n+ATTCAAAAAACATTTTCTTGTGTTCGCTTGGTGTATAATTTAATGTTACAAGACCGGATT\n+GATATCTACAAAGAGATGCGAAAAAATCCTCAACAAACGTTTAAAATGCCAACGCCAGCT\n+AAATATAAGAAACAATACCCTGTCCTCAGAGAAGTTGATAGTTTAGCTTTGGCAAATGCA\n+CAAGTTTATTTGGATCGAGCCTTTAAAAATTTTTATCGGGAAAAAGGGATGGGCTTTCCA\n+AAAAAGAAAAAGAAAGAAACGGTGCATTCCTACACTACGAACAATCAACATGGCACGGTC\n+AAAATTTTGGATAATCGTTATTTGAAAGTACCTAAATTGAAATCTTTAATTAAAATGAAG\n+GTACACCGCCAACCGCTGGGGGAGATAAAATCTGTAACTATTTCTATGAGTGCGAGTCAC\n+AATTATTATGTTTCCATTTTGTGTGAAGCGCCGATTGAAACGAAAACAAAGCAACAAAAA\n+ATGGTGGGAATTTGTAGCAGTAGGGAAAAATTTGCGCTGCTTTCGAATGGTGAAAGCTTC\n+GAAAAAAGCTATTGTTCAAAGCATTTAAAGCAAAAACTATGTCAAGAAGAACGAAAATTA\n+AACAAGCGTAAAATGATTGCTTTAGAAAAAGGTGTCGATCTTTCACAAGCAAAAAATTAT\n+CAAAAACAAAAAATAAAAGTCGCAAAAATTCGCGAAAAAATAGCCAACCAACGAACGGAT\n+ATTTTAAACAAAATTACAACGGAATTGGTTTCAAGTTACGATGTTATTTGTATTGAAAAA\n+GCCCATCACAGTAATGAGCGGCCGCCAAAACATGATCGTTCTGAACTGGCTTGGTCTTTA\n+TTTTTAGCTAAACTGTTGTATAAAGCACAATGGTATGGCAAAGAACTCATTTGTATTGAG\n+TCAGAGGAGATCGAAACAGAGTTGTCTTTTTCTGAAAGTACAGAAAATTCAGAGTATCTT\n+AGAAGCCAAAAAATCTTAGAACGTGGCTTGTCTAAACGAGAAACCTTATAA\n+>contig00002_210541_214169_-\n+TTGAAAGGAAATCGGCAAAGAATCCAACCAAAAAATATTTTTCAAGCGGTTATTGATTCA\n+CCGCTTTCTGATCAAGAGAAAGAGGTTTTAACCTTTTTATATCAACCAATTGTCGGCGCC\n+AATGCGTTTAGTTTATATTGGCTTTTGTTATCTGAAACAACAGACTCAGAGGAGAATGGC\n+TCGCTGTTTCATGCAGATTTAATTAGTTTGCTGGACTTGAGTTGTCAACAATTAGAAGAA\n+GCTTGCTACAAATTAGAAGGCATTGGGTTGCTAGAAACGTATAAAAAAACAGATCGGGAA\n+TTAGGAGATTGTTATTTATATTATTTAAAAGCACCTGAAACAGCCGCTCGTTTTTTTAAA\n+GATGAAGTGTTAGCTTTAGTGTTATTTAATCGGGTTGGACAACGGAAATTTGATCAATTA\n+GTGCAAAAGTTTCAACCGCATCCTACCAAAACAGAGGGCTATCAAAATGTTTCCGCTAGC\n+TTTCAAGAGGTTTATGCCTTTAAAGAAGAACAAATTGTTTCCGAAGCGAACCGATTGACA\n+ACGATTCAAGAAACTTTTTCTCAAAAAGAAAAATCGAAGAAAATTTCTGTATCAACGGAT\n+TCTTTTGATTGGCACTATTTTGTGGAAGGTTTGCACCGTTTAGGTTTACAACTGCCTGAA\n+GATGAGGCTAGTTTTCAAGAAGAAGTCTATGTTTTTCATCAATTATATGGCATCAATGAG\n+TTAGATATGGTAGACTTTGCTTCGAAATCATTTGACTATTATACAAGTCGAATTTTGCCT\n+AAGGAATTAGTGCGAACGATTCATCAAGCGTTTGATCCTGATAAAAAACCACAATCAACA\n+AACGTAGTGACAAACAAGCAAGCACAATTGACGGTGGAAGAGCAACAAACGTATCGATAT\n+AACGCATTAAAAATGAATGGTTTTTCTGAACTGGATATTCAAATGATTATGGATAGTGAA\n+AAGAATCCGCCTATTCAATATTTAGAAGCTTTAAAAAATAGTCGAGGCGGCTATACGACA\n+CCACAAGAACGTTCATTAGTGAAATATTTGGTTGCCAAATCAGGCTTACCGACTAGTGTG\n+ATTAATATTTTGATTAACTATGTTTACAATATTCAACAACAACCGACTTTAAAAGCGGAG\n+TATGTGAATCGAATTGCGAATGAATGGGGACAAAGTGGCATTCATTCACCAGAAAAAGCA\n+ATTGAACATGTCAGAGAATTGGCAAAACAAAGCCAAACCAAACAAAAACAGCGACAACAA\n+AATTATTCAGGGAAACGCCAAACTGTTCGACAAGAGCGATTGCCAGAATGGGCAGATCAG\n+CCAAACGATGAAACAAAACTTTCCCCAGCAGAACAAGCCGAGTTAGATCGACAAATTCAA\n+GAATTTTTAAACCAAGGAGGTGACCAATGATGGAAGACGTAGGAAAAGAAATGTCAAAAA\n+TTATCCAGAAGCGTGACATCAATGAACGATATGAAGAGCTGGTTAACGAAGTATTGAAAG\n+ATCAAGATGTTCAAGCCTTTATACAAGCAAACCGAGAGCGTTTAACCGATGAAGATATTC\n+GTAAAAGTTATGCTAAGTTGTATGAATTTGTTCAAGAAAAAAAGAAATTTCAAGTAAACG\n+ATCCGGCAATGATTGCCCCCGGCTATGAGCCAAGATTAATGTTGAATTTTCATTACATTG\n+ATGTAACGTATGTCCCAACGGCTGATTTAATCGCCCGTCAGAAGGAAGAAGAAATTCGTA\n+ATCGAGTAAGGGCAATGGACATTCCAAAAGATGTCCGAGAAGCAAATTTACGAGATTTCG\n+ATCCATCTTCTCAAGGTCGAGCCAAAGCGTTAGCAGAAGCAATGCAATTT'..b'ig00059_1_652_+\n+CGTGCTATACAAACTATTTATAATGTAGTCAATAAGTTCAAGCAAGGCAAGACTGCTCTT\n+GATTATTGGCACCAGTATAAAGAAAATAAGAAAAAATGTGGTAGAAAAGTCATTCAATTA\n+CCTGCTCATGAAGTAGATTACATTAAAGAGAAAGTCACTCTTGGTTGGACGCCTGACGTC\n+ATTATCGGGCGAAAAGAAAGGCCTGTTTCATGCGGTATGAGAACACTTTATCGTTTATTT\n+TCTAAAGGGATATTTGATATTGACACACTACCGATGAAAGGTAAAAGAAAACCCAATGGC\n+CATCAGGAAAAACGGGGAAAACAACAATATCAGCGCTCAATCCATGATCGACCTGATAAT\n+TATCCTGATTTCAATTCTGAGTTTGGTCACCTTGAAGGTGATACGATCGTTGGCATTCAT\n+CATAAAAGTGCCGTCATTACTTTAGTTGAAAGATTATCTAAAGTCATTATCACGATTAAA\n+CCCAACGGCCGTAAGGCATTAGATATTGAAACCGCCCTTAATCAATGGTTTTCTCGCTTC\n+CCTAAAAACTTCTTTAAATCTATTACGTTTGACTGTGGAAAAGAATTTTCTAACTGGAAA\n+GCCATTAGTAACCAACACGATATTGATATATATTTTGCGGACCCTGGAACAC\n+>contig00062_1_525_-\n+TCATTTTAAAGGAAAGCAATTTCAGCAGGATGTGATTATTGTAGCCGTGGGCTACTATCT\n+TCGTTATAACCTTAGCTATCGTGAAGTTCAAGAAATCTTATATGATCGTGGCATTAACGT\n+TTCTCATACGACGATTTATCGTTGGGTGCAAGAATATGGCAAACTACTCTATCAAATTTG\n+GAAAAAGAAAAATAAAAAATCCTTTTATTCATGGAAAATGGATGAAACATACATCAAAAT\n+TAAAGGAAAATGGCATTATTTGTATCGAGCCATCGATGCAGATGGTTTAACCTTGGATAT\n+TTGGTTACGTAAAAAACGGGACACACAAGCAGCCTATGCTTTTCTTAAGCGGTTAGTGAA\n+GCAGTTTGATGAACCGAAGGTTGTAGTCACAGATAAAGCCCCCTCTATTACAAGTGCCTT\n+TAAGAAACTAAAAGAATACGGCTTTTATCAAGGGACAGAACATCGTACCATTAAATACCT\n+GAATAATTTGATTGAACAAGACCATCGTCCAGTAAAGAGACGCAA\n+>contig00070_1_332_-\n+CCCCCTCTATTACAAGTGCCTTTAAGAAACTAAAAGAATACGGCTTTTATCAAGGGACAG\n+AACATCGTACCATTAAATACCTGAATAATTTGATTGAACAAGACCATCGTCCAGTAAAGA\n+GACGCAATAAATTCTATCGAAGTTTACGCACTGCCTCTACCACGATTAAAGGCATGGAAG\n+CCATTCGAGGATTATATAAGAAAACCCGAAAAGAAGGCACTCTCTTCGGGTTTTCGGTCT\n+GTACTGAAATCAAGGTATTATTGGGAATCCCAGCTTAAATCATAGATACCGTAAGGGATT\n+TTATTCTTTATTTAAAACTTTGCAACAGAACC\n+>contig00076_1_223_-\n+ATGACCTACAAACATCTTACCATAGACGAACTGACAATGATAGAATCATATTATCTTCAA\n+CATAATAAACCGGTTGAAATCGCTAACCGAATGGGACGTGCTATACAAACTATTTATAAT\n+GTAGTCAATAAGTTCAAGCAAGGCAAGACTGCTCTTGATTATTGGCACCAGTATAAAGAA\n+AATAAGAAAAAATGTGGTAGAAAAGTCATTCAATTACCTGCTC\n+>contig00079_1_255_-\n+CTATTACGTTTGACTGTGGAAAAGAATTTTCTAACTGGAAAGCCATTAGTAACCAACACG\n+ATATTGATATATATTTTGCGGACCCTGGAACACTTTCTCAACGCCCATTAAACGAGAATT\n+CTAACGGGATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATC\n+AGACATTTATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATT\n+ACAGAACACCAATTG\n+>contig00083_1_128_+\n+ATACGACGATTTATCGTTGGGTGCAAGAATATGGCAAACTACTCTATCAAATTTGGAAAA\n+AGAAAAATAAAAAATCCTTTTATTCATGGAAAATGGATGAAACGTACATCAAAATTAAAG\n+GAAAATGA\n+>contig00083_135_255_+\n+TTGTATCGAGCCATCGATGCAGATGGTTTAACCTTGGATATTTGGTTACGTAAAAAACGG\n+GACACACAAGCAGCCTATGCTTTTCTTAAGCGGTTAGTGAAGCAGTTTGATGAACCGAAG\n+G\n+>contig00085_1_255_+\n+CTATTACGTTTGACTGTGGAAAAGAATTTTCTAACTGGAAAGCCATTAGTAACCAACACG\n+ATATTGATATATATTTTGCGGACCCTGGAACACTTTCTCAACGCCCATTAAACGAGAATT\n+CTAACGGTATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATC\n+AGACATTTATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATT\n+ACAGAACACCAATTG\n+>contig00090_1_250_-\n+TGCAGATGGTTTAACCTTGGATATTTGGTTACGTAAAAAACGGGACACACAAGCAGCCTA\n+TGCTTTTCTTAAGCGGTTAGTGAAGCAGTTTGATGAACCGAAGGTTGTAGTCACAGATAA\n+AGCCCCCCTCTATTACAAGTGCCTTTAAGAAACTAAAAGAATACGGCTTTTATCAAGGGA\n+CAGAACATCGTACCATTAAATACCTGAATAATTTGATTGAACAAGACCATCGTCCAGTAA\n+AGAGACGCAA\n+>contig00093_1_231_-\n+ATACGACGATTTATCGTTGGGTGCAAGAATATGGCAAACTACTCTATCAAATTTGGAAAA\n+AGAAAAATAAAAAATCCTTTTATTCATGGAAAATGGATGAAACGTACATCAAAATTAAAG\n+GAAAATGGCATTATTTGTATCGAGCCATCGATGCAGATGGTTTAACCTTGGATATTTGGT\n+TACGTAAAAAACGGGACACACAAGCAGCCTATGCTTTTCTTAAGCGGTTAG\n+>contig00094_69_206_+\n+ATGACGATGAGTCATTTTAAAGGAAAGCAATTTCAGCAGGATGTGATTATTGTAGCCGTG\n+GGCTACTATCTTCGTTATAACCTTAGCTATCGTGAAGTTCAAGAAATCTTATATGATCGT\n+GGCATTAACGTTTCTCAT\n+>contig00096_1_161_-\n+TGGTTTTCTCGCTTCCCTAAAAACTTCTTTAAATCTATTACGTTTGACTGTGGAAAAGAA\n+TTTTCTAACTGGAAAGCCATTAGTAACCAACACGATATTGATATATATTTTGCGGACCCT\n+GGAACACTTTCTCAACGCCCATTAAACGAGAATTCTAACGG\n+>contig00097_1_151_-\n+ATGATCGTGGCATTAACGTTTCTCATACGACGATTTATCGTTGGGTGCAAGAATATGGCA\n+AACTACTCTATCAAATTTGGAAAAAGAAAAATAAAAAATCCTTTTATTCATGGAAAATGG\n+ATGAAACGTACATCAAAATTAAAGGAAAATG\n+>contig00098_1_138_+\n+ATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATCAGACATTT\n+ATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATTACAGAACA\n+CCAATTGAGATATTTTTG\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/isescan/results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isescan/results.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,44 @@ +seqID family cluster isBegin isEnd isLen ncopy4is start1 end1 start2 end2 score irId irLen nGaps orfBegin orfEnd strand orfLen E-value E-value4copy type ov tir +contig00001 IS21 IS21_259 104722 106001 1280 1 104722 104735 105988 106001 20 12 14 0 105201 106043 + 843 2.1e-13 2.1e-13 p 1 TTGAAAAAAATAGC:TTGGAAAACATAGC +contig00002 IS200/IS605 IS200/IS605_96 179502 180572 1071 1 0 0 0 0 0 0 0 0 179502 180572 - 1071 1.2e-69 1.2e-69 c 1 -:- +contig00002 IS21 IS21_288 210210 214514 4305 1 210210 210236 214488 214514 26 20 27 0 210541 214169 - 3629 6.1e-11 6.1e-11 p 1 ATTAAGCCAAATGGCAATGGTGATGAA:ATCAAGAAAAATGGGGATCGTGAAGAA +contig00002 IS30 IS30_241 252678 252900 223 1 0 0 0 0 0 0 0 0 252678 252900 + 223 8.3e-32 8.3e-32 p 1 -:- +contig00005 IS30 IS30_241 54 3033 2980 1 54 67 3020 3033 20 12 14 0 1 2892 + 2892 6.2e-51 6.2e-51 p 1 AAAAGAATTTTCTA:AAATGAATGTTCTA +contig00005 IS21 IS21_259 84142 85683 1542 1 84142 84174 85651 85683 34 25 33 0 84182 85525 - 1344 6.3e-15 6.3e-15 p 1 TGTGGATAACTTTGTTCTTTTTTGTTTAGTTTT:TGTGGAAAACTTTTTTCACCCTTGTGTACTTTT +contig00008 IS30 IS30_241 99798 99915 118 1 0 0 0 0 0 0 0 0 99798 99915 - 118 4.6e-11 4.6e-11 p 1 -:- +contig00010 IS6 IS6_292 1 138 138 1 0 0 0 0 0 0 0 0 1 138 - 138 7.2e-22 7.2e-22 p 1 -:- +contig00010 IS256 IS256_47 63216 65257 2042 1 63216 63259 65215 65257 26 30 44 1 63507 64842 - 1336 4.3e-136 4.3e-136 c 1 AGGGATTCTTAGAAGTAGAAGCTCAACATTTTGAACTTATAGAA:AGGCATTTGTGGAATTATACTTTCAATA-TTAGAACTTTTTGAA +contig00010 IS3 IS3_176 65906 67630 1725 1 65906 65936 67600 67630 34 24 31 0 65942 67421 + 1480 2.5e-113 2.5e-113 c 1 TGGATAGGCTACAATTAACTAGACAGAAAAA:TGGATAGATGTCAATAAAGTAGACACAAAAA +contig00010 IS256 IS256_162 70798 72118 1321 1 70798 70826 72090 72118 38 24 29 0 71048 72069 + 1022 1.9e-148 1.9e-148 c 1 TAGCGTAAAATATTTTGTGTAAATAGAAA:TAGCGTCAAGAATTATGTGTAAATGGAAA +contig00010 ISL3 ISL3_126|ISL3||protein:plasmid:139408 74315 76017 1703 1 74315 74360 75974 76017 24 32 46 2 74651 75803 + 1153 5.1e-56 5.1e-56 c 1 TTATTCCCTCTCTTATCATATTATCATCTTCAACAGTTAATATTTT:TTAGTACTTCTTGTATCAT-TGATTAT-TTCTTCATTCAATATATT +contig00010 IS256 IS256_162 81227 82564 1338 1 81227 81253 82538 82564 34 22 27 0 81322 82512 + 1191 2e-192 2e-192 c 1 TGAGAGTGTAAAATATTTTGTGTAAAT:TGGGAGCGTCAATAATTTTGTGTAAAT +contig00017 ISL3 ISL3_126|ISL3||protein:plasmid:139408 93 1807 1715 1 93 102 1798 1807 20 10 10 0 192 1618 + 1427 1.4e-44 1.4e-44 p 1 TTTTTATTTT:TTTTTATTTT +contig00029 IS30 IS30_241 15381 16432 1052 1 15381 15402 16411 16432 36 20 22 0 15385 16344 - 960 1.7e-143 1.7e-143 c 1 ATTGTCAAATTAAGTTAGACAA:ATTGTAAAATTAAGCTAGACAA +contig00030 IS30 IS30_241 23835 23952 118 1 0 0 0 0 0 0 0 0 23835 23952 - 118 4.6e-11 4.6e-11 p 1 -:- +contig00035 IS3 IS3_61 7068 7978 911 1 7068 7091 7955 7978 20 17 24 0 7039 8102 + 1064 6.2e-50 6.2e-50 p 1 AATTCAGTTATTTTTAAAATATGA:AAATCAGCAATTTTGTAAAAGTGA +contig00036 IS30 IS30_241 1 117 117 1 0 0 0 0 0 0 0 0 1 117 + 117 4.6e-11 4.6e-11 p 1 -:- +contig00036 IS3 IS3_97 1131 2606 1476 1 1131 1154 2583 2606 32 20 24 0 1090 2554 - 1465 6.2e-133 6.2e-133 c 1 GTGCACCCCAAAAGTTAGACTTTT:GTGACCCCCAAAATATAGACTTTT +contig00036 ISL3 ISL3_126|ISL3||protein:plasmid:139408 6170 7474 1305 1 6170 6184 7460 7474 22 13 15 0 6652 7530 + 879 2.6e-54 2.6e-54 c 1 TTAGTGTAAAATTGA:TTAGCGTAAAACTGA +contig00036 IS256 IS256_162 9125 10401 1277 1 9125 9140 10386 10401 20 13 16 0 9092 10351 - 1260 1.5e-189 1.5e-189 c 1 TCTGTCAAATAGTGTT:TCTGTAGAATAGAGTT +contig00036 IS256 IS256_162 13800 15146 1347 1 13800 13820 15126 15146 30 18 21 0 13804 15031 - 1228 6.9e-136 6.9e-136 c 1 AGCGTCAAGAATCTTGTGTAA:AGCGTAAAATATCTTGTGTAA +contig00043 IS256 IS256_162 211 1174 964 1 211 230 1155 1174 28 17 20 0 591 1213 + 623 2.8e-67 2.8e-67 p 1 CAATGATTTCGTGTGAATAA:CAATAATTTTGTGTAAATAA +contig00043 IS6 IS6_292 5366 6174 809 1 5366 5383 6157 6174 32 17 18 0 5661 6221 + 561 5.3e-63 5.3e-63 c 1 GGTTCTGTTGCAAAGTTT:GGTTCTGTTGCGAAGTTT +contig00045 IS30 IS30_241 1 117 117 1 0 0 0 0 0 0 0 0 1 117 + 117 4.6e-11 4.6e-11 p 1 -:- +contig00053 IS110 IS110_139 261 1613 1353 1 261 280 1594 1613 20 15 20 0 385 1635 + 1251 1e-33 1e-33 p 1 GGTGGCTTAGAGGTTTAATG:GGTGGCATATAGAGTTGATG +contig00056 ISL3 ISL3_126|ISL3||protein:plasmid:139408 75 1478 1404 1 75 118 1433 1478 40 36 46 2 84 1367 - 1284 2.1e-50 2.1e-50 p 1 CTTTTTTAG-TTATTTAATTTTAATA-AGGCCGTTTATCAAGAAAA:CTTTTTTAGTTTATTTAAATATAAAACATGTCGTCTATCTAGTAAA +contig00057 IS3 IS3_97 7 1510 1504 1 7 25 1492 1510 34 18 19 0 58 1460 - 1403 6.1e-131 6.1e-131 c 1 CGACCCCAAAAAGTTAGAC:CGACCCCCAAAAGTTAGAC +contig00058 IS30 IS30_241 1 1299 1299 1 1 127 1173 1299 254 127 127 0 201 1160 - 960 1.1e-160 1.1e-160 c 1 CGGCTACAATAATCACATCCTGCTGAAATTGCTTTCCTTTAAAATGATTCATCGTCATTCCTCCTGCTATCTTTTTCTATTATTCTACCTTATTTGATAGTAGATTTAAAACTTTGCAACAGAACCG:CGGCTACAATAATCACATCCTGCTGAAATTGCTTTCCTTTAAAATGATTCATCGTCATTCCTCCTGCTATCTTTTTCTATTATTCTACCTTATTTGATAGTAGATTTAAAACTTTGCAACAGAACCG +contig00059 IS30 IS30_241 102 592 491 1 102 114 580 592 18 11 13 0 1 652 + 652 6.1e-113 6.1e-113 p 1 TAGAAAAGTCATT:TAGAAAATTCTTT +contig00062 IS6 IS6_292 140 474 335 1 140 151 463 474 16 10 12 0 1 525 - 525 2.3e-92 2.3e-92 p 1 CTACAACCTTCG:CTACTATCTTCG +contig00070 IS6 IS6_292 1 332 332 1 0 0 0 0 0 0 0 0 1 332 - 332 3.3e-26 3.3e-26 p 1 -:- +contig00076 IS30 IS30_241 1 223 223 1 0 0 0 0 0 0 0 0 1 223 - 223 8.3e-32 8.3e-32 p 1 -:- +contig00079 IS30 IS30_241 1 255 255 1 0 0 0 0 0 0 0 0 1 255 - 255 1.2e-41 1.2e-41 p 1 -:- +contig00083 IS6 IS6_292 1 128 128 1 0 0 0 0 0 0 0 0 1 128 + 128 7.1e-19 7.1e-19 p 1 -:- +contig00083 IS6 IS6_292 135 255 121 1 0 0 0 0 0 0 0 0 135 255 + 121 9.9e-18 9.9e-18 p 1 -:- +contig00085 IS30 IS30_241 1 255 255 1 0 0 0 0 0 0 0 0 1 255 + 255 1.2e-41 1.2e-41 p 1 -:- +contig00090 IS6 IS6_292 1 250 250 1 0 0 0 0 0 0 0 0 1 250 - 250 1.4e-34 1.4e-34 p 1 -:- +contig00093 IS6 IS6_292 1 231 231 1 0 0 0 0 0 0 0 0 1 231 - 231 4.5e-41 4.5e-41 p 1 -:- +contig00094 IS6 IS6_292 69 206 138 1 0 0 0 0 0 0 0 0 69 206 + 138 1.4e-20 1.4e-20 p 1 -:- +contig00096 IS30 IS30_241 1 161 161 1 0 0 0 0 0 0 0 0 1 161 - 161 6.2e-24 6.2e-24 p 1 -:- +contig00097 IS6 IS6_292 1 151 151 1 0 0 0 0 0 0 0 0 1 151 - 151 2.5e-24 2.5e-24 p 1 -:- +contig00098 IS30 IS30_241 1 138 138 1 0 0 0 0 0 0 0 0 1 138 + 138 1.5e-18 1.5e-18 p 1 -:- |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/isescan/summary.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isescan/summary.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,41 @@ +# seqid family nIS %Genome bps4IS dnaLen +contig00001 IS21 1 0.29 1280 436224 +contig00002 IS200/IS605 1 0.42 1071 252900 +contig00002 IS21 1 1.70 4305 252900 +contig00002 IS30 1 0.09 223 252900 +contig00005 IS21 1 1.16 1542 132811 +contig00005 IS30 1 2.24 2980 132811 +contig00008 IS30 1 0.12 118 99915 +contig00010 IS256 3 5.11 4701 92075 +contig00010 IS3 1 1.87 1725 92075 +contig00010 IS6 1 0.15 138 92075 +contig00010 ISL3 1 1.85 1703 92075 +contig00017 ISL3 1 2.66 1715 64537 +contig00029 IS30 1 4.33 1052 24296 +contig00030 IS30 1 0.49 118 23952 +contig00035 IS3 1 5.84 911 15587 +contig00036 IS256 2 17.14 2624 15306 +contig00036 IS3 1 9.64 1476 15306 +contig00036 IS30 1 0.76 117 15306 +contig00036 ISL3 1 8.53 1305 15306 +contig00043 IS256 1 10.78 964 8939 +contig00043 IS6 1 9.05 809 8939 +contig00045 IS30 1 1.69 117 6929 +contig00053 IS110 1 76.23 1353 1775 +contig00056 ISL3 1 92.01 1404 1526 +contig00057 IS3 1 99.27 1504 1515 +contig00058 IS30 1 100.00 1299 1299 +contig00059 IS30 1 75.31 491 652 +contig00062 IS6 1 63.81 335 525 +contig00070 IS6 1 100.00 332 332 +contig00076 IS30 1 87.45 223 255 +contig00079 IS30 1 100.00 255 255 +contig00083 IS6 2 97.65 249 255 +contig00085 IS30 1 100.00 255 255 +contig00090 IS6 1 100.00 250 250 +contig00093 IS6 1 100.00 231 231 +contig00094 IS6 1 66.99 138 206 +contig00096 IS30 1 100.00 161 161 +contig00097 IS6 1 100.00 151 151 +contig00098 IS30 1 100.00 138 138 +10_Enterococcus_faecalis_S17_L001.fasta total 43 1.31 39763 3027634 |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/kraken2/taxonomy_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken2/taxonomy_report.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,10 @@ +100.00 95 0 R 1 root +100.00 95 0 R1 131567 cellular organisms +100.00 95 4 D 2 Bacteria + 95.79 91 0 D1 1783272 Terrabacteria group + 95.79 91 0 P 1239 Firmicutes + 95.79 91 4 C 91061 Bacilli + 89.47 85 8 O 186826 Lactobacillales + 78.95 75 0 F 81852 Enterococcaceae + 78.95 75 7 G 1350 Enterococcus + 66.32 63 42 S 1351 Enterococcus faecalis \ No newline at end of file |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/kraken2/taxonomy_result.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken2/taxonomy_result.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,5 @@ +C contig00063 1351 412 0:7 2:2 0:16 2:5 0:16 91061:3 0:21 91061:2 0:22 1351:2 0:5 1351:1 0:21 2:5 0:4 2:1 0:1 2:7 0:3 2:5 0:3 2:4 0:13 2:2 0:5 2:2 1351:1 0:22 1351:1 0:14 1351:5 0:7 1350:5 0:2 1350:1 0:2 1350:5 0:6 1350:3 0:42 91061:5 0:15 91061:4 0:10 91061:1 0:11 91061:5 0:9 91061:2 0:19 91061:3 +C contig00075 1351 255 0:3 91061:5 0:1 91061:1 0:2 91061:4 0:18 91061:2 0:5 91061:12 0:5 91061:3 0:4 91061:3 0:13 91061:5 0:13 1351:5 0:3 91061:8 0:2 91061:7 0:19 91061:3 0:12 91061:2 0:14 91061:5 1783272:1 91061:1 0:9 91061:4 0:7 91061:5 0:5 91061:2 0:5 2:3 +C contig00085 186826 254 0:16 2:5 0:9 1:4 0:51 2:8 0:30 186826:1 0:5 2:1 0:27 2:2 0:5 2:2 0:6 2:5 0:41 2:2 +C contig00091 1350 161 0:4 1350:6 0:1 1350:1 0:19 186826:2 0:11 1350:5 0:7 1350:5 0:3 1350:2 0:8 186826:10 0:9 186826:1 0:9 186826:3 0:3 186826:5 0:7 186826:1 0:5 +C contig00095 2 128 2:2 0:1 2:5 0:1 2:3 0:9 2:6 0:7 2:4 0:16 2:5 0:1 2:5 0:3 2:3 0:1 2:5 0:14 2:3 |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/plasmidfinder/genome_hit.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmidfinder/genome_hit.fasta Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,94 @@ +>repUS12:WARNING ID:100.0% COV:88.01% Best_match:contig00051 len=2083 cov=17.5 corr=0 origname=NODE_51_length_2083_cov_17.526074_pilon sw=shovill-spades/1.1.0 date=20230213:127..897:repUS12_2_repB(SAP014A)_GQ900379:88.013699 +ATGTGTCCTAATAGTAGCATTTATTCAGATGAAAAATCAAGGGTTTTAGTGGACAAGACA +AAAAGTGGAAAAGTGAGACCATGGAGAGAAAAGAAAATCGCTAATGTTGATTACTTTGAA +CTTCTGCATATTCTTGAATTTAAAAAGGCTGAAAGAGTAAAAGATTGTGCTGAAATATTA +GAGTATAAACAAAATCGTGAAACAGGCGAAAGAAAGTTGTATCGAGTGTGGTTTTGTAAA +TCCAGGCTTTGTCCAATGTGCAACTGGAGGAGAGCAATGAAACATGGCATTCAGTCACAA +AAGGTTGTTGCTGAAGTTATTAAACAAAAGCCAACAGTTCGTTGGTTGTTTCTCACATTA +ACAGTTAAAAATGTTTATGATGGCGAAGAATTAAATAAGAGTTTGTCAGATATGGCTCAA +GGATTTCGCCGAATGATGCAATATAAAAAAATTAATAAAAATCTTGTTGGTTTTATGCGT +GCAACGGAAGTGACAATAAATAATAAAGATAATTCTTATAATCAGCACATGCATGTATTG +GTATGTGTGGAACCAACTTATTTTAAGAATACAGAAAACTACGTGAATCAAAAACAATGG +ATTCAATTTTGGAAAAAGGCAATGAAATTAGACTATGATCCAAATGTAAAAGTTCAAATG +ATTCGACCGAAAAATAAATATAAATCGGATATACAATCGGCAATTGACGAAACTGCAAAA +TATCCTGTAAAGGATACGGATTTTATGACCGATGATGAAGAAAAGAATTTGGGTTCTGTT +GCAAAGTTTTAAATAAAGAATAAAATCCCTTACGGTATCTATGATTTAAGCTGGGATTCC +CAATAATACCTTGATTTCAGTACAGACCGAAAACCC +>repUS40:WARNING ID:100.0% COV:100.0% Best_match:contig00026 len=35051 cov=66.2 corr=0 origname=NODE_26_length_35051_cov_66.162954_pilon sw=shovill-spades/1.1.0 date=20230213:21156..22313:repUS40_1_repB(pE394)_KP399637:100.000000 +ATGCTCAATTCTAGTATATCACGAAAGGTACTTATGATGAATGACATTCAAAACAAAAAA +ATAGTTCAAGACAATGATTTAATTGTAAGTGTCGCAAAAATGGATAAGACACCCATGAAA +TTTTTTGAATTAGCAGTCGCCAGTTTAGATATTAAGAATATTCCTGCTGATCGAACTGTT +CATGTTTCTAAAGAATTATTGTATTCCTTCTTTGACGCAAAAAGTGAAAATAAACATACA +CGCTTTAAAGACGCTGTTCTAACTGTTCATGAGCAAGCAGTGTTTCTAATGCGAGAATTA +AATGAGCGCAAAGGAAAATATGAATATCAAGTGATTAGTCCATTGGAAAGAACTTCTTGG +AATGATTATGAAGATATTGTTTCTTTTAAGTTTACTGAATCTATTTTTCCGTATCTGATA +GATTTAAAAGGAACATACACGCAATATTTATTGTCAGACATTGCACAACTAAATAGCAAG +TATTCCATCATTATTTATAAATGGTTAAGCATGAATTATAACCAGTATGACTATTATAAT +GCAAAAGGTGGGCGCAGAGAAAAACAGTTAAATGAATATAAAAATCCAATTATTCCGATT +GAAGAATTACGAAGAATAACTGATACAGAAAAAGAGTATTTAAAATTTTCCAATTTTGAA +GCAAGAGTTTTAAAAAAAGCTGTTGAAGAAATCAACCAATTTACAGTTTTAAATGCGACG +TATGAAAAAATAAAAAAAGGAAACCGAATTGGTTCGATTCAGTTCCATATTACGAAAAAA +CAAATTGCTCCTAATCCTTCTTACAAAATTGGCGATTCTGTGTATGAAGCGCAACAAGCA +GAAAAAGAACAAAATCAAATTACTTTATTTGCGCAGGCAATGCAAAGTCAATACACTACC +ATTTTGATGGAAAATATGTTGATTGGGTACAAAGATATGCAAGATATTGAATTAATGGCA +AGCTTGCAAGAAATGGTTTATCCCTTGTATGACGAGTTGAAAACTCTTAGAGGATTAGAC +GGTGTGAGAAATCACTTAGAATACGTTTCAAGAAAACAAATAGGCTATTCTAAAACTAAT +ATTGTCAAGTATTTAAAAACAGCTATCACACAATATTTGCCAACGGTAAAAATGATGGAT +ATGGATAATAGAGTGTAA +>rep9b:WARNING ID:100.0% COV:100.0% Best_match:contig00023 len=45935 cov=46.6 corr=0 origname=NODE_23_length_45935_cov_46.624847_pilon sw=shovill-spades/1.1.0 date=20230213:3630..4643:rep9b_2_prgW(EF62pC)_CP002494:100.000000 +ATGAACGATTTTCAATTTATTTCAGCTAATGAAACCTATAGAAATTTGTATTACCAATTA +CCTAAAGTACTTTTTACATCAGAATTTTATAAGACTATGTCTAATGATAGTAAAATAGCT +TACGCAATGTTGCAAGACCGATGTGAATATTCAATACAAAATAATTGGATTGATCAAGAT +GGGCATATATATTTTATCTTTACACGAAATGAACTGATGGATATTTTAGGGTGTAAAGAA +AATAAAATTGCAAAAATAAAAAAAGAATTAAAAGACAAAAATTTACTTTATGAAAAACGT +ATTCCTCCGAAAAAACTCTCTACTGGTGAATTCAAAAACTATCCAAACAGATTGTATTTA +GGTAAGCTGGAAGTTTCAGCAACAGATGTTTACGCCATCAGTAATGCTAGCTATACAAAT +GAGTTTCCCGAAAGTGGGAAAAACCAACCTTCGGATAAACATGATAAAATCGGCATTTCT +TTCGAAAGTGGGAAAAACCAACGTCCAGAAGAATCCAATAATACCAGTACTTTGTTCGAA +AGTGGGAAAAACCAACCCAATCTATATCTAACTAATTCTTTAGATACAATAGATACAATA +GATACTGAAAAAGAACGATTGCAACAACAATTATTGCTCGATCAATTTTCAGAAGTTCAA +GAGCATACATTTCTTAGCAAAAATAGCTTAAAATTTATTGCTGCCTTTTCTGATACTATT +CAAGAAGCACATGAAATGGTTGGAACAATTATTCGTGCTAAAACTAAAGTAGAAAAAGAA +TACAATATCGTTCTAATTGGTGAAGATTATCAAGAAGAAATAGACAAATGTTTGCGTCGT +GTGATGCATAAAATCAAGACAGATTCTACTGTAAAAAGTCCAAAAGGCCTATTCTACAAG +TCGTTTTACAATTTATTTGTTGAATGTACAATAGAGAAAAAAAGTCATTTAAATAAAAAT +AGTACGGACAACACCCCAGAAATAACTACACATAACTGGATTGAGTATCAATAA +>rep7a:WARNING ID:100.0% COV:100.0% Best_match:contig00048 len=5336 cov=19.5 corr=0 origname=NODE_48_length_5336_cov_19.468228_pilon sw=shovill-spades/1.1.0 date=20230213:3276..4214:rep7a_8_ORF11(pRE25)_X92945:100.000000 +ATGAAGAAAATTGATGAAAAATTAGCTGCAGAAATCTCACTAAAAAAACCGGCCGTCTCT +AATAGCCGGTTAAGTAATAGCCGGTTAAGTGGTCAAACTTTGGGAAAATCTCAACCCGCA +TTAAGTTTTGATGCCATGACAATCGTTGGAAATTTGAACAAAACTAATGCTAAAAAGCTA +TCTGACTTTATGAGTGTAGAGCCACAAATACGACTTTGGGATATACTTCAAACAAAGTTT +AAAGCTAAGGCACTTCAAGAAAAAGTTTATATCGAATATGACAAAGTAAAAGCAGATACT +TGGGATAGACGTAATATGCGTGTTGAATTTAATCCCAATAAACTCACACATGAAGAAATG +ATTTGGTTAAAACAAAATATTATCGACTACATGGAAGATGACGGTTTTACAAGATTAGAC +TTAGCTTTTGATTTTGAAGATGATTTGAGCGATTACTATGCAATGACTGATAAAGCAGTT +AAGAAAACTGTTTTTTATGGTCGTAATGGCAAGCCAGAAACAAAATATTTTGGTGTCCGT +GATAGTGATAGATTTATTAGAATTTATAATAAAAAACAAGAACGTAAAGATAACGCAGAT +GTTGAAGTTGTGTCTGAACATTTATGGCGTGTAGAAGTTGAATTAAAAAGAGATATGGTT +GATTACTGGAATGATTGTTTTAATGATTTACACATCTTGAAACCTGCGTGGGCTACTTTA +GAAAAAATTAATGAGCAAGCTATGGTTTATACTTTGTTGCATGAAGAAAGTATGTGGGGA +AAGCTAAGTAAGAATACTAAGACTAAATTTAAAAAATTGATTAGAGAAATATCTCCAATT +GATTTAACGGAATTAATGAAATCGACTTTAAAAGCGAACGAAAAACAATTGCAAAAGCAG +ATTGATTTTTGGCAACGTGAATTTAGGTTTTGGAAGTAA +>repUS43:WARNING ID:100.0% COV:100.0% Best_match:contig00040 len=12074 cov=69.2 corr=0 origname=NODE_40_length_12074_cov_69.205993_pilon sw=shovill-spades/1.1.0 date=20230213:8225..9430:repUS43_1_CDS12738(DOp1)_CP003584:100.000000 +TTGGAGGGATTTTTACTGAATGAACAAACTTGGTTACAGCATTTAAAAGAAAAACGCTTG +GCTTATGGACTATCTCAAAACCGTTTAGCTGTTGCGACTGGTATTACAAGGCAGTATCTA +AGCGATATTGAAACAGGAAAAGTCAAGCCATCAGAGGATTTACAGCAGTCCCTTTGGGAA +GCTCTGGAACGCTTCAATCCCGACGCTCCCCTTGAAATGCTGTTTGATTATGTAAGAATT +CGCTTTCCGACAACAGACGTACAGCAGGTGGTCGAAAACATCTTACAACTGAAACTGTCC +TATTTTCTTCATGAGGACTATGGTTTCTATTCTTATTCAGAGCATTATGCTTTAGGCGAC +ATATTCGTCCTTTGCTCCCATGAACTGGACAAAGGAGTTCTGGTGGAATTGAAAGGTCGT +GGGTGCAGACAATTTGAAAGCTATCTTCTGGCACAACAAAGAAGCTGGTATGAGTTCTTT +ATGGACGTTTTGGTGGCTGGCGGTGTGATGAAACGCCTTGACCTTGCCATTAACGATAAG +ACAGGGATTTTAAATATCCCTGTACTCACTGAAAAGTGCCAACAGGAAGAATGTATCTCC +GTCTTCCGCAGTTTTAAAAGCTATCGCAGTGGCGAACTGGTACGCAAAGAGGAAAAGGAA +TGTATGGGAAACACCCTCTATATCGGTTCATTACAAAGTGAAGTTTATTTCTGTATCTAT +GAAAAGGACTACGAGCAGTACAAGAAAAATGATATTCCCATTGAAGACGCAGAAGTAAAA +AACCGTTTTGAGATTCGATTGAAAAATGAGCGTGCCTATTATGCAGTCCGTGATTTACTC +GTCTATGACAATCCAGAGCATACCGCCTTTAAAATTATCAATCGGTATATCCGTTTTGTA +GATAAAGACGATTCCAAACCTCGTTCTGATTGGAAACTGAATGAAGAATGGGCTTGGTTT +ATTGGGAACAATCGTGAACGATTAAAACTAACCACAAAACCAGAGCCTTACTCCTTCCAA +AGGACGCTGAACTGGCTATCTCATCAAGTTGCCCCGACCTTAAAGGTTGCGATTAAACTT +GATGAAATCAACCAGACGCAGGTTGTAAAAGACATTCTCGACCATGCGAAACTGACAGAC +CGACACAAGCAGATTTTGAAGCAACAGTCAGTAAAAGAACAGGACGTGATAACAACAAAA +AAATAA |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/plasmidfinder/plasmid_hit.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmidfinder/plasmid_hit.fasta Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,94 @@ +>contig00051 len=2083 cov=17.5 corr=0 origname=NODE_51_length_2083_cov_17.526074_pilon sw=shovill-spades/1.1.0 date=20230213:127..897:repUS12_2_repB(SAP014A)_GQ900379:88.013699 +ATGTGTCCTAATAGTAGCATTTATTCAGATGAAAAATCAAGGGTTTTAGTGGACAAGACA +AAAAGTGGAAAAGTGAGACCATGGAGAGAAAAGAAAATCGCTAATGTTGATTACTTTGAA +CTTCTGCATATTCTTGAATTTAAAAAGGCTGAAAGAGTAAAAGATTGTGCTGAAATATTA +GAGTATAAACAAAATCGTGAAACAGGCGAAAGAAAGTTGTATCGAGTGTGGTTTTGTAAA +TCCAGGCTTTGTCCAATGTGCAACTGGAGGAGAGCAATGAAACATGGCATTCAGTCACAA +AAGGTTGTTGCTGAAGTTATTAAACAAAAGCCAACAGTTCGTTGGTTGTTTCTCACATTA +ACAGTTAAAAATGTTTATGATGGCGAAGAATTAAATAAGAGTTTGTCAGATATGGCTCAA +GGATTTCGCCGAATGATGCAATATAAAAAAATTAATAAAAATCTTGTTGGTTTTATGCGT +GCAACGGAAGTGACAATAAATAATAAAGATAATTCTTATAATCAGCACATGCATGTATTG +GTATGTGTGGAACCAACTTATTTTAAGAATACAGAAAACTACGTGAATCAAAAACAATGG +ATTCAATTTTGGAAAAAGGCAATGAAATTAGACTATGATCCAAATGTAAAAGTTCAAATG +ATTCGACCGAAAAATAAATATAAATCGGATATACAATCGGCAATTGACGAAACTGCAAAA +TATCCTGTAAAGGATACGGATTTTATGACCGATGATGAAGAAAAGAATTTGAAACGTTTG +TCTGATTTGGAGGAAGGTTTACACCGTAAAAGGTTAATCTCCTATGGTGGTTTGTTAAAA +GAAATACATAAAAAATTAGGTTCTGTTGCAAAGTAA +>contig00026 len=35051 cov=66.2 corr=0 origname=NODE_26_length_35051_cov_66.162954_pilon sw=shovill-spades/1.1.0 date=20230213:21156..22313:repUS40_1_repB(pE394)_KP399637:100.000000 +ATGCTCAATTCTAGTATATCACGAAAGGTACTTATGATGAATGACATTCAAAACAAAAAA +ATAGTTCAAGACAATGATTTAATTGTAAGTGTCGCAAAAATGGATAAGACACCCATGAAA +TTTTTTGAATTAGCAGTCGCCAGTTTAGATATTAAGAATATTCCTGCTGATCGAACTGTT +CATGTTTCTAAAGAATTATTGTATTCCTTCTTTGACGCAAAAAGTGAAAATAAACATACA +CGCTTTAAAGACGCTGTTCTAACTGTTCATGAGCAAGCAGTGTTTCTAATGCGAGAATTA +AATGAGCGCAAAGGAAAATATGAATATCAAGTGATTAGTCCATTGGAAAGAACTTCTTGG +AATGATTATGAAGATATTGTTTCTTTTAAGTTTACTGAATCTATTTTTCCGTATCTGATA +GATTTAAAAGGAACATACACGCAATATTTATTGTCAGACATTGCACAACTAAATAGCAAG +TATTCCATCATTATTTATAAATGGTTAAGCATGAATTATAACCAGTATGACTATTATAAT +GCAAAAGGTGGGCGCAGAGAAAAACAGTTAAATGAATATAAAAATCCAATTATTCCGATT +GAAGAATTACGAAGAATAACTGATACAGAAAAAGAGTATTTAAAATTTTCCAATTTTGAA +GCAAGAGTTTTAAAAAAAGCTGTTGAAGAAATCAACCAATTTACAGTTTTAAATGCGACG +TATGAAAAAATAAAAAAAGGAAACCGAATTGGTTCGATTCAGTTCCATATTACGAAAAAA +CAAATTGCTCCTAATCCTTCTTACAAAATTGGCGATTCTGTGTATGAAGCGCAACAAGCA +GAAAAAGAACAAAATCAAATTACTTTATTTGCGCAGGCAATGCAAAGTCAATACACTACC +ATTTTGATGGAAAATATGTTGATTGGGTACAAAGATATGCAAGATATTGAATTAATGGCA +AGCTTGCAAGAAATGGTTTATCCCTTGTATGACGAGTTGAAAACTCTTAGAGGATTAGAC +GGTGTGAGAAATCACTTAGAATACGTTTCAAGAAAACAAATAGGCTATTCTAAAACTAAT +ATTGTCAAGTATTTAAAAACAGCTATCACACAATATTTGCCAACGGTAAAAATGATGGAT +ATGGATAATAGAGTGTAA +>contig00023 len=45935 cov=46.6 corr=0 origname=NODE_23_length_45935_cov_46.624847_pilon sw=shovill-spades/1.1.0 date=20230213:3630..4643:rep9b_2_prgW(EF62pC)_CP002494:100.000000 +ATGAACGATTTTCAATTTATTTCAGCTAATGAAACCTATAGAAATTTGTATTACCAATTA +CCTAAAGTACTTTTTACATCAGAATTTTATAAGACTATGTCTAATGATAGTAAAATAGCT +TACGCAATGTTGCAAGACCGATGTGAATATTCAATACAAAATAATTGGATTGATCAAGAT +GGGCATATATATTTTATCTTTACACGAAATGAACTGATGGATATTTTAGGGTGTAAAGAA +AATAAAATTGCAAAAATAAAAAAAGAATTAAAAGACAAAAATTTACTTTATGAAAAACGT +ATTCCTCCGAAAAAACTCTCTACTGGTGAATTCAAAAACTATCCAAACAGATTGTATTTA +GGTAAGCTGGAAGTTTCAGCAACAGATGTTTACGCCATCAGTAATGCTAGCTATACAAAT +GAGTTTCCCGAAAGTGGGAAAAACCAACCTTCGGATAAACATGATAAAATCGGCATTTCT +TTCGAAAGTGGGAAAAACCAACGTCCAGAAGAATCCAATAATACCAGTACTTTGTTCGAA +AGTGGGAAAAACCAACCCAATCTATATCTAACTAATTCTTTAGATACAATAGATACAATA +GATACTGAAAAAGAACGATTGCAACAACAATTATTGCTCGATCAATTTTCAGAAGTTCAA +GAGCATACATTTCTTAGCAAAAATAGCTTAAAATTTATTGCTGCCTTTTCTGATACTATT +CAAGAAGCACATGAAATGGTTGGAACAATTATTCGTGCTAAAACTAAAGTAGAAAAAGAA +TACAATATCGTTCTAATTGGTGAAGATTATCAAGAAGAAATAGACAAATGTTTGCGTCGT +GTGATGCATAAAATCAAGACAGATTCTACTGTAAAAAGTCCAAAAGGCCTATTCTACAAG +TCGTTTTACAATTTATTTGTTGAATGTACAATAGAGAAAAAAAGTCATTTAAATAAAAAT +AGTACGGACAACACCCCAGAAATAACTACACATAACTGGATTGAGTATCAATAA +>contig00048 len=5336 cov=19.5 corr=0 origname=NODE_48_length_5336_cov_19.468228_pilon sw=shovill-spades/1.1.0 date=20230213:3276..4214:rep7a_8_ORF11(pRE25)_X92945:100.000000 +ATGAAGAAAATTGATGAAAAATTAGCTGCAGAAATCTCACTAAAAAAACCGGCCGTCTCT +AATAGCCGGTTAAGTAATAGCCGGTTAAGTGGTCAAACTTTGGGAAAATCTCAACCCGCA +TTAAGTTTTGATGCCATGACAATCGTTGGAAATTTGAACAAAACTAATGCTAAAAAGCTA +TCTGACTTTATGAGTGTAGAGCCACAAATACGACTTTGGGATATACTTCAAACAAAGTTT +AAAGCTAAGGCACTTCAAGAAAAAGTTTATATCGAATATGACAAAGTAAAAGCAGATACT +TGGGATAGACGTAATATGCGTGTTGAATTTAATCCCAATAAACTCACACATGAAGAAATG +ATTTGGTTAAAACAAAATATTATCGACTACATGGAAGATGACGGTTTTACAAGATTAGAC +TTAGCTTTTGATTTTGAAGATGATTTGAGCGATTACTATGCAATGACTGATAAAGCAGTT +AAGAAAACTGTTTTTTATGGTCGTAATGGCAAGCCAGAAACAAAATATTTTGGTGTCCGT +GATAGTGATAGATTTATTAGAATTTATAATAAAAAACAAGAACGTAAAGATAACGCAGAT +GTTGAAGTTGTGTCTGAACATTTATGGCGTGTAGAAGTTGAATTAAAAAGAGATATGGTT +GATTACTGGAATGATTGTTTTAATGATTTACACATCTTGAAACCTGCGTGGGCTACTTTA +GAAAAAATTAATGAGCAAGCTATGGTTTATACTTTGTTGCATGAAGAAAGTATGTGGGGA +AAGCTAAGTAAGAATACTAAGACTAAATTTAAAAAATTGATTAGAGAAATATCTCCAATT +GATTTAACGGAATTAATGAAATCGACTTTAAAAGCGAACGAAAAACAATTGCAAAAGCAG +ATTGATTTTTGGCAACGTGAATTTAGGTTTTGGAAGTAA +>contig00040 len=12074 cov=69.2 corr=0 origname=NODE_40_length_12074_cov_69.205993_pilon sw=shovill-spades/1.1.0 date=20230213:8225..9430:repUS43_1_CDS12738(DOp1)_CP003584:100.000000 +TTGGAGGGATTTTTACTGAATGAACAAACTTGGTTACAGCATTTAAAAGAAAAACGCTTG +GCTTATGGACTATCTCAAAACCGTTTAGCTGTTGCGACTGGTATTACAAGGCAGTATCTA +AGCGATATTGAAACAGGAAAAGTCAAGCCATCAGAGGATTTACAGCAGTCCCTTTGGGAA +GCTCTGGAACGCTTCAATCCCGACGCTCCCCTTGAAATGCTGTTTGATTATGTAAGAATT +CGCTTTCCGACAACAGACGTACAGCAGGTGGTCGAAAACATCTTACAACTGAAACTGTCC +TATTTTCTTCATGAGGACTATGGTTTCTATTCTTATTCAGAGCATTATGCTTTAGGCGAC +ATATTCGTCCTTTGCTCCCATGAACTGGACAAAGGAGTTCTGGTGGAATTGAAAGGTCGT +GGGTGCAGACAATTTGAAAGCTATCTTCTGGCACAACAAAGAAGCTGGTATGAGTTCTTT +ATGGACGTTTTGGTGGCTGGCGGTGTGATGAAACGCCTTGACCTTGCCATTAACGATAAG +ACAGGGATTTTAAATATCCCTGTACTCACTGAAAAGTGCCAACAGGAAGAATGTATCTCC +GTCTTCCGCAGTTTTAAAAGCTATCGCAGTGGCGAACTGGTACGCAAAGAGGAAAAGGAA +TGTATGGGAAACACCCTCTATATCGGTTCATTACAAAGTGAAGTTTATTTCTGTATCTAT +GAAAAGGACTACGAGCAGTACAAGAAAAATGATATTCCCATTGAAGACGCAGAAGTAAAA +AACCGTTTTGAGATTCGATTGAAAAATGAGCGTGCCTATTATGCAGTCCGTGATTTACTC +GTCTATGACAATCCAGAGCATACCGCCTTTAAAATTATCAATCGGTATATCCGTTTTGTA +GATAAAGACGATTCCAAACCTCGTTCTGATTGGAAACTGAATGAAGAATGGGCTTGGTTT +ATTGGGAACAATCGTGAACGATTAAAACTAACCACAAAACCAGAGCCTTACTCCTTCCAA +AGGACGCTGAACTGGCTATCTCATCAAGTTGCCCCGACCTTAAAGGTTGCGATTAAACTT +GATGAAATCAACCAGACGCAGGTTGTAAAAGACATTCTCGACCATGCGAAACTGACAGAC +CGACACAAGCAGATTTTGAAGCAACAGTCAGTAAAAGAACAGGACGTGATAACAACAAAA +AAATAA |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/plasmidfinder/plasmidfinder_result.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmidfinder/plasmidfinder_result.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +{"plasmidfinder": {"user_input": {"filename(s)": ["/storage/scratch/piemari/60579090/plasmidfinder/10_Enterococcus_faecalis_S17_L001.fasta"], "method": "blast", "file_format": "fasta"}, "run_info": {"date": "13.02.2023", "time": "14:26:18"}, "results": {"Enterobacteriaceae": {"enterobacteriaceae": "No hit found"}, "Gram Positive": {"Inc18": "No hit found", "NT_Rep": "No hit found", "Rep1": {"contig00051 len=2083 cov=17.5 corr=0 origname=NODE_51_length_2083_cov_17.526074_pilon sw=shovill-spades/1.1.0 date=20230213:127..897:repUS12_2_repB(SAP014A)_GQ900379:88.013699": {"plasmid": "repUS12", "identity": 100.0, "HSP_length": 771, "template_length": 876, "position_in_ref": "1..771", "contig_name": "contig00051 len=2083 cov=17.5 corr=0 origname=NODE_51_length_2083_cov_17.526074_pilon sw=shovill-spades/1.1.0 date=20230213", "positions_in_contig": "127..897", "note": "repB(SAP014A)", "accession": "GQ900379", "coverage": 88.01, "hit_id": "contig00051 len=2083 cov=17.5 corr=0 origname=NODE_51_length_2083_cov_17.526074_pilon sw=shovill-spades/1.1.0 date=20230213:127..897:repUS12_2_repB(SAP014A)_GQ900379:88.013699"}}, "Rep2": "No hit found", "Rep3": {"contig00026 len=35051 cov=66.2 corr=0 origname=NODE_26_length_35051_cov_66.162954_pilon sw=shovill-spades/1.1.0 date=20230213:21156..22313:repUS40_1_repB(pE394)_KP399637:100.000000": {"plasmid": "repUS40", "identity": 100.0, "HSP_length": 1158, "template_length": 1158, "position_in_ref": "1..1158", "contig_name": "contig00026 len=35051 cov=66.2 corr=0 origname=NODE_26_length_35051_cov_66.162954_pilon sw=shovill-spades/1.1.0 date=20230213", "positions_in_contig": "21156..22313", "note": "repB(pE394)", "accession": "KP399637", "coverage": 100.0, "hit_id": "contig00026 len=35051 cov=66.2 corr=0 origname=NODE_26_length_35051_cov_66.162954_pilon sw=shovill-spades/1.1.0 date=20230213:21156..22313:repUS40_1_repB(pE394)_KP399637:100.000000"}}, "RepA_N": {"contig00023 len=45935 cov=46.6 corr=0 origname=NODE_23_length_45935_cov_46.624847_pilon sw=shovill-spades/1.1.0 date=20230213:3630..4643:rep9b_2_prgW(EF62pC)_CP002494:100.000000": {"plasmid": "rep9b", "identity": 100.0, "HSP_length": 1014, "template_length": 1014, "position_in_ref": "1..1014", "contig_name": "contig00023 len=45935 cov=46.6 corr=0 origname=NODE_23_length_45935_cov_46.624847_pilon sw=shovill-spades/1.1.0 date=20230213", "positions_in_contig": "3630..4643", "note": "prgW(EF62pC)", "accession": "CP002494", "coverage": 100.0, "hit_id": "contig00023 len=45935 cov=46.6 corr=0 origname=NODE_23_length_45935_cov_46.624847_pilon sw=shovill-spades/1.1.0 date=20230213:3630..4643:rep9b_2_prgW(EF62pC)_CP002494:100.000000"}}, "RepL": "No hit found", "Rep_trans": {"contig00040 len=12074 cov=69.2 corr=0 origname=NODE_40_length_12074_cov_69.205993_pilon sw=shovill-spades/1.1.0 date=20230213:8225..9430:repUS43_1_CDS12738(DOp1)_CP003584:100.000000": {"plasmid": "repUS43", "identity": 100.0, "HSP_length": 1206, "template_length": 1206, "position_in_ref": "1..1206", "contig_name": "contig00040 len=12074 cov=69.2 corr=0 origname=NODE_40_length_12074_cov_69.205993_pilon sw=shovill-spades/1.1.0 date=20230213", "positions_in_contig": "8225..9430", "note": "CDS12738(DOp1)", "accession": "CP003584", "coverage": 100.0, "hit_id": "contig00040 len=12074 cov=69.2 corr=0 origname=NODE_40_length_12074_cov_69.205993_pilon sw=shovill-spades/1.1.0 date=20230213:8225..9430:repUS43_1_CDS12738(DOp1)_CP003584:100.000000"}, "contig00048 len=5336 cov=19.5 corr=0 origname=NODE_48_length_5336_cov_19.468228_pilon sw=shovill-spades/1.1.0 date=20230213:3276..4214:rep7a_8_ORF11(pRE25)_X92945:100.000000": {"plasmid": "rep7a", "identity": 100.0, "HSP_length": 939, "template_length": 939, "position_in_ref": "1..939", "contig_name": "contig00048 len=5336 cov=19.5 corr=0 origname=NODE_48_length_5336_cov_19.468228_pilon sw=shovill-spades/1.1.0 date=20230213", "positions_in_contig": "3276..4214", "note": "ORF11(pRE25)", "accession": "X92945", "coverage": 100.0, "hit_id": "contig00048 len=5336 cov=19.5 corr=0 origname=NODE_48_length_5336_cov_19.468228_pilon sw=shovill-spades/1.1.0 date=20230213:3276..4214:rep7a_8_ORF11(pRE25)_X92945:100.000000"}}}}}} \ No newline at end of file |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/quast/quast_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/quast/quast_report.html Tue Apr 30 08:41:54 2024 +0000 |
| b |
| b'@@ -0,0 +1,4826 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ <meta http-equiv="Content-Type" content="text/html;charset=utf-8" >\n+\n+ <style rel="stylesheet">\n+/*!\n+ * Bootstrap v2.0.4\n+ *\n+ * Copyright 2012 Twitter, Inc\n+ * Licensed under the Apache License v2.0\n+ * http://www.apache.org/licenses/LICENSE-2.0\n+ *\n+ * Designed and built with all the love in the world @twitter by @mdo and @fat.\n+ */\n+.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";}\n+.clearfix:after{clear:both;}\n+.hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;}\n+.input-block-level{display:block;width:100%;min-height:28px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;}\n+.tooltip{position:absolute;z-index:1020;display:block;visibility:visible;padding:5px;font-size:11px;opacity:0;filter:alpha(opacity=0);}.tooltip.in{opacity:0.8;filter:alpha(opacity=80);}\n+.tooltip.top{margin-top:-2px;}\n+.tooltip.right{margin-left:2px;}\n+.tooltip.bottom{margin-top:2px;}\n+.tooltip.left{margin-left:-2px;}\n+.tooltip.top .tooltip-arrow{bottom:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-top:5px solid #000000;}\n+.tooltip.left .tooltip-arrow{top:50%;right:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;}\n+.tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-bottom:5px solid #000000;}\n+.tooltip.right .tooltip-arrow{top:50%;left:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-right:5px solid #000000;}\n+.tooltip-inner{max-width:200px;padding:3px 8px;color:#ffffff;text-align:center;text-decoration:none;background-color:#000000;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;}\n+.tooltip-arrow{position:absolute;width:0;height:0;}\n+\n+</style>\n+\n+ <style rel="stylesheet">\n+/* Main things */\n+html, body, div, span, h1, h3, h4, h5, h6, blockquote, pre,\n+em, sub, sup, dl, dt, dd, ol, ul, li,\n+fieldset, form, label,\n+table, caption, tbody, tfoot, thead,\n+article, aside, canvas, details, figure, figcaption, footer, header, hgroup,\n+menu, nav, output, section, time {\n+ margin: 0;\n+ padding: 0;\n+ border: 0;\n+ font-size: 100%;\n+ font: inherit;\n+ vertical-align: baseline;\n+}\n+body {\n+ margin: 0;\n+ font-family: Lucida Grande, Verdana, Arial, sans-serif;\n+ font-size: 12px;\n+ color: black;\n+ padding-bottom: 30px;\n+}\n+a {\n+ text-decoration: none;\n+ /*color: #0c4f72;*/\n+ color: #0077B5;\n+ border-bottom: 1px solid #487b95;\n+ border-color: #487b95; /* #487b95 */\n+ border-color: rgba(12, 79, 114, 0.2); /* #0c4f72; */ /* #a0d2eb; */ /*rgba(0, 88, cc, 0.3);*/\n+}\n+a:visited {\n+ text-decoration: none;\n+ color: #8C66B2;\n+ border-bottom: 1px solid #8c66b2;\n+ border-color: #8c66b2;\n+ border-color: rgba(102, 51, 153, 0.2);\n+}\n+a:hover {\n+ text-decoration: none;\n+ color: #b33; /* #0088cc; */\n+ border-bottom: 1px solid #ffcccc;\n+ border-color: #ffcccc;\n+ border-color: rgba(255, 0, 0, 0.2); /* #55b2e0; */ /*#005580;*/\n+}\n+a.dark_bg_link {\n+ color: white; /* #0088cc; */\n+ border-bottom: 1px solid #cccccc;\n+ border-color: #cccccc;\n+}\n+a.dark_bg_link:hover {\n+ color: white; /* #0088cc; */\n+ border-bottom: 1px solid white;\n+}\n+\n+.leading_link_dot {\n+ border-bottom: white solid 1px;\n+}\n+\n+a.header_link, a.header_link:hover, a.header_link:visited {\n+ color: black;\n+ border-bottom: 1px solid #bbb;\n+}\n+\n+\n+.dotted-link {\n+ cursor: pointer;\n+ text-decoration: none;\n+ /*color: #0c4f72;*/\n+ color: #0077B5;\n+ border-bottom: 1px dashed #487b95;\n+ border-color: #487b95; /* #487b95 */\n+ border-color: rgba(12, 79, 114, 0.2);\n+}\n+.dotted-link:hover {\n+ text-decoration: none;\n+ color: #b33 !im'..b'. This metric is computed only if a reference genome is provided.</span>",\n+ "NGAx" : "<span>plot shows the NGAx metric value as x varies from 0 to 100.</span><span>NGAx is computed similarly to NGx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken at misassembly breakpoints. NGAx is the minimum block length <b>y</b> such that using blocks of length at least <b>y</b> accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>",\n+ "GC content" : "<span>plot shows the distribution of GC percentage among the contigs, i.e., the total number of bases in contigs with such GC content. Typically, the distribution is approximately Gaussian. However, for some genomes it is not Gaussian. For assembly projects with contaminants, the GC distribution of the contaminants often differs from the reference genome and may give a superposition of multiple curves with different peaks.</span>",\n+\n+ "Duplication ratio" : "<span>is the total number of aligned bases in the assembly, divided by the total number of aligned bases in the reference (see the <b>Genome fraction (%)</b> metric). If the assembly contains many contigs that cover the same regions of the reference, its <i>Duplication ratio</i> may be much larger than 1. This may occur due to overestimating repeat multiplicities and due to small overlaps between contigs, among other reasons.</span>",\n+ "Largest alignment" : "<span>is the length of the largest continuous alignment in the assembly. This metric is always equal to the <i>Largest contig</i> metric but it can be smaller if the largest contig of the assembly contains a misassembly event.</span>",\n+ "Total aligned length" : "<span>is the total number of aligned bases in the assembly.</span>",\n+ "Avg contig read support" : "<span>is the average coverage of contigs that have large unique alignments to the reference. Read coverage is extracted from contig names (SPAdes/Velvet naming scheme only).</span>",\n+\n+ "# N\'s" : "<span>is the total number of uncalled bases (N\'s) in the assembly.</span>",\n+ "# N\'s per 100 kbp" : "<span>is the average number of uncalled bases (N\'s) per 100,000 assembly bases.</span>",\n+\n+ "# mapped" : "<span>is the number of reads that mapped to the assembly.</span>",\n+ "Mapped (%)" : "<span>is the percent of reads that mapped to the assembly.</span>",\n+ "# properly paired" : "<span>is the number of reads that mapped within expected range and orientation of each other to the assembly.</span>",\n+ "Properly paired (%)" : "<span>is the percent of reads that mapped within expected range and orientation of each other to the assembly.</span>",\n+ "# singletons" : "<span>is the number of reads which do not overlap any other reads.</span>",\n+ "Singletons (%)" : "<span>is the percent of reads which do not overlap any other reads.</span>",\n+ "# misjoint mates" : "<span>is the number of reads with mate mapped to a different contig.</span>",\n+ "Misjoint mates (%)" : "<span>is the percent of reads with mate mapped to a different contig.</span>",\n+ "Avg. coverage depth" : "<span>is the average depth of coverage.</span>",\n+ "Coverage >= 1x (%)" : "<span>is the total number of bases with at least 1x coverage, divided by the total length of the assembly.</span>",\n+\n+ "# similar correct contigs" : "<span>is the number of correct contigs similar among > 50% assemblies (see Icarus for visualization).</span>",\n+ "# similar misassembled blocks" : "<span>is the number of misassembled blocks similar among > 50% assemblies (see Icarus for visualization).</span>"\n+}\n+\n+ </div>\n+ </div>\n+</div>\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/quast/quast_result.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/quast/quast_result.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,30 @@ +Assembly 10_Enterococcus_faecalis_S17_L001 +# contigs (>= 0 bp) 100 +# contigs (>= 1000 bp) 58 +# contigs (>= 5000 bp) 48 +# contigs (>= 10000 bp) 41 +# contigs (>= 25000 bp) 28 +# contigs (>= 50000 bp) 20 +Total length (>= 0 bp) 3027634 +Total length (>= 1000 bp) 3015201 +Total length (>= 5000 bp) 2996428 +Total length (>= 10000 bp) 2944723 +Total length (>= 25000 bp) 2735277 +Total length (>= 50000 bp) 2421445 +# contigs 62 +Largest contig 436224 +Total length 3017519 +GC (%) 37.31 +N50 99915 +N90 27780 +auN 154096.4 +L50 8 +L90 28 +# total reads 3489582 +# left 1744791 +# right 1744791 +Mapped (%) 99.85 +Properly paired (%) 98.83 +Avg. coverage depth 230 +Coverage >= 1x (%) 100.0 +# N's per 100 kbp 0.00 |
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| diff -r 000000000000 -r 05c1bcba20c9 test-data/recentrifuge/rcf_data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/recentrifuge/rcf_data.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| b'@@ -0,0 +1,296 @@\n+Samples\t/storage/scratch/piemari/60579059/recentrifuge/10_Enterococcus_faecalis_S17_L001\t/storage/scratch/piemari/60579059/recentrifuge/10_Enterococcus_faecalis_S17_L001\t/storage/scratch/piemari/60579059/recentrifuge/10_Enterococcus_faecalis_S17_L001\tDetails\tDetails\n+Stats\tcount\tunassigned\tscore\tRank\tName\n+Id\t\t\t\t\t\n+1\t1705098\t8766\t23.406576938256993\tno_rank\troot\n+2\t1696077\t41771\t23.395425082794883\tsuperkingdom\tBacteria\n+1224\t656\t8\t2.5291006275765358\tphylum\tProteobacteria\n+1236\t626\t12\t2.482047572064056\tclass\tGammaproteobacteria\n+91347\t614\t1\t2.457941868298954\torder\tEnterobacterales\n+543\t613\t320\t2.460424106929107\tfamily\tEnterobacteriaceae\n+2890311\t293\t0\t3.246096990938595\tno_rank\tKlebsiella/Raoultella group\n+570\t293\t0\t3.246096990938595\tgenus\tKlebsiella\n+573\t37\t37\t0.8707595857425035\tspecies\tKlebsiella pneumoniae\n+1463165\t256\t256\t3.5894074752833425\tspecies\tKlebsiella quasipneumoniae\n+28211\t14\t3\t3.5108263106101574\tclass\tAlphaproteobacteria\n+204455\t11\t0\t3.9118522954498163\torder\tRhodobacterales\n+31989\t11\t5\t3.9118522954498163\tfamily\tRhodobacteraceae\n+2083206\t6\t0\t5.003000134822521\tgenus\tTritonibacter\n+379347\t6\t6\t5.003000134822521\tspecies\tTritonibacter mobilis\n+68525\t8\t2\t6.4392025411184886\tsubphylum\tdelta/epsilon subdivisions\n+29547\t6\t0\t6.491794757763988\tclass\tEpsilonproteobacteria\n+213849\t6\t6\t6.491794757763988\torder\tCampylobacterales\n+203691\t8\t0\t2.670556919903863\tphylum\tSpirochaetes\n+203692\t8\t0\t2.670556919903863\tclass\tSpirochaetia\n+1643686\t8\t0\t2.670556919903863\torder\tBrachyspirales\n+143786\t8\t0\t2.670556919903863\tfamily\tBrachyspiraceae\n+29521\t8\t0\t2.670556919903863\tgenus\tBrachyspira\n+52584\t8\t0\t2.670556919903863\tspecies\tBrachyspira pilosicoli\n+759914\t8\t8\t2.670556919903863\tstrain\tBrachyspira pilosicoli 95/1000\n+1783257\t9\t1\t5.666318593923775\tno_rank\tPVC group\n+204428\t8\t0\t6.1710253562749955\tphylum\tChlamydiae\n+204429\t8\t0\t6.1710253562749955\tclass\tChlamydiia\n+1963360\t8\t0\t6.1710253562749955\torder\tParachlamydiales\n+92713\t8\t0\t6.1710253562749955\tfamily\tParachlamydiaceae\n+83551\t8\t0\t6.1710253562749955\tgenus\tParachlamydia\n+83552\t8\t0\t6.1710253562749955\tspecies\tParachlamydia acanthamoebae\n+765952\t8\t8\t6.1710253562749955\tstrain\tParachlamydia acanthamoebae UV-7\n+1783270\t66\t0\t2.006752928257857\tno_rank\tFCB group\n+68336\t66\t0\t2.006752928257857\tno_rank\tBacteroidetes/Chlorobi group\n+976\t66\t0\t2.006752928257857\tphylum\tBacteroidota\n+117743\t16\t0\t4.41718651898131\tclass\tFlavobacteriia\n+200644\t16\t0\t4.41718651898131\torder\tFlavobacteriales\n+49546\t10\t10\t5.956891819839705\tfamily\tFlavobacteriaceae\n+2762318\t6\t0\t1.8510110175506516\tfamily\tWeeksellaceae\n+2782232\t6\t0\t1.8510110175506516\tno_rank\tChryseobacterium group\n+59732\t6\t6\t1.8510110175506516\tgenus\tChryseobacterium\n+200643\t50\t0\t1.2354141792263518\tclass\tBacteroidia\n+171549\t50\t0\t1.2354141792263518\torder\tBacteroidales\n+815\t50\t0\t1.2354141792263518\tfamily\tBacteroidaceae\n+816\t50\t0\t1.2354141792263518\tgenus\tBacteroides\n+817\t50\t50\t1.2354141792263518\tspecies\tBacteroides fragilis\n+1783272\t1653567\t1652\t23.34001268644121\tno_rank\tTerrabacteria group\n+1239\t1651848\t2786\t23.34408417992166\tphylum\tFirmicutes\n+91061\t1648513\t26463\t23.367281250244677\tclass\tBacilli\n+1385\t1549\t105\t1.5310126165432292\torder\tBacillales\n+90964\t933\t3\t1.6488807818855296\tfamily\tStaphylococcaceae\n+1279\t922\t364\t1.6529169672137187\tgenus\tStaphylococcus\n+1280\t172\t172\t4.134921158621555\tspecies\tStaphylococcus aureus\n+1283\t9\t9\t1.1011853849280868\tspecies\tStaphylococcus haemolyticus\n+29382\t169\t169\t0.8554142297734083\tspecies\tStaphylococcus cohnii\n+2815305\t208\t0\t0.9949576979684763\tspecies_group\tStaphylococcus intermedius group\n+283734\t208\t208\t0.9949576979684763\tspecies\tStaphylococcus pseudintermedius\n+2803850\t8\t0\t0.793093163911496\tgenus\tMammaliicoccus\n+1296\t8\t8\t0.793093163911496\tspecies\tMammaliicoccus sciuri\n+186817\t455\t134\t1.2032272261636583\tfamily\tBacillaceae\n+1386\t97\t13\t1.0549176203970638\tgenus\tBacillus\n+86661\t41\t9\t1.1850461843452467\tspecies_group\tBacillus cereus group\n+1392\t13\t13\t1.1096346346273416\tspecies\tBacillus anthracis\n+1396\t8\t8\t1.0777632709036333\tspecies\tBac'..b'47787\tfamily\tMethanobacteriaceae\n+2172\t7\t1\t2.6483733912147787\tgenus\tMethanobrevibacter\n+83816\t6\t0\t2.9956069978485034\tspecies\tMethanobrevibacter ruminantium\n+634498\t6\t6\t2.9956069978485034\tstrain\tMethanobrevibacter ruminantium M1\n+1783275\t24\t2\t4.701969383935966\tno_rank\tTACK group\n+651137\t22\t0\t4.833030004650398\tphylum\tThaumarchaeota\n+31932\t22\t0\t4.833030004650398\torder\tNitrosopumilales\n+338190\t22\t0\t4.833030004650398\tfamily\tNitrosopumilaceae\n+338191\t22\t0\t4.833030004650398\tgenus\tNitrosopumilus\n+1580092\t22\t22\t4.833030004650398\tspecies\tNitrosopumilus adriaticus\n+2759\t158\t0\t3.7577410515006657\tsuperkingdom\tEukaryota\n+33154\t158\t0\t3.7577410515006657\tno_rank\tOpisthokonta\n+4751\t25\t0\t1.1301603777565976\tkingdom\tFungi\n+451864\t25\t0\t1.1301603777565976\tsubkingdom\tDikarya\n+4890\t25\t0\t1.1301603777565976\tphylum\tAscomycota\n+716545\t25\t0\t1.1301603777565976\tno_rank\tsaccharomyceta\n+147537\t25\t0\t1.1301603777565976\tsubphylum\tSaccharomycotina\n+4891\t25\t0\t1.1301603777565976\tclass\tSaccharomycetes\n+4892\t25\t0\t1.1301603777565976\torder\tSaccharomycetales\n+115784\t10\t0\t1.3132361338061045\tfamily\tPhaffomycetaceae\n+460517\t10\t0\t1.3132361338061045\tgenus\tKomagataella\n+460519\t10\t0\t1.3132361338061045\tspecies\tKomagataella phaffii\n+644223\t10\t10\t1.3132361338061045\tstrain\tKomagataella phaffii GS115\n+2916678\t15\t0\t1.008109873723593\tno_rank\tCUG-Ser1 clade\n+766764\t15\t0\t1.008109873723593\tfamily\tDebaryomycetaceae\n+1535325\t15\t0\t1.008109873723593\tno_rank\tCandida/Lodderomyces clade\n+5475\t15\t0\t1.008109873723593\tgenus\tCandida\n+42374\t15\t0\t1.008109873723593\tspecies\tCandida dubliniensis\n+573826\t15\t15\t1.008109873723593\tstrain\tCandida dubliniensis CD36\n+33208\t133\t0\t4.251647193181881\tkingdom\tMetazoa\n+6072\t133\t0\t4.251647193181881\tno_rank\tEumetazoa\n+33213\t133\t0\t4.251647193181881\tno_rank\tBilateria\n+33511\t133\t0\t4.251647193181881\tno_rank\tDeuterostomia\n+7711\t133\t0\t4.251647193181881\tphylum\tChordata\n+89593\t133\t0\t4.251647193181881\tsubphylum\tCraniata\n+7742\t133\t0\t4.251647193181881\tno_rank\tVertebrata\n+7776\t133\t0\t4.251647193181881\tno_rank\tGnathostomata\n+117570\t133\t0\t4.251647193181881\tno_rank\tTeleostomi\n+117571\t133\t0\t4.251647193181881\tno_rank\tEuteleostomi\n+8287\t133\t0\t4.251647193181881\tsuperclass\tSarcopterygii\n+1338369\t133\t0\t4.251647193181881\tno_rank\tDipnotetrapodomorpha\n+32523\t133\t0\t4.251647193181881\tno_rank\tTetrapoda\n+32524\t133\t0\t4.251647193181881\tno_rank\tAmniota\n+40674\t133\t0\t4.251647193181881\tclass\tMammalia\n+32525\t133\t0\t4.251647193181881\tno_rank\tTheria\n+9347\t133\t0\t4.251647193181881\tno_rank\tEutheria\n+1437010\t133\t0\t4.251647193181881\tno_rank\tBoreoeutheria\n+314146\t133\t0\t4.251647193181881\tsuperorder\tEuarchontoglires\n+9443\t133\t0\t4.251647193181881\torder\tPrimates\n+376913\t133\t0\t4.251647193181881\tsuborder\tHaplorrhini\n+314293\t133\t0\t4.251647193181881\tinfraorder\tSimiiformes\n+9526\t133\t0\t4.251647193181881\tparvorder\tCatarrhini\n+314295\t133\t0\t4.251647193181881\tsuperfamily\tHominoidea\n+9604\t133\t0\t4.251647193181881\tfamily\tHominidae\n+207598\t133\t0\t4.251647193181881\tsubfamily\tHomininae\n+9605\t133\t0\t4.251647193181881\tgenus\tHomo\n+9606\t133\t133\t4.251647193181881\tspecies\tHomo sapiens\n+10239\t66\t0\t4.761562706518553\tsuperkingdom\tViruses\n+2731341\t41\t0\t4.775296347886017\tno_rank\tDuplodnaviria\n+2731360\t41\t0\t4.775296347886017\tkingdom\tHeunggongvirae\n+2731618\t41\t0\t4.775296347886017\tphylum\tUroviricota\n+2731619\t41\t0\t4.775296347886017\tclass\tCaudoviricetes\n+10699\t41\t0\t4.775296347886017\tfamily\tSiphoviridae\n+196894\t41\t0\t4.775296347886017\tno_rank\tunclassified Siphoviridae\n+1747326\t41\t41\t4.775296347886017\tspecies\tEnterococcus phage vB_EfaS_IME197\n+2732004\t25\t0\t4.7390395346759115\tno_rank\tVaridnaviria\n+2732005\t25\t0\t4.7390395346759115\tkingdom\tBamfordvirae\n+2732007\t25\t0\t4.7390395346759115\tphylum\tNucleocytoviricota\n+2732523\t25\t0\t4.7390395346759115\tclass\tMegaviricetes\n+2732554\t25\t0\t4.7390395346759115\torder\tImitervirales\n+549779\t25\t0\t4.7390395346759115\tfamily\tMimiviridae\n+985780\t25\t0\t4.7390395346759115\tno_rank\tunclassified Mimiviridae\n+985782\t25\t0\t4.7390395346759115\tspecies\tMoumouvirus\n+1269028\t25\t25\t4.7390395346759115\tno_rank\tAcanthamoeba polyphaga moumouvirus\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/recentrifuge/rcf_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/recentrifuge/rcf_report.html Tue Apr 30 08:41:54 2024 +0000 |
| b |
| b'@@ -0,0 +1,6581 @@\n+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\n+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta charset="utf-8"><link rel="shortcut icon" 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href="2509511">2509511</val></tid><rank><val>subgenus</val></rank><score><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>24.2</val><val>0</val><val>0</val><val>0</val><val>0</val></score><node name="Severe acute respiratory syndrome-related coronavirus" href="https://www.google.com/search?q=Severe acute respiratory syndrome-related coronavirus"><count><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val>16</val><val></val><val></val><val></val><val></val></count><unassigned><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val></unassigned><tid><val href="694009">694009</val></tid><rank><val>species</val></rank><score><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>24.2</val><val>0</val><val>0</val><val>0</val><val>0</val></score><node name="Severe acute respiratory syndrome coronavirus 2" href="https://www.google.com/search?q=Severe acute respiratory syndrome coronavirus 2"><count><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val>16</val><val></val><val></val><val></val><val></val></count><unassigned><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val>16</val><val></val><val></val><val></val><val></val></unassigned><tid><val href="2697049">2697049</val></tid><rank><val>no_rank</val></rank><score><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>24.2</val><val>0</val><val>0</val><val>0</val><val>0</val></score></node></node></node></node></node></node></node></node></node></node></node></node></node></node></krona></div></body></html>\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/recentrifuge/rcf_stat.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/recentrifuge/rcf_stat.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,16 @@ + /storage/scratch/piemari/60579059/recentrifuge/10_Enterococcus_faecalis_S17_L001 +Seqs. read 1720128.0 +Seqs. unclass. 15028.0 +Seqs. class. 1705100.0 +Seqs. filtered 1705100.0 +Score min 35.0 +Score mean 111.25451527769633 +Score max 295.0 +Length min 70.0 +Length mean 403.0 +Length max 602.0 +Total nt read 690189277.0 +TIDs class. 426.0 +TIDs filtered 425.0 +TIDs folded 166.0 +Score limit |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/refseqmasher/refsesqmasher.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refseqmasher/refsesqmasher.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,6 @@ +sample top_taxonomy_name distance pvalue matching full_taxonomy taxonomic_species taxonomic_genus taxonomic_family taxonomic_order taxonomic_class taxonomic_phylum taxonomic_superkingdom subspecies serovar plasmid bioproject biosample taxid assembly_accession match_id +10_Enterococcus_faecalis_S17_L001 Enterococcus faecalis EnGen0295 0.00802142 0.0 314/400 Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; EnGen0295 Enterococcus faecalis Enterococcus Enterococcaceae Lactobacillales Bacilli Firmicutes Bacteria PRJNA224116 SAMN00809230 1158669 GCF_000395135.1 ./rcn/refseq-NZ-1158669-PRJNA224116-SAMN00809230-GCF_000395135.1-.-Enterococcus_faecalis_EnGen0295.fna +10_Enterococcus_faecalis_S17_L001 Enterococcus faecalis EnGen0425 0.00869982 0.0 308/400 Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; EnGen0425 Enterococcus faecalis Enterococcus Enterococcaceae Lactobacillales Bacilli Firmicutes Bacteria PRJNA224116 SAMN02333901 1391495 GCF_000519925.1 ./rcn/refseq-NZ-1391495-PRJNA224116-SAMN02333901-GCF_000519925.1-.-Enterococcus_faecalis_EnGen0425.fna +10_Enterococcus_faecalis_S17_L001 Enterococcus faecalis ATCC 4200 0.00916272 0.0 304/400 Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; ATCC 4200 Enterococcus faecalis Enterococcus Enterococcaceae Lactobacillales Bacilli Firmicutes Bacteria PRJNA224116 SAMN02595252 565642 GCF_000157195.1 ./rcn/refseq-NZ-565642-PRJNA224116-SAMN02595252-GCF_000157195.1-.-Enterococcus_faecalis_ATCC_4200.fna +10_Enterococcus_faecalis_S17_L001 Enterococcus faecalis ATCC 29212 0.00975375 0.0 299/400 Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; ATCC 29212 Enterococcus faecalis Enterococcus Enterococcaceae Lactobacillales Bacilli Firmicutes Bacteria PRJNA224116 SAMN02870637 1201292 GCF_000742975.1 ./rcn/refseq-NZ-1201292-PRJNA224116-SAMN02870637-GCF_000742975.1-.-Enterococcus_faecalis_ATCC_29212.fna +10_Enterococcus_faecalis_S17_L001 Enterococcus faecalis EnGen0417 0.0101152 0.0 296/400 Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; EnGen0417 Enterococcus faecalis Enterococcus Enterococcaceae Lactobacillales Bacilli Firmicutes Bacteria PRJNA224116 SAMN02333893 1391487 GCF_000519765.1 ./rcn/refseq-NZ-1391487-PRJNA224116-SAMN02333893-GCF_000519765.1-.-Enterococcus_faecalis_EnGen0417.fna |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/shovill/alignment.bam |
| b |
| Binary file test-data/shovill/alignment.bam has changed |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/shovill/contigs.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shovill/contigs.fa Tue Apr 30 08:41:54 2024 +0000 |
| b |
| b'@@ -0,0 +1,16825 @@\n+>contig00001 len=436224 cov=31.3 corr=0 origname=NODE_1_length_436224_cov_31.255918_pilon sw=shovill-spades/1.1.0 date=20220302\n+CTTTCTATCTTAGATTTTTGGTCGTACTTAAATTTTACTAGATAGACGACATGTTTTATA\n+TTTAAATAAACTAAAAAAGGACTGATGAATCAAAATTTGATTCATCAGTCCTTTAAATTA\n+TAGAGCCGTTAAAGACAGCCACAGCACGTGGCTGTCTTTTTTATTTTTTGTTATTTTTTC\n+ATTCTATTAAAATACCTGAGAAGTTTTCTTTTTTCTTAAGCTTGATTATGATAGAATGAT\n+TGGGTAGTTTATTTAGAAAACGTATATTACAGATAGGTGAGAATATAAATGAAAAAAATC\n+GTAATCAATGGGAATCGTCCATTAAAGGGCGAAGTAACCATTAGCGGCGCCAAAAATAGT\n+GTGGTCGCTTTAATTCCAGCTGCTATTTTAGCAGATTCGCCCGTGACTTTAGATGGCGTT\n+CCTGACATTCAGGATGTTCACTCATTAATTGAAATATTAGAAATTATGGGTGCTAAAATT\n+ACTTTTGAAAATAATACATTAATTATTGACCCAACAGAAGTTGTTTCTGTGCCTATGCCA\n+AAAGGAAAAATCAATAGCTTACGTGCATCCTATTATTTTATGGGCTCACTTCTTGGTCGA\n+TTTGGGGAAGGCGTTGTCGGCTTACCTGGCGGTTGTTACTTAGGACCTCGTCCAATTGAT\n+TTACATATCAAAGGATTTGAAGCATTAGGCGCTCATGTAACCAACGAACATGGGGCGATG\n+TACTTGAGAACAGACGAAGCTGGCTTACAAGGAACACGAATTTTTATGGATATGGTATCT\n+ATTGGCGCTACAATCAATGTCATGTTAGCCGCAGTTAAAGCCAAAGGCAAAACGATTATT\n+GAAAATGCTGCGCGTGAGCCAGAAATCATTGATATTGCTACATTATTAAATAACATGGGT\n+GCAAAAGTTCGAGGAGCTGGAACGGACGTTATTCGGATTGAAGGTGTCGAAGAATTACAT\n+GGCTGTCGTCACTCGATTATTCCAGATCGAATTGAAGCTGGGACTTATTTAGCTATGGCA\n+GCAGCTATGGGTGAAGGAATCAAGGTTCGAAATGTTATTTATGAGCATTTAGAAAGCTTC\n+ATTGCGAAATTGCAAGAAATGGGCGTTAAGATGACAATTGAAGAAGACATGATTGAAGTT\n+CATCCGTCACATGATCTGAAAATGACGACGGTGAAAACCTATCCGTATCCTGGTTTTGCC\n+ACAGACTTGCAACAACCGTTAACGCCATTACTTTTAAAAGCACAAGGAACTGGTGAAATT\n+ATTGATACGATTTATGCTCAACGAAATAAGCATATCCCTGAGTTGGTGCGGATGGGGGCT\n+GATGCTTCGGTTGAAGGCAATATGATTATCTTAAATGGCCCAAATCAATTGCACGGTGCA\n+GAAGTAGTCGCCTCTGATTTACGGGCAGGCGCTTGCCTAGTCACTGCCGGCTTGATGGCT\n+GAAGGTACGACCACTATTTATAATGTAGAATATATTTTACGTGGGTACGACCACATTATC\n+GAAAAGTTAACTGCTTTAGGCGCTGATATTCAAATGCTAGAAACCGAAGAACAAGAAGGT\n+CCGTTTGAGGTGGATCAATGAGCGACTATTTAACAATGGCTGAATTGGAAAACAGTACGT\n+TAAAAGATATTTATGCATACGCGAAAGAGTTTAAAATTCCTTATTATAGCCAAATGAACA\n+AAAAAGAATTGTCTTTAGCTGTGATTCGTGCACAAGCTGAGAAGCAAGGGTTTTTCTTCA\n+TGGAAGGAATTTTAGATATTGTTTCTCAGGATGGTTATGGTTTTTTGCGACCAATTAATT\n+ATGGACCAAGTGCAGAAGACATTTATATTTCTTCTTCTCAAATTCGTCGTTTCGGATTGA\n+GAAATGGGGACAAAGTAGCTGGCAAGGCGCGTCCGCCAAAGGAATCAGAACGTTACTATG\n+GACTCATGCATGTTGAAAGTGTCAATGGGAAAGATCCTGAAGAAGCGAAAGAGCGGCCAC\n+ATTTTCCAGCGCTAACACCGTTGTATCCTGAAAAACAATTAACGTTAGAAACAACGGCTG\n+GCAGATTATCAACACGAATGATTGATGTATTTGCCCCAATTGGTTTTGGGCAACGTGGTT\n+TAATTGTAGCGCCGCCAAAAGCGGGGAAAACAAGTGTTTTAAAGGAAATTGCTAATGGGA\n+TTACAGAAAATCATCCTGATGTGGAATTGATTCTGTTGTTAATTGACGAGCGTCCTGAAG\n+AAGTGACTGATTTAGAGCGAAGTGTTAAAGGCGATGTGGTTTCTTCAACTTTTGATCAAC\n+AACCACAAAATCATACGCGAGTTGCTGAATTGGTTCTGGATCGAGCAATGCGCTTAGTTG\n+AAGACAAACGGGACGTAGTTATTTTAATGGACAGCATCACTCGTTTAGCAAGGGCCTATA\n+ATTTAGTGGTCCCGCCTAGTGGTCGAACCTTAAGTGGTGGAATAGATCCAGCTGCGTTTT\n+TCAAACCTAAACGATTTTTTGGTGCTGCCAGAAATATCGAAGAAGGGGGCAGTCTGACTA\n+TTTTAGCCACGGCATTGGTGGATACAGGTAGCCGAATGGATGATGTCATCTATGAAGAAT\n+TCAAAGGCACAGGCAACATGGAGCTCCATTTATCTCGTGAATTAGCAGAGCGCCGTATTT\n+TCCCAGCAATTGATATTAAAAAATCAAGTACGCGAAAAGAAGAGTTGCTAATGACACCAG\n+AACAACTAGAAGAAACGTGGAAATTGAGAAATAATATGTCAGGAGACTCGCTGGAATATA\n+CGGATCAATTCATAAAAATGTTGAAACGGACCCAAAATAATCAACAATTATTTGAAGTTT\n+TCCATGATGTTTCGTTTGGCAAACAAATTAAAAGAAATCCAAAAAGATAATTGCATACCA\n+ACTGAAAACATGGTAAGATAGCATTGTTGTATACCGACAAAATAACTCTGATACAGCAAA\n+TGGATCAGGGCAAAGGAGCGAAAAAACGTATGAAACAAGATATCCATCCAAATTACCAAC\n+CAGTAGTATTCATGGATTCAACAACAGGTTTCAAATTCCTTTCAGGTTCAACTAAAGGAT\n+CTTCAGAAACTGTTGAATGGGAAGATGGCAACACTTATCCATTATTACGTGTTGAGGTTA\n+CTTCAGACTCACACCCATTCTACACTGGTCGTCAAAAATTCACACAAGCCGACGGACGTG\n+TGGACCGTTTCAACAAAAAATACGGTCTCAAAGACGAAAACGCAAATCCAGACGCATAGT\n+CTTTCAAAACATTGTTATGACAAGGTTTATAGAGGTTTTCCACTGTGGTGGGAAACCTCT\n+TTTTTGCGTTAAATATGTAGTTTTAATTCAGAGAAAAGAAATAAAGCAACTTACCAATCT\n+TTTCCTCTTTCTTTTCAAGATTATCCTTCCCAAAAGTCAAAGATTGATCAGCATTGTTTC\n+GCTGATTTGTTAGACTAGTAGGTACATTCAGCTTTATAAAGGAGATCTTGAAGAAATGAG\n+TAGAAAAAAAGTCGGTGTTTTCTGTCTATTTCTGTTTTTCACATTTTTTATTATTGTTCC\n+AAAAGTAGAAGCTACAGAAGAAATGAAGACTAAATTTACAGTAACGCCTGTTTTACCAGA\n+AAATCAAGTGTCAGGAACATCTAGTTATTATGATTTAATTCTGGCACCAAAGCAATCTTC\n+CACTATTGTCTTAGACATAAAAAATAAGACAGACGAAAAATTGTCCATTGTATTGACTCT\n+AGCAA'..b'CA\n+GTGGTTAATTGTTTTTCTGCGTTTTGCAGATTTGTTTGAAGAGTGGTAGCCTCTGTCGTG\n+GTTTCACTGTTCGTTTCCAGTTGCTCTTCCAATTCAAAAATTTCATGTTCCTTTTGATTT\n+AGTGTTTCAAGTAATGCCTGATTTTTTTCTTCTAATGCTTGTTTTTCCGTTTCTTGTTGG\n+TTCTTTAATTGCTCATTTTCTTCTTGAAGTTTTTTAAAGGCTGTTTCTTTTTTCTGATAG\n+TAGGCGAGCCTTTCTCTTAACGTCGCCATTTCTTTTTCCTGTTGTTCCGGTTTGATTCCG\n+CTAATTATTTTTTCTGGTTCGAATCCTGGCTGAAAAAAGACTTCTTTTTCAAGCGTATCA\n+TCCGAAATATCTTTAATTTTTTTGATTAAACGTCTTTTTGTCATATATATGTCCTTTCTC\n+TCGTCCTTTTAACTAATCACGACAGGCTCCAAATTTGTTTCAAGCGTCTCACGAGCATAC\n+GTATCAATGGATTTGACAAGGGTTTGCTCTTGATCTCGATAAGTAAAATTAAAATCAATC\n+ATGGTAATTTCTTTAACTGAATTCAACGCTGCAATAAGTGCTACAATATTGTCTTGGCCT\n+GTTTGAAATTCATGGTAACTTAAGCCAACTGAAAAAACAGACAGTGTCAAGGTTTGTGTT\n+TTTTCACTTCTAATCATTGTGATACTCGTCTCTCCGAGGTAAGGACGCCATTCACGCGCT\n+AATTGTAATTCATAATTAGTCAAGACAGCGGCCGATTCTGCCGAAACAGCTTGCTTCCAG\n+GGAAACTGATTTAAGGCTGTTTTTTTAATCGCTTGTTTTTTTATTTTGTCACCTTGAGTA\n+GCTTGGCCTTGTGCCAAACGCTCAATCCGTTGTTCCATGCGGATATTTCGTTGATTTAAT\n+TGATAATATGTATAAACAATTCCTAACAATAATACGCTAAGTAGACAAACACTAAACAAT\n+AAATAAATCATTAAACGACTATTTTTCTGATACTTATAGAAATTTATTTTCCTCTTTAAT\n+GTCCGGTCCTCTGAATCCAGTTTTTCGACAAGTAATCGCAAATACAATTGATAGCTTACA\n+AATAAAAATAAGCAACTACTCATTAAAAGTACAACAATCATCATACAAATATAATCTCCT\n+TTATGTCATCGCTCGACAATCAAAACTTGTAAAATCACCTGTTACGCTCTTTAAAAACTC\n+TATATAGTATTGATTGTAACATTCCGTTTGAGCCTTGCCAACAACTTTATTTAAAATACA\n+ATGATAAAATTTTATATTTTATATTTATATTTTAATTTTTAAAATATAAAACAAAAAAAG\n+AGAGATGCCACTTGGCCATCTCTCTCGCTTTTACTCAAACTATGTTTAGCGAACCGTACT\n+AGATCAGTCGCTTTTAAAAAAATCCAATTAGTCTTTGTTGATTTCATAGTAGCTATCGTT\n+CTTTATGTAGCTGAATTTGCTTTTGCTGGGGCTGAATCGCTACTAAGTCCAACACTGATG\n+CCTAAGGCACGATCAACTTCTTCCATAATATCAAGTCTCAAATGACAAACTTTTTCTTTC\n+AAGCGACCCTTATCGATTGTTCGAATCTGCTCTAAAAGAATCACTGAATCTTTTTCAATG\n+CCTGTTTCATCAGAATTAATCCCGATATGTGTTGGCAATTTTGGCTTTGCCATTTTGGCT\n+GTGATCGCCGCAACGATAATCGTTGGGCTAAAATGATTACCTAAGTTATTTTGGACAACA\n+AGGACAGGTCTGACGCCACCTTGTTCCGAGCCCACTACTGGGGAAAGGTCTGCAAAATAA\n+ATATCTCCGCGTTTGACCATAGTGGAACCTCCTATCTAGTTATATTCTCTGGGGATTCTT\n+TGTGAGAAAGTACATGCAACTTCATAATGAATGGTTTCTAATTTTTCGGCTACCATTTGT\n+AACGTATTTTCTTCATTGCCATCTTTTCCAACTAATGTAACGACTGAGCCGACAGGAACT\n+TCTTCTGCTAAACGAATCATACATTGATCCATACACACTCGTCCGACGATTTCGCAACGC\n+TTACCATTCACGAGCACTGTAAATCCTTGGAGATGACGCAACCAGCCATCTGCATAGCCG\n+ATTGGCACTGTCCCAATCCATTCTTCAGCTTCAGTTACGTAGGTTTCGCCATAGCCAATC\n+CCTTCACCAGCCGCTAAGCGTTTTACATGGATAAGTTCACTGGTCAACCGTAAGGCCGGC\n+TTTAACGCATAGCTTGGGGCAAGCTTATTACCTGAAGGGTTCAATCCATACATGGCTACT\n+CCATAGCGAATCATGTTTCCTGGCACATCAGGATGCCATAACGCTGTCGCACTATTGCTA\n+ACATGGACATACCGTGGTAACTCTTCTAAAACTGCTAGAACAGCCTTAAAACGCCCTGCT\n+TGTTTTTCAAAATAGCTTGTATCGATTTCATCAGCTGTTGAAAAATGAGTAAAAATCCCT\n+TCCCATAAAAATTCTTTGTGGGATTGAACAAACCGCACTGCTTGCTTAGTCTCTTCCGGG\n+GTTAAAAAGCCAATCCGTCCCATGCCAGTATCGACTTTTAAGTGAACACGTAATGGCGTG\n+TTACTCTCAGGCGTTAGTTGTTGAAGAGCAGCTTCTAACCATTCTTGTGTAGCTACCGTT\n+ACAGACAAATCATATTGAATCAACAAAGGCACATAAGCTAAGTCTACCACACTCAAAATT\n+AAAATGGGGTCCTGAACACCTGCTTCTCTCAATTCAATTGCTTCATCCAATAAGGCGACA\n+CAAAAACCTGTCGCGCCACCTTTTTTCGCCGCTTTAGCGGATTCTACGGCGCCATGCCCA\n+TAGCCGTTCGCTTTCACAACCGCAAATAAAGCAGTTCCTTCTGGCAAACGTTGACATTCC\n+TTTTGGACATTTTCAGTAATTGCTTGCGTATCGATATGTAACCGTGTAGGACGATGCCAT\n+CCAACGACCATTGTACATCCTTCTTTCTTCGTTGCTTCTGTTATTCGCTTTCTAAAACAA\n+TTTGTGCAATCGCCATAGTATCTGTGTGCGTAATTGAGACAAACACTTTACCATTATGGG\n+GCGAGTTTGCTACGTATGGTGCACCTGTTTTTTCAGTCAGCACCTCAATATCTTGTAAAC\n+CAACTTTACCAATCCCTGTGCCCCATGCTTTAGAAAACGCTTCTTTACAAGCAAAACGAC\n+CAGCTAAAAATTCTATTTGACGTTTTGTAGATAACTTTTCAAAAAGGGTCAATTCGTTAG\n+GTGTTAAAACCCGTTGAATAAACGATCCTTGTTTTTCAACAATCGGTTTTATCCGACTTA\n+ATTCTACTGCGTCAATACCAATTCCCTTTATCATTTTCCGCCTTACTTCCTATTTAATAT\n+AGTTACTCCGAATTACCTTTCATTTTAACAAAATTTCAAAATTTTTCCACTGATTCGCTA\n+AAAAAATAAAGAATGTTTTACAAGATCCTCACACAAATTGAAGTACCATACGTTTTCTTC\n+CTATTTACATTTTTATAAAATTTTTCTGAATTTTTATAAAACGCGAATTGTAAAATTAAG\n+TTAGAAAAATAAAAAGGCATTTATGGTACACTCAAATTGTATTTCCGACGAAAGAAAACA\n+AAGGAGTGTAACCATAAATGACCTACAAACATCTTACCATAGACGAACTGACAATGATAG\n+AATCATATTATCTTCAACATAATAAACCGGTTGAAATCGCTAACCGAATGGGTCGTGCTA\n+TACAAACTATTTATAATGTAGTCAATAAGTTCAAGCAAGGCAAGACTGCTCTTGATTATT\n+GGCACCAGTATAAAGAAAATAAGAAAAAATGTGGTAGAAAAGTCATTCAATTACCTGCTC\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/shovill/contigs.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shovill/contigs.gfa Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +S 141 AAGAAGTAAAAAAGGGCTCTTTTCCAATCAAACGTGCGATTGACTTGGTATTAAGTATCGTTTTATTATTTTTAACATTTCCGATTATGTTCATATTCGCCATTGCTATCGTCATAGATTCGCCAGGAAACCCTATTTATAGTCAGGTTAGAGTTGGGAAGATGGGTAAATTAATTAAAATATACAAATTACGTTCGATGTGTAAAAACGCAGAGAAAAACGGTGCGCAATGGGCTGATAAAGATGATGATCGTATAACAAATGTCGGGAAGTTTATTCGTAAAACACGCATTGATGAATTACCACAACTAATTAATGTTGTTAAAGGGGAAATGAGTTTTATTGGACCACGCCCGGAACGTCCAGAATTTGTAGAATTATTTAGTTCAGAAATAATAGGATTTGAGCAAAGATGTCTTGTTACACCAGGATTAACAGGTCTTGCGCAAATTCAAGGTGGATATGACTTAACACCACAACAAAAATTAAAATATGACATGAAATATATACATAAAGGTAGCTTAATGATGGAATTATATATATCAATTAGAACATTGATGGTTGTTATTACAGGGGAAGGCTCAAGGTAGTCTTAATTTGCTTAATAAGTTTAAATAAAAGTTACATTTTAAAGATTGTGACCAATTGTTACAGTATAACGAGGAATCCCTTGAGACAGTATCAAATGGCATTAAGAAATATTTGCCATCATTGATTTGCATGGCTATAAATACTATTCATCTGATGAGATAGCCATGTTAAGAAATTGAAAGTATAGCATTAAAGGGGTTTGTAACAGTTGAAAATTATATATTGTATTACTAAAGCAGATAATGGTGGTGCACAAACACATCTCATTCAACTCGCTAACCATTTTTGCGTACACCATGATGTTTATGTCATTGTAGGCAATCATGGACCAATGATTGAACAACTAGATGCAAGAGTCAATGTAATTATTATCGAACATTTAGTAGGTCCAATTGACTTTAAACAAGATATTTTAGCTGTCAAAGTGTTAGCACAGTTATTCTCGAAAATTAAACCTGATGTTATCCATCTACATTCTTCCAAAGCTGGAACGGTCGGACGAATTGCGAAGTTCATTTCGAAATCGAAAGACACACGTGTAGTTTTTACTGCGCATGGATGGGCTTTTACAGAGGGTGTTAAACCAGCTAAAAAATTTCTATATCTAGTTATTGAAAAATTAATGTCACGTATTACAGATAGCATTATTTGTGTTTCAGATT DP:f:36.5639 KC:i:41756 +P NODE_1_length_1253_cov_36.563923_1 141+ * |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/staramr/mlst.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/staramr/mlst.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Isolate ID Scheme Sequence Type Locus 1 Locus 2 Locus 3 Locus 4 Locus 5 Locus 6 Locus 7 +10_Enterococcus_faecalis_S17_L001 efaecalis 768 gdh(27) gyd(29) pstS(11) gki(21) aroE(4) xpt(2) yqiL(1) |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/staramr/plasmidfinder.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/staramr/plasmidfinder.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,6 @@ +Isolate ID Plasmid %Identity %Overlap HSP Length/Total Length Contig Start End Accession +10_Enterococcus_faecalis_S17_L001 rep7a 100.00 100.00 939/939 contig00048 3276 4214 X92945 +10_Enterococcus_faecalis_S17_L001 rep9b 100.00 100.00 1014/1014 contig00023 3630 4643 CP002494 +10_Enterococcus_faecalis_S17_L001 repUS12 99.75 99.62 792/795 contig00051 918 127 AF181950 +10_Enterococcus_faecalis_S17_L001 repUS40 100.00 100.00 1158/1158 contig00026 21156 22313 KP399637 +10_Enterococcus_faecalis_S17_L001 repUS43 100.00 100.00 1206/1206 contig00040 9430 8225 CP003584 |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/staramr/pointfinder.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/staramr/pointfinder.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Isolate ID Gene Predicted Phenotype Type Position Mutation %Identity %Overlap HSP Length/Total Length Contig Start End +SRR1952908 gyrA (S83Y) ciprofloxacin I/R, nalidixic acid codon 83 TCC -> TAC (S -> Y) 99.96 100.00 2637/2637 contig00008 22801 20165 |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/staramr/resfinder.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/staramr/resfinder.tsv Tue Apr 30 08:41:54 2024 +0000 |
| b |
| b"@@ -0,0 +1,11 @@\n+Isolate ID\tGene\tPredicted Phenotype\t%Identity\t%Overlap\tHSP Length/Total Length\tContig\tStart\tEnd\tAccession\tSequence\n+10_Enterococcus_faecalis_S17_L001\tant(6)-Ia\tstreptomycin\t100.00\t100.00\t909/909\tcontig00046\t4769\t3861\tAF330699\tATGAGATCAGAAAAAGAAATGATGGATTTAGTACTTTCTTTAGCAGAACAGGATGAACGTATTCGAATTGTGACCCTTGAGGGGTCACGCGCAAATATTAATATACCTAAAGATGAATTTCAGGATTATGATATTACATATTTTGTAAGTGATATAGAACCGTTTATATCTAATGATGACTGGCTTAATCAATTTGGGAATATAATAATGATGCAAAAGCCGGAGGATATGGAATTATTCCCACCTGAAGAAAAGGGATTTTCCTATCTTATGCTATTTGATGATTACAATAAAATTGATCTTACCTTATTGCCCTTGGAAGAGTTAGATAATTACCTAAAGGGCGATAAATTAATAAAGGTTCTAATTGATAAAGATTGTAGAATTAAAAGGGACATAGTTCCGACTGATATAGATTATCATGTAAGAAAGCCAAGCGCAAGGGAGTATGATGATTGCTGCAATGAATTTTGGAATGTAACACCTTATGTTATTAAAGGATTGTGCCGTAAGGAAATTTTATTTGCTATTGATCATTTTAATCAGATTGTTCGCCATGAGCTGCTGAGAATGATATCATGGAAGGTCGGCATCGAAACAGGCTTTAAATTAAGTGTAGGCAAGAACTATAAGTTTATTGAAAGGTATATATCCGAGGATTTGTGGGAGAAACTTTTGTCCACCTACCGGATGGATTCCTATGAAAACATATGGGAAGCATTATTTCTATGCCATCAATTGTTCAGGGCGGTATCCGGTGAGGTGGCGGAAAGGCTTCATTATGCCTATCCGGAGTATGATAGGAATATAACAAAATATACCAGGGACATGTATAAAAAATACACTGGTAAAACCGGCTGCCTGGATAGCACATATGCCGCTGATATAGAAGAGAGGCGGGAACAGTGA\n+10_Enterococcus_faecalis_S17_L001\taph(3')-III\tkanamycin, amikacin\t100.00\t100.00\t795/795\tcontig00046\t3229\t2435\tM26832\tATGGCTAAAATGAGAATATCACCGGAATTGAAAAAACTGATCGAAAAATACCGCTGCGTAAAAGATACGGAAGGAATGTCTCCTGCTAAGGTATATAAGCTGGTGGGAGAAAATGAAAACCTATATTTAAAAATGACGGACAGCCGGTATAAAGGGACCACCTATGATGTGGAACGGGAAAAGGACATGATGCTATGGCTGGAAGGAAAGCTGCCTGTTCCAAAGGTCCTGCACTTTGAACGGCATGATGGCTGGAGCAATCTGCTCATGAGTGAGGCCGATGGCGTCCTTTGCTCGGAAGAGTATGAAGATGAACAAAGCCCTGAAAAGATTATCGAGCTGTATGCGGAGTGCATCAGGCTCTTTCACTCCATCGACATATCGGATTGTCCCTATACGAATAGCTTAGACAGCCGCTTAGCCGAATTGGATTACTTACTGAATAACGATCTGGCCGATGTGGATTGCGAAAACTGGGAAGAAGACACTCCATTTAAAGATCCGCGCGAGCTGTATGATTTTTTAAAGACGGAAAAGCCCGAAGAGGAACTTGTCTTTTCCCACGGCGACCTGGGAGACAGCAACATCTTTGTGAAAGATGGCAAAGTAAGTGGCTTTATTGATCTTGGGAGAAGCGGCAGGGCGGACAAGTGGTATGACATTGCCTTCTGCGTCCGGTCGATCAGGGAGGATATCGGGGAAGAACAGTATGTCGAGCTATTTTTTGACTTACTGGGGATCAAGCCTGATTGGGAGAAAATAAAATATTATATTTTACTGGATGAATTGTTTTAG\n+10_Enterococcus_faecalis_S17_L001\tcat(pC221)\tchloramphenicol\t97.69\t100.00\t648/648\tcontig00048\t4344\t4991\tX02529\tATGACTTTTAATATTATTGAATTAGAAAATTGGGATAGAAAAGAATATTTTGAACACTATTTTAATCAGCAAACTACTTATAGCATTACTAAAGAAATTGATATTACTTTGTTTAAAGATATGATAAAAAAGAAAGGATATGAAATTTATCCCTCTTTAATTTATGCAATTATGGAAGTTGTAAATAAAAATAAAGTGTTTAGAACAGGAATTAATAGTGAGAATAAATTAGGTTATTGGGATAAGTTAAATCCTTTGTATACAGTTTTTAATAAGCAAACTGAAAAATTTACTAACATTTGGACTGAATCTGATAAAAACTTCATTTCTTTTTATAATAATTATAAAAATGACTTGCTTGAATATAAAGATAAAGAAGAAATGTTTCCTAAAAAACCGATACCTGAAAACACCATACCGATTTCAATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAATATTGGTAACAATAGCAGCTTTTTATTGCCTATTATTACGATAGGTAAATTTTATAGTGAGAATAATAAAATTTATATACCAGTTGCTCTGCAACTTCATCATTCTGTATGTGATGGTTACCATGCTTCACTATTTATGAATGAATTTCAAGATATAATTCATAGGGTAGATGATTGGATTTAG\n+10_Enterococcus_faecalis_S17_L001\tdfrG\ttrimethoprim\t100.00\t100.00\t498/498\tcontig00049\t275\t772\tAB205645\tATGAAAGTTTCTTTGATTGCTGCGATGGATAAGAATAGAGTGATTGGCAAAGAGAATGACATTCCTTGGAGGATTCCCAAGGACTGGGAATATGTTAAAAATACTACAAAGGGACATCCGATAATATTAGGTAGGAAGAACCTTGAATCAATCGGAAGAGCCTTACCTGACAGAAGAAATATTATTCTGACGAGAGATAAGGGGTTTACCTTTAATGGTTGTGAAATTGTTCATTCAATAGAAGATGTTTTTGAGTTATGTAAAAACGAAGAAGAAATTTTTATTTTCGGAGGAGAACAGATTTATAATTTGTTTTTCCCTTATGTTGAGAAAATGTACATCACAAAAATACATCATGAATTCGAAGGAGATACTTTTTTTCCAGAAGTGAATTATGAGGAATGGAATGAGGTATTTGCCCAAAAAGGGATAAAGAATGATAAAAATCCGTATAACTACTATTTTCATGTATATGAAAGAAAAAACTTATTGAGTTAA\n+10_Enterococcus_faecalis_S17_L001\term(B)\terythromycin, azithromycin\t99.21\t100.13\t763/762\tcontig00048\t961\t199\tX66468\tATGTAATCACTTCAGGAGTGATTACATGAACAAAAATATAAAATATTCTCAAAACTTTTTAACGAGTGAAAAAGTACTCAACCAAATAATAAAACAATTGAATTTAAAAGAAACCGATACCGTTTACGAAATTGGAACAGGTAAAGGGCATTTAACGACGAAACTGGCTAAAATAAGTAAACAGGTAACGTCTATTGAATTAGACAGTCATCTATTCAACTTATCGTCAGAAAAATTAAAACTGAATACTCGTGTCACTTTAATTCACCAAGATATTCTACAGTTTCAATTCCCTAACAAACAGAGGTATAAAATTGTTGGGAGTATTCCTTACCATTTAAGCACACAAATTATTAAAAAAGTGGTTTTTGAAAGCCATGCGTCTGACATCTATCTGATTGTTGAAGAAGGATTCTACAAGCGTACCTTGGATATTCACCGAACACTAGG"..b'TTATTGGAAAAGAGAATTTAGAGAATATCTTATGCAGTTATCAAGGTACAATTATTTTTGTGTCACATGATAGATATTTTACTAATAAGATTGCTGACAGATTACTTGTTTTTGATAAGGATGGTGTAGAGTTTGTACAATCTACTTATGGTGAGTACGAGAAAAAAAGGATGAATTCTGAAAAGCCATTTAATAACATTAAAGTTGAGCAGAAAGTAGAGAAAAATAACACAGTAAAAGGCGATCGTAACTCCATTGAGAAGGAGAAGGTTAAGAAGGAGAAACGAATTGAAAAGCTTGAAGTGTTAATAAATCAATATGATGAAGAATTAGAAAGATTGAATAAAATCATTTCTGAACCAAACAATTCTTCTGATTATATAGTACTGACGGAAATACAAAAATCAATTGATGATGTTAAAAGGTGTCAGGGTAATTATTTTAATGAATGGGAACAGTTGATGAGAGAATTGGAAGTTATGTAA\n+10_Enterococcus_faecalis_S17_L001\ttet(L)\ttetracycline\t100.00\t100.00\t1377/1377\tcontig00050\t282\t1658\tM29725\tGTGAATACATCCTATTCACAATCGAATTTACGACACAACCAAATTTTAATTTGGCTTTGCATTTTATCTTTTTTTAGCGTATTAAATGAAATGGTTTTGAACGTCTCATTACCTGATATTGCAAATGATTTTAATAAACCACCTGCGAGTACAAACTGGGTGAACACAGCCTTTATGTTAACCTTTTCCATTGGAACAGCTGTATATGGAAAGCTATCTGATCAATTAGGCATCAAAAGGTTACTCCTATTTGGAATTATAATAAATTGTTTCGGGTCGGTAATTGGGTTTGTTGGCCATTCTTTCTTTTCCTTACTTATTATGGCTCGTTTTATTCAAGGGGCTGGTGCAGCTGCATTTCCAGCACTCGTAATGGTTGTAGTTGCGCGCTATATTCCAAAGGAAAATAGGGGTAAAGCATTTGGTCTTATTGGATCGATAGTAGCCATGGGAGAAGGAGTCGGTCCAGCGATTGGTGGAATGATAGCCCATTATATTCATTGGTCCTATCTTCTACTCATTCCTATGATAACAATTATCACTGTTCCGTTTCTTATGAAATTATTAAAGAAAGAAGTAAGGATAAAAGGTCATTTTGATATCAAAGGAATTATACTAATGTCTGTAGGCATTGTATTTTTTATGTTGTTTACAACATCATATAGCATTTCTTTTCTTATCGTTAGCGTGCTGTCATTCCTGATATTTGTAAAACATATCAGGAAAGTAACAGATCCTTTTGTTGATCCCGGATTAGGGAAAAATATACCTTTTATGATTGGAGTTCTTTGTGGGGGAATTATATTTGGAACAGTAGCAGGGTTTGTCTCTATGGTTCCTTATATGATGAAAGATGTTCACCAGCTAAGTACTGCCGAAATCGGAAGTGTAATTATTTTCCCTGGAACAATGAGTGTCATTATTTTCGGCTACATTGGTGGGATACTTGTTGATAGAAGAGGTCCTTTATACGTGTTAAACATCGGAGTTACATTTCTTTCTGTTAGCTTTTTAACTGCTTCCTTTCTTTTAGAAACAACATCATGGTTCATGACAATTATAATCGTATTTGTTTTAGGTGGGCTTTCGTTCACCAAAACAGTTATATCAACAATTGTTTCAAGTAGCTTGAAACAGCAGGAAGCTGGTGCTGGAATGAGTTTGCTTAACTTTACCAGCTTTTTATCAGAGGGAACAGGTATTGCAATTGTAGGTGGTTTATTATCCATACCCTTACTTGATCAAAGGTTGTTACCTATGGAAGTTGATCAGTCAACTTATCTGTATAGTAATTTGTTATTACTTTTTTCAGGAATCATTGTCATTAGTTGGCTGGTTACCTTGAATGTATATAAACATTCTCAAAGGGATTTCTAA\n+10_Enterococcus_faecalis_S17_L001\ttet(M)\ttetracycline\t98.12\t100.00\t1920/1920\tcontig00047\t5912\t3993\tX90939\tATGAAAATTATTAATATTGGAGTTTTAGCTCATGTTGATGCGGGAAAAACTACCTTAACAGAAAGCTTATTATATAACAGTGGAGCGATTACAGAATTAGGAAGCGTGGACAAAGGTACAACGAGGACGGATAATACGCTTTTAGAACGTCAGAGAGGAATTACAATTCAGACAGGAATAACCTCTTTTCAGTGGGAAAATACGAAGGTGAACATCATAGACACGCCAGGACATATGGATTTCTTAGCAGAAGTATATCGTTCATTATCAGTTTTAGATGGGGCAATTCTACTGATTTCTGCAAAAGATGGCGTACAAGCACAAACTCGTATATTATTTCATGCACTTAGGAAAATGGGGATTCCCACAATCTTTTTTATCAATAAGATTGACCAAAATGGAATTGATTTATCAACGGTTTATCAGGATATTAAAGAGAAACTTTCTGCCGAAATTGTAATCAAACAGAAGGTAGAACTGTATCCTAATATGTGTGTGACGAACTTTACCGAATCTGAACAATGGGATACGGTAATAGAGGGAAACGATGACCTTTTAGAGAAATATATGTCCGGTAAATCATTAGAAGCATTGGAACTCGAACAAGAGGAAAGCATAAGATTTCAGAATTGTTCCCTGTTCCCTGTTTATCACGGAAGTGCAAAAAACAATATAGGGATTGATAACCTTATAGAAGTGATTACGAATAAATTTTATTCATCAACACATCGAGGTCAGTCTGAACTTTGCGGAAATGTTTTCAAAATTGAATATACAAAAAAAAGACAACGTCTTGCATATATACGTCTTTATAGTGGCGTACTGCATTTGCGAGATTCGGTTAGAATATCGGAAAAGGAAAAAATAAAAATTACAGAAATGTATACTTCAATAAATGGTGAATTATGTAAAATCGATAAGGCTTATTCCGGGGAAATTGTTATTTTGCAGAATGAGTTTTTGAAGTTAAATAGTGTTCTTGGAGATACAAAGCTATTGCCACAGAGAGAGAGAATTGAAAATCCCCTCCCTCTGCTGCAAACGACTGTTGAACCGAGCAAACCTCAACAAAGGGAAATGTTGCTTGATGCCCTTTTGGAAATCTCAGATAGTGATCCGCTTCTACGATATTACGTGGATTCTACGACACATGAAATTATACTTTCTTTCTTAGGGAAAGTACAAATGGAAGTGATTAGTGCACTGTTGCAAGAAAAGTATCATGTGGAGATAGAACTAAAAGAGCCTACAGTCATTTATATGGAGAGACCGTTAAAAAATGCAGAATATACCATTCACATCGAAGTGCCGCCAAATCCTTTCTGGGCTTCCATTGGTTTATCTGTATCACCGCTTCCATTAGGGAGCGGAGTGCAGTATGAGAGCTCGGTTTCTCTTGGATACTTAAATCAATCGTTTCAAAATGCAGTTATGGAGGGGATACGCTATGGCTGTGAACAAGGATTGTATGGTTGGAATGTGACGGACTGTAAAATCTGTTTTAAGTATGGCTTATACTATAGCCCTGTTAGTACCCCAGCAGATTTTCGGATGCTTGCTCCTATTGTATTGGAACAAGTCTTAAAAAAAGCTGGAACAGAATTGTTAGAGCCATATCTTAGTTTTAAAATTTATGCGCCACAGGAATATCTTTCACGAGCATACAACGATGCTCCTAAATATTGTGCGAACATCGTAGACACTCAATTGAAAAATAATGAGGTCATTCTTAGTGGAGAAATCCCTGCTCGGTGTATTCAAGAATATCGTAGTGATTTAACTTTCTTTACAAATGGACGTAGTGTTTGTTTAACAGAGTTAAAAGGGTACCATGTTACTACCGGTGAACCTGTTTGCCAGCCCCGTCGTCCAAATAGTCGGATAGATAAAGTACGATATATGTTCAATAAAATAACTTAG\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/staramr/settings.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/staramr/settings.txt Tue Apr 30 08:41:54 2024 +0000 |
| b |
| @@ -0,0 +1,23 @@ +command_line = /home/piemari/apps/conda/envs/amr/bin/staramr search --nprocs 4 --no-exclude-genes --pid-threshold 95 --percent-length-overlap-resfinder 90 --percent-length-overlap-pointfinder 90 --percent-length-overlap-plasmidfinder 90 --output-dir /storage/scratch/piemari/60579242/staramr/staramr_10_Enterococcus_faecalis_S17_L001 /storage/scratch/piemari/60579242/staramr/10_Enterococcus_faecalis_S17_L001.fasta +version = 0.9.1 +start_time = 2023-02-13 14:26:11 +end_time = 2023-02-13 14:26:13 +total_minutes = 0.04 +resfinder_db_dir = /home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/resfinder +resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git +resfinder_db_commit = 23661dbb58797b302464855611223b7ba4a21f75 +resfinder_db_date = Fri, 02 Dec 2022 11:36 +pointfinder_db_dir = /home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/pointfinder +pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git +pointfinder_db_commit = a25ac32c7a7a904dff14ffbd17e3b3f7cd732954 +pointfinder_db_date = Fri, 28 Oct 2022 10:19 +pointfinder_organisms_all = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, klebsiella, mycobacterium_tuberculosis, neisseria_gonorrhoeae, plasmodium_falciparum, salmonella, staphylococcus_aureus +pointfinder_organisms_valid = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, salmonella +plasmidfinder_db_dir = /home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/plasmidfinder +plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git +plasmidfinder_db_commit = b1c9ddac0e618e07630a94452293d84f296a6de5 +plasmidfinder_db_date = Thu, 12 Jan 2023 12:51 +mlst_version = 2.23.0 +pointfinder_organism = None +pointfinder_gene_drug_version = 072621.1 +resfinder_gene_drug_version = 072621 |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/abricate_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/abricate_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"analysis_software_version": "1.0", "reference_database_version": "1.0", "analysis_software_name": "abricate", "results": [{"name": "abricate_report", "file_path": "tests/data/dummy/abricate/report.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00002", "START": 142975, "END": 143985, "STRAND": "+", "GENE": "bopD", "COVERAGE": "1-1011/1011", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 98.91, "DATABASE": "vfdb", "ACCESSION": "NP_814691", "PRODUCT": "(bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00003", "START": 7884, "END": 11111, "STRAND": "-", "GENE": "fss3", "COVERAGE": "1-3228/3228", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.38, "DATABASE": "vfdb", "ACCESSION": "NP_815578", "PRODUCT": "(fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00003", "START": 162314, "END": 163240, "STRAND": "+", "GENE": "efaA", "COVERAGE": "1-927/927", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.89, "DATABASE": "vfdb", "ACCESSION": "NP_815739", "PRODUCT": "(efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00006", "START": 33703, "END": 37014, "STRAND": "+", "GENE": "ebpA", "COVERAGE": "1-3312/3312", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.49, "DATABASE": "vfdb", "ACCESSION": "NP_814821", "PRODUCT": "(ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00006", "START": 37018, "END": 38448, "STRAND": "+", "GENE": "ebpB", "COVERAGE": "1-1431/1431", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.3, "DATABASE": "vfdb", "ACCESSION": "NP_814822", "PRODUCT": "(ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00006", "START": 38445, "END": 40328, "STRAND": "+", "GENE": "ebpC", "COVERAGE": "1-1878/1878", "GAPS": "1/6", "%COVERAGE": 100.0, "%IDENTITY": 98.99, "DATABASE": "vfdb", "ACCESSION": "NP_814823", "PRODUCT": "(ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00006", "START": 40422, "END": 41276, "STRAND": "+", "GENE": "srtC", "COVERAGE": "1-855/855", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.3, "DATABASE": "vfdb", "ACCESSION": "NP_814824", "PRODUCT": "(srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00006", "START": 44356, "END": 46374, "STRAND": "+", "GENE": "ace", "COVERAGE": "1-2025/2025", "GAPS": "2/6", "%COVERAGE": 99.7, "%IDENTITY": 96.74, "DATABASE": "vfdb", "ACCESSION": "NP_814829", "PRODUCT": "(ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00010", "START": 49447, "END": 50301'..b'UENCE": "contig00018", "START": 18214, "END": 20666, "STRAND": "-", "GENE": "cpsG", "COVERAGE": "1-2454/2454", "GAPS": "1/1", "%COVERAGE": 99.96, "%IDENTITY": 99.51, "DATABASE": "vfdb", "ACCESSION": "NP_816135", "PRODUCT": "(cpsG) MurB family protein [Capsule (VF0361)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00018", "START": 20736, "END": 23245, "STRAND": "-", "GENE": "cpsE", "COVERAGE": "1-2510/2511", "GAPS": "0/0", "%COVERAGE": 99.96, "%IDENTITY": 99.4, "DATABASE": "vfdb", "ACCESSION": "NP_816137", "PRODUCT": "(cpsE) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00018", "START": 23315, "END": 24781, "STRAND": "-", "GENE": "cpsD", "COVERAGE": "1-1467/1467", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 98.91, "DATABASE": "vfdb", "ACCESSION": "NP_816138", "PRODUCT": "(cpsD) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00018", "START": 24800, "END": 25969, "STRAND": "-", "GENE": "cpsC", "COVERAGE": "1-1170/1170", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.57, "DATABASE": "vfdb", "ACCESSION": "NP_816139", "PRODUCT": "(cpsC) teichoic acid biosynthesis protein putative [Capsule (VF0361)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00018", "START": 26443, "END": 27243, "STRAND": "-", "GENE": "cpsB", "COVERAGE": "1-801/801", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.5, "DATABASE": "vfdb", "ACCESSION": "NP_816140", "PRODUCT": "(cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00018", "START": 27240, "END": 28055, "STRAND": "-", "GENE": "cpsA", "COVERAGE": "1-816/816", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.51, "DATABASE": "vfdb", "ACCESSION": "NP_816141", "PRODUCT": "(cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00018", "START": 36270, "END": 40580, "STRAND": "-", "GENE": "fss2", "COVERAGE": "1-4305/4956", "GAPS": "11/22", "%COVERAGE": 86.7, "%IDENTITY": 92.92, "DATABASE": "vfdb", "ACCESSION": "NP_816151", "PRODUCT": "(fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00023", "START": 14087, "END": 18004, "STRAND": "+", "GENE": "prgB/asc10", "COVERAGE": "1-3918/3918", "GAPS": "2/4", "%COVERAGE": 99.95, "%IDENTITY": 94.26, "DATABASE": "vfdb", "ACCESSION": "NP_817031", "PRODUCT": "(prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00042", "START": 2539, "END": 8502, "STRAND": "-", "GENE": "fss1", "COVERAGE": "1-5964/5964", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 98.31, "DATABASE": "vfdb", "ACCESSION": "NP_813892", "PRODUCT": "(fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]", "RESISTANCE": null}]}], "tool_has_database": true}]\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/bakta_all_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/bakta_all_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[{"analysis_software_version": "1.8.1", "reference_database_version": "5.0", "analysis_software_name": "bakta", "results": [{"name": "bakta_report", "file_path": "tests/data/dummy/bakta/bakta.json", "hid": "12345", "galaxy_id": null, "content": [{"genome": {"genus": null, "species": null, "strain": null, "complete": true, "gram": "?", "translation_table": 11}, "stats": {"no_sequences": 1, "size": 1330, "gc": 0.4518796992481203, "n_ratio": 0.0, "n50": 1330, "coding_ratio": 0.6203007518796992}, "features": [{"type": "cds", "contig": "contig_1", "start": 413, "stop": 736, "strand": "+", "frame": 2, "gene": null, "product": "hypothetical protein", "db_xrefs": [], "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", "start_type": "ATG", "rbs_motif": "GGAG/GAGG", "hypothetical": true, "genes": [], "seq_stats": {"molecular_weight": 12072.9082, "isoelectric_point": 10.3678861618}, "id": "IHHALPPJCH_1", "locus": "IHHALP_00005", "edge": null}, {"type": "cds", "contig": "contig_1", "start": 971, "stop": 141, "strand": "-", "frame": 1, "gene": null, "product": "hypothetical protein", "db_xrefs": [], "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584", "start_type": "ATG", "rbs_motif": "AGGA/GGAG/GAGG", "hypothetical": true, "genes": [], "seq_stats": {"molecular_weight": 18866.3258, "isoelectric_point": 7.6965906143}, "id": "IHHALPPJCH_2", "locus": "IHHALP_00010", "edge": true}], "run": {"start": "2024-02-11 00:24:53", "end": "2024-02-11 00:25:06"}, "summary": {"tRNAs": 0, "tmRNAs": 0, "rRNAs": 0, "ncRNAs": 0, "ncRNAregions": 0, "CRISPRarrays": 0, "CDSs": 2, "pseudogenes": 0, "hypotheticals": 2, "signalpeptides": 0, "sORFs": 0, "gaps": 0, "oriCs": 0, "oriVs": 0, "oriTs": 0}}]}, {"name": "annotation_tabular_path", "file_path": "tests/data/dummy/bakta/bakta_annotation.tsv", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "gff_file_path", "file_path": "tests/data/dummy/bakta/bakta_annotation.gff3", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "annotation_genbank_path", "file_path": "tests/data/dummy/bakta/bakta_gbff.gbff", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "annotation_embl_path", "file_path": "tests/data/dummy/bakta/bakta_embl.embl", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "contig_sequences_path", "file_path": "tests/data/dummy/bakta/bakta_contigs_sequences.fna", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "nucleotide_annotation_path", "file_path": "tests/data/dummy/bakta/bakta_nucleotide_annotation.ffn", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "amino_acid_annotation_path", "file_path": "tests/data/dummy/bakta/bakta_aminoacid.faa", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "hypothetical_protein_path", "file_path": "tests/data/dummy/bakta/bakta_hypothetical.faa", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "hypothetical_tabular_path", "file_path": "tests/data/dummy/bakta/bakta_hypothetical.tsv", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "summary_result_path", "file_path": "tests/data/dummy/bakta/bakta_summary.txt", "hid": "98765", "galaxy_id": null, "content": []}, {"name": "plot_file_path", "file_path": "tests/data/dummy/bakta/bakta_plot.svg", "hid": "98765", "galaxy_id": null, "content": []}], "tool_has_database": true}] \ No newline at end of file |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/bandage_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/bandage_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[{"analysis_software_version": "1.0", "reference_database_version": "", "analysis_software_name": "bandage", "results": [{"name": "bandage_report", "file_path": "tests/data/dummy/bandage/bandage_info.txt", "hid": "12345", "galaxy_hid": "", "content": {"Node_count": "222", "Edge_count": "299", "Smallest_edge_overlap_(bp)": "127", "Largest_edge_overlap_(bp)": "127", "Total_length_(bp)": "3042326", "Total_length_no_overlaps_(bp)": "3014132", "Dead_ends": "0", "Percentage_dead_ends": "0%", "Connected_components": "2", "Largest_component_(bp)": "3042198", "Total_length_orphaned_nodes_(bp)": "3042198", "N50_(bp)": "79920", "Shortest_node_(bp)": "128", "Lower_quartile_node_(bp)": "151", "Median_node_(bp)": "256", "Upper_quartile_node_(bp)": "7566", "Longest_node_(bp)": "239204", "Median_depth": "22.997", "Estimated_sequence_length_(bp)": "3234717"}}, {"name": "bandage_plot_path", "file_path": "tests/data/dummy/bandage/bandage_plot.svg", "hid": "12345", "galaxy_id": "", "content": {}}], "tool_has_database": false}] \ No newline at end of file |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/bracken_full_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/bracken_full_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[{"analysis_software_version": "2.8", "reference_database_version": "PlusPF_16", "analysis_software_name": "bracken", "results": [{"name": "bracken_report", "file_path": "tests/data/dummy/bracken/bracken_report.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"name": "Enterococcus_faecalis", "taxonomy_id": 1351, "taxonomy_lvl": "S", "kraken_assigned_reads": 63, "added_reads": 21, "new_est_reads": 84, "fraction_total_reads": 0.88421}, {"name": "Enterococcus_faecium", "taxonomy_id": 1352, "taxonomy_lvl": "S", "kraken_assigned_reads": 4, "added_reads": 0, "new_est_reads": 4, "fraction_total_reads": 0.04211}, {"name": "Enterococcus_casseliflavus", "taxonomy_id": 37734, "taxonomy_lvl": "S", "kraken_assigned_reads": 1, "added_reads": 0, "new_est_reads": 1, "fraction_total_reads": 0.01053}, {"name": "Streptococcus_cristatus", "taxonomy_id": 45634, "taxonomy_lvl": "S", "kraken_assigned_reads": 1, "added_reads": 0, "new_est_reads": 1, "fraction_total_reads": 0.01053}, 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| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/fastp_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/fastp_output.json Tue Apr 30 08:41:54 2024 +0000 |
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"tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/integronfinder2_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/integronfinder2_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"analysis_software_version": "1.6.1", "reference_database_version": "", "analysis_software_name": "integronfinder2", "results": [{"name": "integronfinder2_report", "file_path": "tests/data/dummy/integronfinder2/results.integrons", "hid": "12345", "galaxy_hid": "", "content": [{"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "contig00017_42", "pos_beg": 41235, "pos_end": 41546, "strand": -1, "evalue": null, "type_elt": "protein", "annotation": "protein", "model": null, "type": "CALIN", "default": "No", "distance_2attC": null, "considered_topology": "lin"}, {"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "contig00017_43", "pos_beg": 41543, "pos_end": 42391, "strand": -1, "evalue": null, "type_elt": "protein", "annotation": "protein", "model": null, "type": "CALIN", "default": "No", "distance_2attC": null, "considered_topology": "lin"}, {"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "attc_001", "pos_beg": 41600, "pos_end": 41701, "strand": -1, "evalue": 0.15, "type_elt": "attC", "annotation": "attC", "model": "attc_4", "type": "CALIN", "default": "No", "distance_2attC": null, "considered_topology": "lin"}, {"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "contig00017_44", "pos_beg": 42419, "pos_end": 43705, "strand": -1, "evalue": null, "type_elt": "protein", "annotation": "protein", "model": null, "type": "CALIN", "default": "No", "distance_2attC": null, "considered_topology": "lin"}, {"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "contig00017_45", "pos_beg": 43702, "pos_end": 45213, "strand": -1, "evalue": null, "type_elt": "protein", "annotation": "protein", "model": null, "type": "CALIN", "default": "No", "distance_2attC": null, "considered_topology": "lin"}, {"ID_integron": "integron_01", "ID_replicon": "contig00017", "element": "attc_002", "pos_beg": 44054, "pos_end": 44100, "strand": -1, "evalue": 0.095, "type_elt": "attC", "annotation": "attC", "model": "attc_4", "type": "CALIN", "default": "No", "distance_2attC": 2353.0, "considered_topology": "lin"}]}, {"name": "summary", "file_path": "tests/data/dummy/integronfinder2/results.summary", "hid": "12345", "content": [{"ID_replicon": "contig00001", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 436224}, {"ID_replicon": "contig00002", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 252900}, {"ID_replicon": "contig00003", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 206370}, {"ID_replicon": "contig00004", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 168397}, {"ID_replicon": "contig00005", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 132811}, {"ID_replicon": "contig00006", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 115359}, {"ID_replicon": "contig00007", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 113419}, {"ID_replicon": "contig00008", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 99915}, {"ID_replicon": "contig00009", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 97190}, {"ID_replicon": "contig00010", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 92075}, {"ID_replicon": "contig00011", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 86662}, {"ID_replicon": "contig00012", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 82418}, {"ID_replicon": "contig00013", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 81741}, {"ID_replicon": "contig00014", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 81694}, {"ID_replicon": "contig00015", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 71911}, {"ID_replicon": "contig00016", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 66886}, {"ID_replicon": "contig00017", "CALIN": 1, "complete": 0, "In0": 0, "topology": "lin", "size": 645'..b'replicon": "contig00053", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 1775}, {"ID_replicon": "contig00055", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 1578}, {"ID_replicon": "contig00056", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 1526}, {"ID_replicon": "contig00057", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 1515}, {"ID_replicon": "contig00058", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 1299}, {"ID_replicon": "contig00059", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 652}, {"ID_replicon": "contig00060", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 607}, {"ID_replicon": "contig00061", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 534}, {"ID_replicon": "contig00062", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 525}, {"ID_replicon": "contig00063", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 442}, {"ID_replicon": "contig00065", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 405}, {"ID_replicon": "contig00066", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 398}, {"ID_replicon": "contig00067", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 378}, {"ID_replicon": "contig00068", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 372}, {"ID_replicon": "contig00070", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 332}, {"ID_replicon": "contig00074", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 256}, {"ID_replicon": "contig00075", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00076", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00077", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00078", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00079", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00080", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00081", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00082", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00083", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00084", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00085", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 255}, {"ID_replicon": "contig00086", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 254}, {"ID_replicon": "contig00088", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 253}, {"ID_replicon": "contig00089", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 252}, {"ID_replicon": "contig00090", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 250}, {"ID_replicon": "contig00091", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 246}, {"ID_replicon": "contig00092", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 235}, {"ID_replicon": "contig00093", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 231}, {"ID_replicon": "contig00094", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 206}, {"ID_replicon": "contig00095", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 205}, {"ID_replicon": "contig00096", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 161}, {"ID_replicon": "contig00097", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 151}, {"ID_replicon": "contig00098", "CALIN": 0, "complete": 0, "In0": 0, "topology": "lin", "size": 138}]}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/isescan_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/isescan_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"analysis_software_version": "1.7.2.3", "reference_database_version": "", "analysis_software_name": "isescan", "results": [{"name": "isescan_report", "file_path": "tests/data/dummy/isescan/results.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"contig00001": "contig00002", "IS21": "IS200/IS605", "IS21_259": "IS200/IS605_96", "104722": 179502, "106001": 180572, "1280": 1071, "1": 1, "104722.1": 0, "104735": 0, "105988": 0, "106001.1": 0, "20": 0, "12": 0, "14": 0, "0": 0, "105201": 179502, "106043": 180572, "+": "-", "843": 1071, "2.1e-13": 1.2e-69, "2.1e-13.1": 1.2e-69, "p": "c", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "-:-"}, {"contig00001": "contig00002", "IS21": "IS21", "IS21_259": "IS21_288", "104722": 210210, "106001": 214514, "1280": 4305, "1": 1, "104722.1": 210210, "104735": 210236, "105988": 214488, "106001.1": 214514, "20": 26, "12": 20, "14": 27, "0": 0, "105201": 210541, "106043": 214169, "+": "-", "843": 3629, "2.1e-13": 1e-10, "2.1e-13.1": 1e-10, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "ATTAAGCCAAATGGCAATGGTGATGAA:ATCAAGAAAAATGGGGATCGTGAAGAA"}, {"contig00001": "contig00002", "IS21": "IS30", "IS21_259": "IS30_241", "104722": 252678, "106001": 252900, "1280": 223, "1": 1, "104722.1": 0, "104735": 0, "105988": 0, "106001.1": 0, "20": 0, "12": 0, "14": 0, "0": 0, "105201": 252678, "106043": 252900, "+": "+", "843": 223, "2.1e-13": 8.3e-32, "2.1e-13.1": 8.3e-32, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "-:-"}, {"contig00001": "contig00005", "IS21": "IS30", "IS21_259": "IS30_241", "104722": 54, "106001": 3033, "1280": 2980, "1": 1, "104722.1": 54, "104735": 67, "105988": 3020, "106001.1": 3033, "20": 20, "12": 12, "14": 14, "0": 0, "105201": 1, "106043": 2892, "+": "+", "843": 2892, "2.1e-13": 6.2e-51, "2.1e-13.1": 6.2e-51, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "AAAAGAATTTTCTA:AAATGAATGTTCTA"}, {"contig00001": "contig00005", "IS21": "IS21", "IS21_259": "IS21_259", "104722": 84142, "106001": 85683, "1280": 1542, "1": 1, "104722.1": 84142, "104735": 84174, "105988": 85651, "106001.1": 85683, "20": 34, "12": 25, "14": 33, "0": 0, "105201": 84182, "106043": 85525, "+": "-", "843": 1344, "2.1e-13": 0.0, "2.1e-13.1": 0.0, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "TGTGGATAACTTTGTTCTTTTTTGTTTAGTTTT:TGTGGAAAACTTTTTTCACCCTTGTGTACTTTT"}, {"contig00001": "contig00008", "IS21": "IS30", "IS21_259": "IS30_241", "104722": 99798, "106001": 99915, "1280": 118, "1": 1, "104722.1": 0, "104735": 0, "105988": 0, "106001.1": 0, "20": 0, "12": 0, "14": 0, "0": 0, "105201": 99798, "106043": 99915, "+": "-", "843": 118, "2.1e-13": 0.0, "2.1e-13.1": 0.0, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "-:-"}, {"contig00001": "contig00010", "IS21": "IS6", "IS21_259": "IS6_292", "104722": 1, "106001": 138, "1280": 138, "1": 1, "104722.1": 0, "104735": 0, "105988": 0, "106001.1": 0, "20": 0, "12": 0, "14": 0, "0": 0, "105201": 1, "106043": 138, "+": "-", "843": 138, "2.1e-13": 7.2e-22, "2.1e-13.1": 7.2e-22, "p": "p", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "-:-"}, {"contig00001": "contig00010", "IS21": "IS256", "IS21_259": "IS256_47", "104722": 63216, "106001": 65257, "1280": 2042, "1": 1, "104722.1": 63216, "104735": 63259, "105988": 65215, "106001.1": 65257, "20": 26, "12": 30, "14": 44, "0": 1, "105201": 63507, "106043": 64842, "+": "-", "843": 1336, "2.1e-13": 4.3e-136, "2.1e-13.1": 4.3e-136, "p": "c", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "AGGGATTCTTAGAAGTAGAAGCTCAACATTTTGAACTTATAGAA:AGGCATTTGTGGAATTATACTTTCAATA-TTAGAACTTTTTGAA"}, {"contig00001": "contig00010", "IS21": "IS3", "IS21_259": "IS3_176", "104722": 65906, "106001": 67630, "1280": 1725, "1": 1, "104722.1": 65906, "104735": 65936, "105988": 67600, "106001.1": 67630, "20": 34, "12": 24, "14": 31, "0": 0, "105201": 65942, "106043": 67421, "+": "+", "843": 1480, "2.1e-13": 2.5e-113, "2.1e-13.1": 2.5e-113, "p": "c", "1.1": 1, "TTGAAAAAAATAGC:TTGGAAAACATAGC": "TGGATAGGCTACAATTAACTAGACAGAAAAA:TGGATA'..b'ACTCTCTTCGGGTTTTCGGTCTGTACTGAAATCAAGGTATTATTGGGAATCCCAGCTTAAATCATAGATACCGTAAGGGATTTTATTCTTTATTTAAAACTTTGCAACAGAACC"}, "contig00076": {"sequence_informations": {"contig": "contig00076", "start": "1", "end": "223", "strand": "-", "family": "IS30", "cluster": "241"}, "sequence": "ATGACCTACAAACATCTTACCATAGACGAACTGACAATGATAGAATCATATTATCTTCAACATAATAAACCGGTTGAAATCGCTAACCGAATGGGACGTGCTATACAAACTATTTATAATGTAGTCAATAAGTTCAAGCAAGGCAAGACTGCTCTTGATTATTGGCACCAGTATAAAGAAAATAAGAAAAAATGTGGTAGAAAAGTCATTCAATTACCTGCTC"}, "contig00079": {"sequence_informations": {"contig": "contig00079", "start": "1", "end": "255", "strand": "-", "family": "IS30", "cluster": "241"}, "sequence": "CTATTACGTTTGACTGTGGAAAAGAATTTTCTAACTGGAAAGCCATTAGTAACCAACACGATATTGATATATATTTTGCGGACCCTGGAACACTTTCTCAACGCCCATTAAACGAGAATTCTAACGGGATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATCAGACATTTATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATTACAGAACACCAATTG"}, "contig00083": {"sequence_informations": {"contig": "contig00083", "start": "135", "end": "255", "strand": "+", "family": "IS6", "cluster": "292"}, "sequence": "TTGTATCGAGCCATCGATGCAGATGGTTTAACCTTGGATATTTGGTTACGTAAAAAACGGGACACACAAGCAGCCTATGCTTTTCTTAAGCGGTTAGTGAAGCAGTTTGATGAACCGAAGG"}, "contig00085": {"sequence_informations": {"contig": "contig00085", "start": "1", "end": "255", "strand": "+", "family": "IS30", "cluster": "241"}, "sequence": "CTATTACGTTTGACTGTGGAAAAGAATTTTCTAACTGGAAAGCCATTAGTAACCAACACGATATTGATATATATTTTGCGGACCCTGGAACACTTTCTCAACGCCCATTAAACGAGAATTCTAACGGTATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATCAGACATTTATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATTACAGAACACCAATTG"}, "contig00090": {"sequence_informations": {"contig": "contig00090", "start": "1", "end": "250", "strand": "-", "family": "IS6", "cluster": "292"}, "sequence": "TGCAGATGGTTTAACCTTGGATATTTGGTTACGTAAAAAACGGGACACACAAGCAGCCTATGCTTTTCTTAAGCGGTTAGTGAAGCAGTTTGATGAACCGAAGGTTGTAGTCACAGATAAAGCCCCCCTCTATTACAAGTGCCTTTAAGAAACTAAAAGAATACGGCTTTTATCAAGGGACAGAACATCGTACCATTAAATACCTGAATAATTTGATTGAACAAGACCATCGTCCAGTAAAGAGACGCAA"}, "contig00093": {"sequence_informations": {"contig": "contig00093", "start": "1", "end": "231", "strand": "-", "family": "IS6", "cluster": "292"}, "sequence": "ATACGACGATTTATCGTTGGGTGCAAGAATATGGCAAACTACTCTATCAAATTTGGAAAAAGAAAAATAAAAAATCCTTTTATTCATGGAAAATGGATGAAACGTACATCAAAATTAAAGGAAAATGGCATTATTTGTATCGAGCCATCGATGCAGATGGTTTAACCTTGGATATTTGGTTACGTAAAAAACGGGACACACAAGCAGCCTATGCTTTTCTTAAGCGGTTAG"}, "contig00094": {"sequence_informations": {"contig": "contig00094", "start": "69", "end": "206", "strand": "+", "family": "IS6", "cluster": "292"}, "sequence": "ATGACGATGAGTCATTTTAAAGGAAAGCAATTTCAGCAGGATGTGATTATTGTAGCCGTGGGCTACTATCTTCGTTATAACCTTAGCTATCGTGAAGTTCAAGAAATCTTATATGATCGTGGCATTAACGTTTCTCAT"}, "contig00096": {"sequence_informations": {"contig": "contig00096", "start": "1", "end": "161", "strand": "-", "family": "IS30", "cluster": "241"}, "sequence": "TGGTTTTCTCGCTTCCCTAAAAACTTCTTTAAATCTATTACGTTTGACTGTGGAAAAGAATTTTCTAACTGGAAAGCCATTAGTAACCAACACGATATTGATATATATTTTGCGGACCCTGGAACACTTTCTCAACGCCCATTAAACGAGAATTCTAACGG"}, "contig00097": {"sequence_informations": {"contig": "contig00097", "start": "1", "end": "151", "strand": "-", "family": "IS6", "cluster": "292"}, "sequence": "ATGATCGTGGCATTAACGTTTCTCATACGACGATTTATCGTTGGGTGCAAGAATATGGCAAACTACTCTATCAAATTTGGAAAAAGAAAAATAAAAAATCCTTTTATTCATGGAAAATGGATGAAACGTACATCAAAATTAAAGGAAAATG"}, "contig00098": {"sequence_informations": {"contig": "contig00098", "start": "1", "end": "138", "strand": "+", "family": "IS30", "cluster": "241"}, "sequence": "ATTCTGCGTCATAATGGACTGCCGAAATCAATGGATTTTAGAGAAGTGAATCAGACATTTATTTCCAGTGTCAGCAATCAACGTAATCATATTCCAAGAAAATCATTGAATTACAGAACACCAATTGAGATATTTTTG"}}}, {"name": "summary_path", "file_path": "tests/data/dummy/isescan/summary.tsv", "hid": "12345", "galaxy_id": "", "content": {}}, {"name": "annotation_path", "file_path": "tests/data/dummy/isescan/annotation.gff", "hid": "12345", "galaxy_id": "", "content": {}}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/kraken2_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/kraken2_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[{"analysis_software_version": "2.1.2", "reference_database_version": "PlusPF_16", "analysis_software_name": "kraken2", "results": [{"name": "kraken2_report", "file_path": "tests/data/dummy/kraken2/taxonomy_report.tsv", "hid": "12345", "galaxy_id": null, "content": [{"fragment_coverage": 100.0, "fragment_number": 95, "assigned_fragment_number": 0, "rank_code": "R", "ncbi_taxonomic_id": 1, "scientific_name": "root"}, {"fragment_coverage": 100.0, "fragment_number": 95, "assigned_fragment_number": 0, "rank_code": "R1", "ncbi_taxonomic_id": 131567, "scientific_name": "cellular_organisms"}, {"fragment_coverage": 100.0, "fragment_number": 95, "assigned_fragment_number": 4, "rank_code": "D", "ncbi_taxonomic_id": 2, "scientific_name": "Bacteria"}, {"fragment_coverage": 95.79, "fragment_number": 91, "assigned_fragment_number": 0, "rank_code": "D1", "ncbi_taxonomic_id": 1783272, "scientific_name": "Terrabacteria_group"}, {"fragment_coverage": 95.79, "fragment_number": 91, "assigned_fragment_number": 0, "rank_code": "P", "ncbi_taxonomic_id": 1239, "scientific_name": "Firmicutes"}, {"fragment_coverage": 95.79, "fragment_number": 91, "assigned_fragment_number": 4, "rank_code": "C", "ncbi_taxonomic_id": 91061, "scientific_name": "Bacilli"}, {"fragment_coverage": 89.47, "fragment_number": 85, "assigned_fragment_number": 8, "rank_code": "O", "ncbi_taxonomic_id": 186826, "scientific_name": "Lactobacillales"}, {"fragment_coverage": 78.95, "fragment_number": 75, "assigned_fragment_number": 0, "rank_code": "F", "ncbi_taxonomic_id": 81852, "scientific_name": "Enterococcaceae"}, {"fragment_coverage": 78.95, "fragment_number": 75, "assigned_fragment_number": 7, "rank_code": "G", "ncbi_taxonomic_id": 1350, "scientific_name": "Enterococcus"}, {"fragment_coverage": 66.32, "fragment_number": 63, "assigned_fragment_number": 42, "rank_code": "S", "ncbi_taxonomic_id": 1351, "scientific_name": "Enterococcus_faecalis"}]}, {"name": "seq_classification_file_path", "file_path": "tests/data/dummy/kraken2/taxonomy_result.tsv", "hid": "12345", "galaxy_id": null, "content": []}], "tool_has_database": true}] \ No newline at end of file |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/multiqc_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/multiqc_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[{"analysis_software_version": "1.11", "reference_database_version": "", "analysis_software_name": "multiqc", "results": [{"name": "multiqc_report", "file_path": "tests/data/dummy/multiqc/multiqc_report.html", "hid": "12345", "galaxy_hid": "", "content": {}}], "tool_has_database": false}] \ No newline at end of file |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/plasmidfinder_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/plasmidfinder_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"analysis_software_version": "1.0", "reference_database_version": "1.0", "analysis_software_name": "plasmidfinder", "results": [{"name": "plasmidfinder_report", "file_path": "tests/data/dummy/plasmidfinder/plasmidfinder_result.json", "hid": "12345", "galaxy_hid": "", "content": {"Enterobacteriaceae": {"enterobacteriaceae": "No hit found"}, "Gram Positive": {"Inc18": "No hit found", "NT_Rep": "No hit found", "Rep1": {"contig00051 len=2083 cov=17.5 corr=0 origname=NODE_51_length_2083_cov_17.526074_pilon sw=shovill-spades/1.1.0 date=20230213:127..897:repUS12_2_repB(SAP014A)_GQ900379:88.013699": {"plasmid": "repUS12", "identity": 100.0, "HSP_length": 771, "template_length": 876, "position_in_ref": "1..771", "contig_name": "contig00051 len=2083 cov=17.5 corr=0 origname=NODE_51_length_2083_cov_17.526074_pilon sw=shovill-spades/1.1.0 date=20230213", "positions_in_contig": "127..897", "note": "repB(SAP014A)", "accession": "GQ900379", "coverage": 88.01, "hit_id": "contig00051 len=2083 cov=17.5 corr=0 origname=NODE_51_length_2083_cov_17.526074_pilon sw=shovill-spades/1.1.0 date=20230213:127..897:repUS12_2_repB(SAP014A)_GQ900379:88.013699"}}, "Rep2": "No hit found", "Rep3": {"contig00026 len=35051 cov=66.2 corr=0 origname=NODE_26_length_35051_cov_66.162954_pilon sw=shovill-spades/1.1.0 date=20230213:21156..22313:repUS40_1_repB(pE394)_KP399637:100.000000": {"plasmid": "repUS40", "identity": 100.0, "HSP_length": 1158, "template_length": 1158, "position_in_ref": "1..1158", "contig_name": "contig00026 len=35051 cov=66.2 corr=0 origname=NODE_26_length_35051_cov_66.162954_pilon sw=shovill-spades/1.1.0 date=20230213", "positions_in_contig": "21156..22313", "note": "repB(pE394)", "accession": "KP399637", "coverage": 100.0, "hit_id": "contig00026 len=35051 cov=66.2 corr=0 origname=NODE_26_length_35051_cov_66.162954_pilon sw=shovill-spades/1.1.0 date=20230213:21156..22313:repUS40_1_repB(pE394)_KP399637:100.000000"}}, "RepA_N": {"contig00023 len=45935 cov=46.6 corr=0 origname=NODE_23_length_45935_cov_46.624847_pilon sw=shovill-spades/1.1.0 date=20230213:3630..4643:rep9b_2_prgW(EF62pC)_CP002494:100.000000": {"plasmid": "rep9b", "identity": 100.0, "HSP_length": 1014, "template_length": 1014, "position_in_ref": "1..1014", "contig_name": "contig00023 len=45935 cov=46.6 corr=0 origname=NODE_23_length_45935_cov_46.624847_pilon sw=shovill-spades/1.1.0 date=20230213", "positions_in_contig": "3630..4643", "note": "prgW(EF62pC)", "accession": "CP002494", "coverage": 100.0, "hit_id": "contig00023 len=45935 cov=46.6 corr=0 origname=NODE_23_length_45935_cov_46.624847_pilon sw=shovill-spades/1.1.0 date=20230213:3630..4643:rep9b_2_prgW(EF62pC)_CP002494:100.000000"}}, "RepL": "No hit found", "Rep_trans": {"contig00040 len=12074 cov=69.2 corr=0 origname=NODE_40_length_12074_cov_69.205993_pilon sw=shovill-spades/1.1.0 date=20230213:8225..9430:repUS43_1_CDS12738(DOp1)_CP003584:100.000000": {"plasmid": "repUS43", "identity": 100.0, "HSP_length": 1206, "template_length": 1206, "position_in_ref": "1..1206", "contig_name": "contig00040 len=12074 cov=69.2 corr=0 origname=NODE_40_length_12074_cov_69.205993_pilon sw=shovill-spades/1.1.0 date=20230213", "positions_in_contig": "8225..9430", "note": "CDS12738(DOp1)", "accession": "CP003584", "coverage": 100.0, "hit_id": "contig00040 len=12074 cov=69.2 corr=0 origname=NODE_40_length_12074_cov_69.205993_pilon sw=shovill-spades/1.1.0 date=20230213:8225..9430:repUS43_1_CDS12738(DOp1)_CP003584:100.000000"}, "contig00048 len=5336 cov=19.5 corr=0 origname=NODE_48_length_5336_cov_19.468228_pilon sw=shovill-spades/1.1.0 date=20230213:3276..4214:rep7a_8_ORF11(pRE25)_X92945:100.000000": {"plasmid": "rep7a", "identity": 100.0, "HSP_length": 939, "template_length": 939, "position_in_ref": "1..939", "contig_name": "contig00048 len=5336 cov=19.5 corr=0 origname=NODE_48_length_5336_cov_19.468228_pilon sw=shovill-spades/1.1.0 date=20230213", "positions_in_contig": "3276..4214", "note": "ORF11(pRE25)", "accession": "X92945",'..b'AAAAATAAAAAAAGGAAACCGAATTGGTTCGATTCAGTTCCATATTACGAAAAAACAAATTGCTCCTAATCCTTCTTACAAAATTGGCGATTCTGTGTATGAAGCGCAACAAGCAGAAAAAGAACAAAATCAAATTACTTTATTTGCGCAGGCAATGCAAAGTCAATACACTACCATTTTGATGGAAAATATGTTGATTGGGTACAAAGATATGCAAGATATTGAATTAATGGCAAGCTTGCAAGAAATGGTTTATCCCTTGTATGACGAGTTGAAAACTCTTAGAGGATTAGACGGTGTGAGAAATCACTTAGAATACGTTTCAAGAAAACAAATAGGCTATTCTAAAACTAATATTGTCAAGTATTTAAAAACAGCTATCACACAATATTTGCCAACGGTAAAAATGATGGATATGGATAATAGAGTGTAA"}, "contig00023": {"sequence_informations": {"len": "45935", "cov": "46.6", "corr": "0"}, "nucleotide_sequence": "ATGAACGATTTTCAATTTATTTCAGCTAATGAAACCTATAGAAATTTGTATTACCAATTACCTAAAGTACTTTTTACATCAGAATTTTATAAGACTATGTCTAATGATAGTAAAATAGCTTACGCAATGTTGCAAGACCGATGTGAATATTCAATACAAAATAATTGGATTGATCAAGATGGGCATATATATTTTATCTTTACACGAAATGAACTGATGGATATTTTAGGGTGTAAAGAAAATAAAATTGCAAAAATAAAAAAAGAATTAAAAGACAAAAATTTACTTTATGAAAAACGTATTCCTCCGAAAAAACTCTCTACTGGTGAATTCAAAAACTATCCAAACAGATTGTATTTAGGTAAGCTGGAAGTTTCAGCAACAGATGTTTACGCCATCAGTAATGCTAGCTATACAAATGAGTTTCCCGAAAGTGGGAAAAACCAACCTTCGGATAAACATGATAAAATCGGCATTTCTTTCGAAAGTGGGAAAAACCAACGTCCAGAAGAATCCAATAATACCAGTACTTTGTTCGAAAGTGGGAAAAACCAACCCAATCTATATCTAACTAATTCTTTAGATACAATAGATACAATAGATACTGAAAAAGAACGATTGCAACAACAATTATTGCTCGATCAATTTTCAGAAGTTCAAGAGCATACATTTCTTAGCAAAAATAGCTTAAAATTTATTGCTGCCTTTTCTGATACTATTCAAGAAGCACATGAAATGGTTGGAACAATTATTCGTGCTAAAACTAAAGTAGAAAAAGAATACAATATCGTTCTAATTGGTGAAGATTATCAAGAAGAAATAGACAAATGTTTGCGTCGTGTGATGCATAAAATCAAGACAGATTCTACTGTAAAAAGTCCAAAAGGCCTATTCTACAAGTCGTTTTACAATTTATTTGTTGAATGTACAATAGAGAAAAAAAGTCATTTAAATAAAAATAGTACGGACAACACCCCAGAAATAACTACACATAACTGGATTGAGTATCAATAA"}, "contig00048": {"sequence_informations": {"len": "5336", "cov": "19.5", "corr": "0"}, "nucleotide_sequence": "ATGAAGAAAATTGATGAAAAATTAGCTGCAGAAATCTCACTAAAAAAACCGGCCGTCTCTAATAGCCGGTTAAGTAATAGCCGGTTAAGTGGTCAAACTTTGGGAAAATCTCAACCCGCATTAAGTTTTGATGCCATGACAATCGTTGGAAATTTGAACAAAACTAATGCTAAAAAGCTATCTGACTTTATGAGTGTAGAGCCACAAATACGACTTTGGGATATACTTCAAACAAAGTTTAAAGCTAAGGCACTTCAAGAAAAAGTTTATATCGAATATGACAAAGTAAAAGCAGATACTTGGGATAGACGTAATATGCGTGTTGAATTTAATCCCAATAAACTCACACATGAAGAAATGATTTGGTTAAAACAAAATATTATCGACTACATGGAAGATGACGGTTTTACAAGATTAGACTTAGCTTTTGATTTTGAAGATGATTTGAGCGATTACTATGCAATGACTGATAAAGCAGTTAAGAAAACTGTTTTTTATGGTCGTAATGGCAAGCCAGAAACAAAATATTTTGGTGTCCGTGATAGTGATAGATTTATTAGAATTTATAATAAAAAACAAGAACGTAAAGATAACGCAGATGTTGAAGTTGTGTCTGAACATTTATGGCGTGTAGAAGTTGAATTAAAAAGAGATATGGTTGATTACTGGAATGATTGTTTTAATGATTTACACATCTTGAAACCTGCGTGGGCTACTTTAGAAAAAATTAATGAGCAAGCTATGGTTTATACTTTGTTGCATGAAGAAAGTATGTGGGGAAAGCTAAGTAAGAATACTAAGACTAAATTTAAAAAATTGATTAGAGAAATATCTCCAATTGATTTAACGGAATTAATGAAATCGACTTTAAAAGCGAACGAAAAACAATTGCAAAAGCAGATTGATTTTTGGCAACGTGAATTTAGGTTTTGGAAGTAA"}, "contig00040": {"sequence_informations": {"len": "12074", "cov": "69.2", "corr": "0"}, "nucleotide_sequence": "TTGGAGGGATTTTTACTGAATGAACAAACTTGGTTACAGCATTTAAAAGAAAAACGCTTGGCTTATGGACTATCTCAAAACCGTTTAGCTGTTGCGACTGGTATTACAAGGCAGTATCTAAGCGATATTGAAACAGGAAAAGTCAAGCCATCAGAGGATTTACAGCAGTCCCTTTGGGAAGCTCTGGAACGCTTCAATCCCGACGCTCCCCTTGAAATGCTGTTTGATTATGTAAGAATTCGCTTTCCGACAACAGACGTACAGCAGGTGGTCGAAAACATCTTACAACTGAAACTGTCCTATTTTCTTCATGAGGACTATGGTTTCTATTCTTATTCAGAGCATTATGCTTTAGGCGACATATTCGTCCTTTGCTCCCATGAACTGGACAAAGGAGTTCTGGTGGAATTGAAAGGTCGTGGGTGCAGACAATTTGAAAGCTATCTTCTGGCACAACAAAGAAGCTGGTATGAGTTCTTTATGGACGTTTTGGTGGCTGGCGGTGTGATGAAACGCCTTGACCTTGCCATTAACGATAAGACAGGGATTTTAAATATCCCTGTACTCACTGAAAAGTGCCAACAGGAAGAATGTATCTCCGTCTTCCGCAGTTTTAAAAGCTATCGCAGTGGCGAACTGGTACGCAAAGAGGAAAAGGAATGTATGGGAAACACCCTCTATATCGGTTCATTACAAAGTGAAGTTTATTTCTGTATCTATGAAAAGGACTACGAGCAGTACAAGAAAAATGATATTCCCATTGAAGACGCAGAAGTAAAAAACCGTTTTGAGATTCGATTGAAAAATGAGCGTGCCTATTATGCAGTCCGTGATTTACTCGTCTATGACAATCCAGAGCATACCGCCTTTAAAATTATCAATCGGTATATCCGTTTTGTAGATAAAGACGATTCCAAACCTCGTTCTGATTGGAAACTGAATGAAGAATGGGCTTGGTTTATTGGGAACAATCGTGAACGATTAAAACTAACCACAAAACCAGAGCCTTACTCCTTCCAAAGGACGCTGAACTGGCTATCTCATCAAGTTGCCCCGACCTTAAAGGTTGCGATTAAACTTGATGAAATCAACCAGACGCAGGTTGTAAAAGACATTCTCGACCATGCGAAACTGACAGACCGACACAAGCAGATTTTGAAGCAACAGTCAGTAAAAGAACAGGACGTGATAACAACAAAAAAATAA"}}}], "tool_has_database": true}]\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/quast_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/quast_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[{"reference_database_version": "", "analysis_software_version": "5.0.2", "analysis_software_name": "quast", "results": [{"name": "quast_report", "file_path": "tests/data/dummy/quast/quast_result.tsv", "hid": "12345", "galaxy_hid": "", "content": {"Assembly": "10_Enterococcus_faecalis_S17_L001", "contigs_(>=_0_bp)": "100", "contigs_(>=_1000_bp)": "58", "contigs_(>=_5000_bp)": "48", "contigs_(>=_10000_bp)": "41", "contigs_(>=_25000_bp)": "28", "contigs_(>=_50000_bp)": "20", "Total_length_(>=_0_bp)": "3027634", "Total_length_(>=_1000_bp)": "3015201", "Total_length_(>=_5000_bp)": "2996428", "Total_length_(>=_10000_bp)": "2944723", "Total_length_(>=_25000_bp)": "2735277", "Total_length_(>=_50000_bp)": "2421445", "contigs": "62", "Largest_contig": "436224", "Total_length": "3017519", "GC_(%)": "37.31", "N50": "99915", "N90": "27780", "auN": "154096.4", "L50": "8", "L90": "28", "total_reads": "3489582", "left": "1744791", "right": "1744791", "Mapped_(%)": "99.85", "Properly_paired_(%)": "98.83", "Avg._coverage_depth": "230", "Coverage_>=_1x_(%)": "100.0", "N's_per_100_kbp": "0.00"}}, {"name": "quast_html_path", "file_path": "tests/data/dummy/quast/quast_report.html", "hid": "12345", "galaxy_id": "", "content": {}}], "tool_has_database": false}] \ No newline at end of file |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/recentrifuge_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/recentrifuge_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"analysis_software_version": "5.0.2", "reference_database_version": "1.9", "analysis_software_name": "recentrifuge", "results": [{"name": "recentrifuge_report", "file_path": "tests/data/dummy/recentrifuge/rcf_data.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"Stats": "Id", "count": null, "unassigned": null, "score": null, "Rank": null, "Name": null}, {"Stats": "1", "count": 1705098.0, "unassigned": 8766.0, "score": 23.4065769383, "Rank": "no_rank", "Name": "root"}, {"Stats": "2", "count": 1696077.0, "unassigned": 41771.0, "score": 23.3954250828, "Rank": "superkingdom", "Name": "Bacteria"}, {"Stats": "1224", "count": 656.0, "unassigned": 8.0, "score": 2.5291006276, "Rank": "phylum", "Name": "Proteobacteria"}, {"Stats": "1236", "count": 626.0, "unassigned": 12.0, "score": 2.4820475721, "Rank": "class", "Name": "Gammaproteobacteria"}, {"Stats": "91347", "count": 614.0, "unassigned": 1.0, "score": 2.4579418683, "Rank": "order", "Name": "Enterobacterales"}, {"Stats": "543", "count": 613.0, "unassigned": 320.0, "score": 2.4604241069, "Rank": "family", "Name": "Enterobacteriaceae"}, {"Stats": "2890311", "count": 293.0, "unassigned": 0.0, "score": 3.2460969909, "Rank": "no_rank", "Name": "Klebsiella/Raoultellagroup"}, {"Stats": "570", "count": 293.0, "unassigned": 0.0, "score": 3.2460969909, "Rank": "genus", "Name": "Klebsiella"}, {"Stats": "573", "count": 37.0, "unassigned": 37.0, "score": 0.8707595857, "Rank": "species", "Name": "Klebsiellapneumoniae"}, {"Stats": "1463165", "count": 256.0, "unassigned": 256.0, "score": 3.5894074753, "Rank": "species", "Name": "Klebsiellaquasipneumoniae"}, {"Stats": "28211", "count": 14.0, "unassigned": 3.0, "score": 3.5108263106, "Rank": "class", "Name": "Alphaproteobacteria"}, {"Stats": "204455", "count": 11.0, "unassigned": 0.0, "score": 3.9118522954, "Rank": "order", "Name": "Rhodobacterales"}, {"Stats": "31989", "count": 11.0, "unassigned": 5.0, "score": 3.9118522954, "Rank": "family", "Name": "Rhodobacteraceae"}, {"Stats": "2083206", "count": 6.0, "unassigned": 0.0, "score": 5.0030001348, "Rank": "genus", "Name": "Tritonibacter"}, {"Stats": "379347", "count": 6.0, "unassigned": 6.0, "score": 5.0030001348, "Rank": "species", "Name": "Tritonibactermobilis"}, {"Stats": "68525", "count": 8.0, "unassigned": 2.0, "score": 6.4392025411, "Rank": "subphylum", "Name": "delta/epsilonsubdivisions"}, {"Stats": "29547", "count": 6.0, "unassigned": 0.0, "score": 6.4917947578, "Rank": "class", "Name": "Epsilonproteobacteria"}, {"Stats": "213849", "count": 6.0, "unassigned": 6.0, "score": 6.4917947578, "Rank": "order", "Name": "Campylobacterales"}, {"Stats": "203691", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "phylum", "Name": "Spirochaetes"}, {"Stats": "203692", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "class", "Name": "Spirochaetia"}, {"Stats": "1643686", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "order", "Name": "Brachyspirales"}, {"Stats": "143786", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "family", "Name": "Brachyspiraceae"}, {"Stats": "29521", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "genus", "Name": "Brachyspira"}, {"Stats": "52584", "count": 8.0, "unassigned": 0.0, "score": 2.6705569199, "Rank": "species", "Name": "Brachyspirapilosicoli"}, {"Stats": "759914", "count": 8.0, "unassigned": 8.0, "score": 2.6705569199, "Rank": "strain", "Name": "Brachyspirapilosicoli95/1000"}, {"Stats": "1783257", "count": 9.0, "unassigned": 1.0, "score": 5.6663185939, "Rank": "no_rank", "Name": "PVCgroup"}, {"Stats": "204428", "count": 8.0, "unassigned": 0.0, "score": 6.1710253563, "Rank": "phylum", "Name": "Chlamydiae"}, {"Stats": "204429", "count": 8.0, "unassigned": 0.0, "score": 6.1710253563, "Rank": "class", "Name": "Chlamydiia"}, {"Stats": "1963360", "count": 8.0, "unassigned": 0.0, "score": 6.1710253563, "Rank": "order", "Name": "Parachlamydiales"}, {"Stats": "92713", "count": 8'..b'assigned": 0.0, "score": 4.2516471932, "Rank": "suborder", "Name": "Haplorrhini"}, {"Stats": "314293", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "infraorder", "Name": "Simiiformes"}, {"Stats": "9526", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "parvorder", "Name": "Catarrhini"}, {"Stats": "314295", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "superfamily", "Name": "Hominoidea"}, {"Stats": "9604", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "family", "Name": "Hominidae"}, {"Stats": "207598", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "subfamily", "Name": "Homininae"}, {"Stats": "9605", "count": 133.0, "unassigned": 0.0, "score": 4.2516471932, "Rank": "genus", "Name": "Homo"}, {"Stats": "9606", "count": 133.0, "unassigned": 133.0, "score": 4.2516471932, "Rank": "species", "Name": "Homosapiens"}, {"Stats": "10239", "count": 66.0, "unassigned": 0.0, "score": 4.7615627065, "Rank": "superkingdom", "Name": "Viruses"}, {"Stats": "2731341", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "no_rank", "Name": "Duplodnaviria"}, {"Stats": "2731360", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "kingdom", "Name": "Heunggongvirae"}, {"Stats": "2731618", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "phylum", "Name": "Uroviricota"}, {"Stats": "2731619", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "class", "Name": "Caudoviricetes"}, {"Stats": "10699", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "family", "Name": "Siphoviridae"}, {"Stats": "196894", "count": 41.0, "unassigned": 0.0, "score": 4.7752963479, "Rank": "no_rank", "Name": "unclassifiedSiphoviridae"}, {"Stats": "1747326", "count": 41.0, "unassigned": 41.0, "score": 4.7752963479, "Rank": "species", "Name": "EnterococcusphagevB_EfaS_IME197"}, {"Stats": "2732004", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "no_rank", "Name": "Varidnaviria"}, {"Stats": "2732005", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "kingdom", "Name": "Bamfordvirae"}, {"Stats": "2732007", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "phylum", "Name": "Nucleocytoviricota"}, {"Stats": "2732523", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "class", "Name": "Megaviricetes"}, {"Stats": "2732554", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "order", "Name": "Imitervirales"}, {"Stats": "549779", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "family", "Name": "Mimiviridae"}, {"Stats": "985780", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "no_rank", "Name": "unclassifiedMimiviridae"}, {"Stats": "985782", "count": 25.0, "unassigned": 0.0, "score": 4.7390395347, "Rank": "species", "Name": "Moumouvirus"}, {"Stats": "1269028", "count": 25.0, "unassigned": 25.0, "score": 4.7390395347, "Rank": "no_rank", "Name": "Acanthamoebapolyphagamoumouvirus"}]}, {"name": "recentrifuge_statistics", "file_path": "tests/data/dummy/recentrifuge/rcf_stat.tsv", "hid": "12345", "content": [{"infos": "Seqs.read", "value": 1720128.0}, {"infos": "Seqs.unclass", "value": 15028.0}, {"infos": "Seqs.class", "value": 1705100.0}, {"infos": "Seqs.filtered", "value": 1705100.0}, {"infos": "Scoremin", "value": 35.0}, {"infos": "Scoremean", "value": 111.2545152777}, {"infos": "Scoremax", "value": 295.0}, {"infos": "Lengthmin", "value": 70.0}, {"infos": "Lengthmean", "value": 403.0}, {"infos": "Lengthmax", "value": 602.0}, {"infos": "Totalntread", "value": 690189277.0}, {"infos": "TIDsclass", "value": 426.0}, {"infos": "TIDsfiltered", "value": 425.0}, {"infos": "TIDsfolded", "value": 166.0}, {"infos": "Scorelimit", "value": null}]}, {"name": "recentrifuge_report", "file_path": "tests/data/dummy/recentrifuge/rcf_report.html", "hid": "12345", "content": ""}], "tool_has_database": true}]\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/refseqmasher_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/refseqmasher_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[{"reference_database_version": "", "analysis_software_version": "1.0", "analysis_software_name": "refseqmasher", "results": [{"name": "refseqmasher_report", "file_path": "tests/data/dummy/refseqmasher/refsesqmasher.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"sample": "10_Enterococcus_faecalis_S17_L001", "top_taxonomy_name": "Enterococcus faecalis EnGen0295", "distance": 0.00802142, "pvalue": 0.0, "matching": "314/400", "full_taxonomy": "Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; EnGen0295", "taxonomic_species": "Enterococcus faecalis", "taxonomic_genus": "Enterococcus", "taxonomic_family": "Enterococcaceae", "taxonomic_order": "Lactobacillales", "taxonomic_class": "Bacilli", "taxonomic_phylum": "Firmicutes", "taxonomic_superkingdom": "Bacteria", "subspecies": null, "serovar": null, "plasmid": null, "bioproject": "PRJNA224116", "biosample": "SAMN00809230", "taxid": 1158669, "assembly_accession": "GCF_000395135.1", "match_id": "./rcn/refseq-NZ-1158669-PRJNA224116-SAMN00809230-GCF_000395135.1-.-Enterococcus_faecalis_EnGen0295.fna"}, {"sample": "10_Enterococcus_faecalis_S17_L001", "top_taxonomy_name": "Enterococcus faecalis EnGen0425", "distance": 0.00869982, "pvalue": 0.0, "matching": "308/400", "full_taxonomy": "Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; EnGen0425", "taxonomic_species": "Enterococcus faecalis", "taxonomic_genus": "Enterococcus", "taxonomic_family": "Enterococcaceae", "taxonomic_order": "Lactobacillales", "taxonomic_class": "Bacilli", "taxonomic_phylum": "Firmicutes", "taxonomic_superkingdom": "Bacteria", "subspecies": null, "serovar": null, "plasmid": null, "bioproject": "PRJNA224116", "biosample": "SAMN02333901", "taxid": 1391495, "assembly_accession": "GCF_000519925.1", "match_id": "./rcn/refseq-NZ-1391495-PRJNA224116-SAMN02333901-GCF_000519925.1-.-Enterococcus_faecalis_EnGen0425.fna"}, {"sample": "10_Enterococcus_faecalis_S17_L001", "top_taxonomy_name": "Enterococcus faecalis ATCC 4200", "distance": 0.00916272, "pvalue": 0.0, "matching": "304/400", "full_taxonomy": "Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; ATCC 4200", "taxonomic_species": "Enterococcus faecalis", "taxonomic_genus": "Enterococcus", "taxonomic_family": "Enterococcaceae", "taxonomic_order": "Lactobacillales", "taxonomic_class": "Bacilli", "taxonomic_phylum": "Firmicutes", "taxonomic_superkingdom": "Bacteria", "subspecies": null, "serovar": null, "plasmid": null, "bioproject": "PRJNA224116", "biosample": "SAMN02595252", "taxid": 565642, "assembly_accession": "GCF_000157195.1", "match_id": "./rcn/refseq-NZ-565642-PRJNA224116-SAMN02595252-GCF_000157195.1-.-Enterococcus_faecalis_ATCC_4200.fna"}, {"sample": "10_Enterococcus_faecalis_S17_L001", "top_taxonomy_name": "Enterococcus faecalis ATCC 29212", "distance": 0.00975375, "pvalue": 0.0, "matching": "299/400", "full_taxonomy": "Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; ATCC 29212", "taxonomic_species": "Enterococcus faecalis", "taxonomic_genus": "Enterococcus", "taxonomic_family": "Enterococcaceae", "taxonomic_order": "Lactobacillales", "taxonomic_class": "Bacilli", "taxonomic_phylum": "Firmicutes", "taxonomic_superkingdom": "Bacteria", "subspecies": null, "serovar": null, "plasmid": null, "bioproject": "PRJNA224116", "biosample": "SAMN02870637", "taxid": 1201292, "assembly_accession": "GCF_000742975.1", "match_id": "./rcn/refseq-NZ-1201292-PRJNA224116-SAMN02870637-GCF_000742975.1-.-Enterococcus_faecalis_ATCC_29212.fna"}, {"sample": "10_Enterococcus_faecalis_S17_L001", "top_taxonomy_name": "Enterococcus faecalis EnGen0417", "distance": 0.0101152, "pvalue": 0.0, "matching": "296/400", "full_taxonomy": "Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus; faecalis; EnGen0417", "taxonomic_species": "Enterococcus faecalis", "taxonomic_genus": "Enterococcus", "taxonomic_family": "Enterococcaceae", "taxonomic_order": "Lactobacillales", "taxonomic_class": "Bacilli", "taxonomic_phylum": "Firmicutes", "taxonomic_superkingdom": "Bacteria", "subspecies": null, "serovar": null, "plasmid": null, "bioproject": "PRJNA224116", "biosample": "SAMN02333893", "taxid": 1391487, "assembly_accession": "GCF_000519765.1", "match_id": "./rcn/refseq-NZ-1391487-PRJNA224116-SAMN02333893-GCF_000519765.1-.-Enterococcus_faecalis_EnGen0417.fna"}]}], "tool_has_database": false}] \ No newline at end of file |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/shovill_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/shovill_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"analysis_software_version": "1.1.0", "reference_database_version": "", "analysis_software_name": "shovill", "results": [{"name": "shovill_report", "file_path": "tests/data/dummy/shovill/contigs.fa", "hid": "12345", "galaxy_hid": "", "content": {"contig00001": {"length": 436224, "coverage": 31.3, "sequence": "CTTTCTATCTTAGATTTTTGGTCGTACTTAAATTTTACTAGATAGACGACATGTTTTATATTTAAATAAACTAAAAAAGGACTGATGAATCAAAATTTGATTCATCAGTCCTTTAAATTATAGAGCCGTTAAAGACAGCCACAGCACGTGGCTGTCTTTTTTATTTTTTGTTATTTTTTCATTCTATTAAAATACCTGAGAAGTTTTCTTTTTTCTTAAGCTTGATTATGATAGAATGATTGGGTAGTTTATTTAGAAAACGTATATTACAGATAGGTGAGAATATAAATGAAAAAAATCGTAATCAATGGGAATCGTCCATTAAAGGGCGAAGTAACCATTAGCGGCGCCAAAAATAGTGTGGTCGCTTTAATTCCAGCTGCTATTTTAGCAGATTCGCCCGTGACTTTAGATGGCGTTCCTGACATTCAGGATGTTCACTCATTAATTGAAATATTAGAAATTATGGGTGCTAAAATTACTTTTGAAAATAATACATTAATTATTGACCCAACAGAAGTTGTTTCTGTGCCTATGCCAAAAGGAAAAATCAATAGCTTACGTGCATCCTATTATTTTATGGGCTCACTTCTTGGTCGATTTGGGGAAGGCGTTGTCGGCTTACCTGGCGGTTGTTACTTAGGACCTCGTCCAATTGATTTACATATCAAAGGATTTGAAGCATTAGGCGCTCATGTAACCAACGAACATGGGGCGATGTACTTGAGAACAGACGAAGCTGGCTTACAAGGAACACGAATTTTTATGGATATGGTATCTATTGGCGCTACAATCAATGTCATGTTAGCCGCAGTTAAAGCCAAAGGCAAAACGATTATTGAAAATGCTGCGCGTGAGCCAGAAATCATTGATATTGCTACATTATTAAATAACATGGGTGCAAAAGTTCGAGGAGCTGGAACGGACGTTATTCGGATTGAAGGTGTCGAAGAATTACATGGCTGTCGTCACTCGATTATTCCAGATCGAATTGAAGCTGGGACTTATTTAGCTATGGCAGCAGCTATGGGTGAAGGAATCAAGGTTCGAAATGTTATTTATGAGCATTTAGAAAGCTTCATTGCGAAATTGCAAGAAATGGGCGTTAAGATGACAATTGAAGAAGACATGATTGAAGTTCATCCGTCACATGATCTGAAAATGACGACGGTGAAAACCTATCCGTATCCTGGTTTTGCCACAGACTTGCAACAACCGTTAACGCCATTACTTTTAAAAGCACAAGGAACTGGTGAAATTATTGATACGATTTATGCTCAACGAAATAAGCATATCCCTGAGTTGGTGCGGATGGGGGCTGATGCTTCGGTTGAAGGCAATATGATTATCTTAAATGGCCCAAATCAATTGCACGGTGCAGAAGTAGTCGCCTCTGATTTACGGGCAGGCGCTTGCCTAGTCACTGCCGGCTTGATGGCTGAAGGTACGACCACTATTTATAATGTAGAATATATTTTACGTGGGTACGACCACATTATCGAAAAGTTAACTGCTTTAGGCGCTGATATTCAAATGCTAGAAACCGAAGAACAAGAAGGTCCGTTTGAGGTGGATCAATGAGCGACTATTTAACAATGGCTGAATTGGAAAACAGTACGTTAAAAGATATTTATGCATACGCGAAAGAGTTTAAAATTCCTTATTATAGCCAAATGAACAAAAAAGAATTGTCTTTAGCTGTGATTCGTGCACAAGCTGAGAAGCAAGGGTTTTTCTTCATGGAAGGAATTTTAGATATTGTTTCTCAGGATGGTTATGGTTTTTTGCGACCAATTAATTATGGACCAAGTGCAGAAGACATTTATATTTCTTCTTCTCAAATTCGTCGTTTCGGATTGAGAAATGGGGACAAAGTAGCTGGCAAGGCGCGTCCGCCAAAGGAATCAGAACGTTACTATGGACTCATGCATGTTGAAAGTGTCAATGGGAAAGATCCTGAAGAAGCGAAAGAGCGGCCACATTTTCCAGCGCTAACACCGTTGTATCCTGAAAAACAATTAACGTTAGAAACAACGGCTGGCAGATTATCAACACGAATGATTGATGTATTTGCCCCAATTGGTTTTGGGCAACGTGGTTTAATTGTAGCGCCGCCAAAAGCGGGGAAAACAAGTGTTTTAAAGGAAATTGCTAATGGGATTACAGAAAATCATCCTGATGTGGAATTGATTCTGTTGTTAATTGACGAGCGTCCTGAAGAAGTGACTGATTTAGAGCGAAGTGTTAAAGGCGATGTGGTTTCTTCAACTTTTGATCAACAACCACAAAATCATACGCGAGTTGCTGAATTGGTTCTGGATCGAGCAATGCGCTTAGTTGAAGACAAACGGGACGTAGTTATTTTAATGGACAGCATCACTCGTTTAGCAAGGGCCTATAATTTAGTGGTCCCGCCTAGTGGTCGAACCTTAAGTGGTGGAATAGATCCAGCTGCGTTTTTCAAACCTAAACGATTTTTTGGTGCTGCCAGAAATATCGAAGAAGGGGGCAGTCTGACTATTTTAGCCACGGCATTGGTGGATACAGGTAGCCGAATGGATGATGTCATCTATGAAGAATTCAAAGGCACAGGCAACATGGAGCTCCATTTATCTCGTGAATTAGCAGAGCGCCGTATTTTCCCAGCAATTGATATTAAAAAATCAAGTACGCGAAAAGAAGAGTTGCTAATGACACCAGAACAACTAGAAGAAACGTGGAAATTGAGAAATAATATGTCAGGAGACTCGCTGGAATATACGGATCAATTCATAAAAATGTTGAAACGGACCCAAAATAATCAACAATTATTTGAAGTTTTCCATGATGTTTCGTTTGGCAAACAAATTAAAAGAAATCCAAAAAGATAATTGCATACCAACTGAAAACATGGTAAGATAGCATTGTTGTATACCGACAAAATAACTCTGATACAGCAAATGGATCAGGGCAAAGGAGCGAAAAAACGTATGAAACAAGATATCCATCCAAATTACCAACCAGTAGTATTCATGGATTCAACAACAGGTTTCAAATTCCTTTCAGGTTCAACTAAAGGATCTTCAGAAACTGTTGAATGGGAAGATGGCAACACTTATCCATTATTACGTGTTGAGGTTACTTCAGACTCACACCCATTCTACACTGGTCGTCAAAAATTCACACAAGCCGACGGACGTGTGGACCGTTTCAACAAAAAATACGGTCTCAAAGACGAAAACGCAAATCCAGACGCATAGTCTTTCAAAACATTGTTATGACAAGGTTTATAGAGGTTTTCCACTGTGGTGGGAAACCTCTTTTTTGCGTTAAATATGTAGTTTTAATTCAGAGAAAAGAAATAAAGCAACTTACCAATCTTTTCCTCTTTCTTTTCAAGATTATCCTTCCCAAAAGTCAAAGATTGATCAGCATTGTTTCGCTGATTTGTTAGACTAGTAGGTACATTCAGCTTTATAAAGGAGATCTTGAAGAAATGAGTAGAAAAAAAGTCGGTGTTTTCTGTCTATTTCTGTTTTTCACATTTTTTATTATTGTTCCAAAAGTAGAAGCTACAGAAGAAATGAAGACTAAATTTACAGTAACGCCTGTTTTACCAGAAAATCAAGTGTCAGGAACATCTAGTTATTATGATTTAATTCTGGCACCAAAGCAATCTTCCACTATTGT'..b'CGTTTCTTGTTGGTTCTTTAATTGCTCATTTTCTTCTTGAAGTTTTTTAAAGGCTGTTTCTTTTTTCTGATAGTAGGCGAGCCTTTCTCTTAACGTCGCCATTTCTTTTTCCTGTTGTTCCGGTTTGATTCCGCTAATTATTTTTTCTGGTTCGAATCCTGGCTGAAAAAAGACTTCTTTTTCAAGCGTATCATCCGAAATATCTTTAATTTTTTTGATTAAACGTCTTTTTGTCATATATATGTCCTTTCTCTCGTCCTTTTAACTAATCACGACAGGCTCCAAATTTGTTTCAAGCGTCTCACGAGCATACGTATCAATGGATTTGACAAGGGTTTGCTCTTGATCTCGATAAGTAAAATTAAAATCAATCATGGTAATTTCTTTAACTGAATTCAACGCTGCAATAAGTGCTACAATATTGTCTTGGCCTGTTTGAAATTCATGGTAACTTAAGCCAACTGAAAAAACAGACAGTGTCAAGGTTTGTGTTTTTTCACTTCTAATCATTGTGATACTCGTCTCTCCGAGGTAAGGACGCCATTCACGCGCTAATTGTAATTCATAATTAGTCAAGACAGCGGCCGATTCTGCCGAAACAGCTTGCTTCCAGGGAAACTGATTTAAGGCTGTTTTTTTAATCGCTTGTTTTTTTATTTTGTCACCTTGAGTAGCTTGGCCTTGTGCCAAACGCTCAATCCGTTGTTCCATGCGGATATTTCGTTGATTTAATTGATAATATGTATAAACAATTCCTAACAATAATACGCTAAGTAGACAAACACTAAACAATAAATAAATCATTAAACGACTATTTTTCTGATACTTATAGAAATTTATTTTCCTCTTTAATGTCCGGTCCTCTGAATCCAGTTTTTCGACAAGTAATCGCAAATACAATTGATAGCTTACAAATAAAAATAAGCAACTACTCATTAAAAGTACAACAATCATCATACAAATATAATCTCCTTTATGTCATCGCTCGACAATCAAAACTTGTAAAATCACCTGTTACGCTCTTTAAAAACTCTATATAGTATTGATTGTAACATTCCGTTTGAGCCTTGCCAACAACTTTATTTAAAATACAATGATAAAATTTTATATTTTATATTTATATTTTAATTTTTAAAATATAAAACAAAAAAAGAGAGATGCCACTTGGCCATCTCTCTCGCTTTTACTCAAACTATGTTTAGCGAACCGTACTAGATCAGTCGCTTTTAAAAAAATCCAATTAGTCTTTGTTGATTTCATAGTAGCTATCGTTCTTTATGTAGCTGAATTTGCTTTTGCTGGGGCTGAATCGCTACTAAGTCCAACACTGATGCCTAAGGCACGATCAACTTCTTCCATAATATCAAGTCTCAAATGACAAACTTTTTCTTTCAAGCGACCCTTATCGATTGTTCGAATCTGCTCTAAAAGAATCACTGAATCTTTTTCAATGCCTGTTTCATCAGAATTAATCCCGATATGTGTTGGCAATTTTGGCTTTGCCATTTTGGCTGTGATCGCCGCAACGATAATCGTTGGGCTAAAATGATTACCTAAGTTATTTTGGACAACAAGGACAGGTCTGACGCCACCTTGTTCCGAGCCCACTACTGGGGAAAGGTCTGCAAAATAAATATCTCCGCGTTTGACCATAGTGGAACCTCCTATCTAGTTATATTCTCTGGGGATTCTTTGTGAGAAAGTACATGCAACTTCATAATGAATGGTTTCTAATTTTTCGGCTACCATTTGTAACGTATTTTCTTCATTGCCATCTTTTCCAACTAATGTAACGACTGAGCCGACAGGAACTTCTTCTGCTAAACGAATCATACATTGATCCATACACACTCGTCCGACGATTTCGCAACGCTTACCATTCACGAGCACTGTAAATCCTTGGAGATGACGCAACCAGCCATCTGCATAGCCGATTGGCACTGTCCCAATCCATTCTTCAGCTTCAGTTACGTAGGTTTCGCCATAGCCAATCCCTTCACCAGCCGCTAAGCGTTTTACATGGATAAGTTCACTGGTCAACCGTAAGGCCGGCTTTAACGCATAGCTTGGGGCAAGCTTATTACCTGAAGGGTTCAATCCATACATGGCTACTCCATAGCGAATCATGTTTCCTGGCACATCAGGATGCCATAACGCTGTCGCACTATTGCTAACATGGACATACCGTGGTAACTCTTCTAAAACTGCTAGAACAGCCTTAAAACGCCCTGCTTGTTTTTCAAAATAGCTTGTATCGATTTCATCAGCTGTTGAAAAATGAGTAAAAATCCCTTCCCATAAAAATTCTTTGTGGGATTGAACAAACCGCACTGCTTGCTTAGTCTCTTCCGGGGTTAAAAAGCCAATCCGTCCCATGCCAGTATCGACTTTTAAGTGAACACGTAATGGCGTGTTACTCTCAGGCGTTAGTTGTTGAAGAGCAGCTTCTAACCATTCTTGTGTAGCTACCGTTACAGACAAATCATATTGAATCAACAAAGGCACATAAGCTAAGTCTACCACACTCAAAATTAAAATGGGGTCCTGAACACCTGCTTCTCTCAATTCAATTGCTTCATCCAATAAGGCGACACAAAAACCTGTCGCGCCACCTTTTTTCGCCGCTTTAGCGGATTCTACGGCGCCATGCCCATAGCCGTTCGCTTTCACAACCGCAAATAAAGCAGTTCCTTCTGGCAAACGTTGACATTCCTTTTGGACATTTTCAGTAATTGCTTGCGTATCGATATGTAACCGTGTAGGACGATGCCATCCAACGACCATTGTACATCCTTCTTTCTTCGTTGCTTCTGTTATTCGCTTTCTAAAACAATTTGTGCAATCGCCATAGTATCTGTGTGCGTAATTGAGACAAACACTTTACCATTATGGGGCGAGTTTGCTACGTATGGTGCACCTGTTTTTTCAGTCAGCACCTCAATATCTTGTAAACCAACTTTACCAATCCCTGTGCCCCATGCTTTAGAAAACGCTTCTTTACAAGCAAAACGACCAGCTAAAAATTCTATTTGACGTTTTGTAGATAACTTTTCAAAAAGGGTCAATTCGTTAGGTGTTAAAACCCGTTGAATAAACGATCCTTGTTTTTCAACAATCGGTTTTATCCGACTTAATTCTACTGCGTCAATACCAATTCCCTTTATCATTTTCCGCCTTACTTCCTATTTAATATAGTTACTCCGAATTACCTTTCATTTTAACAAAATTTCAAAATTTTTCCACTGATTCGCTAAAAAAATAAAGAATGTTTTACAAGATCCTCACACAAATTGAAGTACCATACGTTTTCTTCCTATTTACATTTTTATAAAATTTTTCTGAATTTTTATAAAACGCGAATTGTAAAATTAAGTTAGAAAAATAAAAAGGCATTTATGGTACACTCAAATTGTATTTCCGACGAAAGAAAACAAAGGAGTGTAACCATAAATGACCTACAAACATCTTACCATAGACGAACTGACAATGATAGAATCATATTATCTTCAACATAATAAACCGGTTGAAATCGCTAACCGAATGGGTCGTGCTATACAAACTATTTATAATGTAGTCAATAAGTTCAAGCAAGGCAAGACTGCTCTTGATTATTGGCACCAGTATAAAGAAAATAAGAAAAAATGTGGTAGAAAAGTCATTCAATTACCTGCTC"}}}, {"name": "contig_graph_path", "file_path": "tests/data/dummy/shovill/contigs.gfa", "hid": "12345", "galaxy_id": "", "content": {}}, {"name": "bam_file_path", "file_path": "tests/data/dummy/shovill/alignment.bam", "hid": "12345", "galaxy_id": "", "content": {}}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/staramr_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/staramr_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"analysis_software_version": "1.1.0", "reference_database_version": "", "analysis_software_name": "staramr", "results": [{"name": "staramr_report", "file_path": "tests/data/dummy/staramr/resfinder.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Gene": "ant(6)-Ia", "Predicted Phenotype": "streptomycin", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "909/909", "Contig": "contig00046", "Start": 4769, "End": 3861, "Accession": "AF330699", "Sequence": "ATGAGATCAGAAAAAGAAATGATGGATTTAGTACTTTCTTTAGCAGAACAGGATGAACGTATTCGAATTGTGACCCTTGAGGGGTCACGCGCAAATATTAATATACCTAAAGATGAATTTCAGGATTATGATATTACATATTTTGTAAGTGATATAGAACCGTTTATATCTAATGATGACTGGCTTAATCAATTTGGGAATATAATAATGATGCAAAAGCCGGAGGATATGGAATTATTCCCACCTGAAGAAAAGGGATTTTCCTATCTTATGCTATTTGATGATTACAATAAAATTGATCTTACCTTATTGCCCTTGGAAGAGTTAGATAATTACCTAAAGGGCGATAAATTAATAAAGGTTCTAATTGATAAAGATTGTAGAATTAAAAGGGACATAGTTCCGACTGATATAGATTATCATGTAAGAAAGCCAAGCGCAAGGGAGTATGATGATTGCTGCAATGAATTTTGGAATGTAACACCTTATGTTATTAAAGGATTGTGCCGTAAGGAAATTTTATTTGCTATTGATCATTTTAATCAGATTGTTCGCCATGAGCTGCTGAGAATGATATCATGGAAGGTCGGCATCGAAACAGGCTTTAAATTAAGTGTAGGCAAGAACTATAAGTTTATTGAAAGGTATATATCCGAGGATTTGTGGGAGAAACTTTTGTCCACCTACCGGATGGATTCCTATGAAAACATATGGGAAGCATTATTTCTATGCCATCAATTGTTCAGGGCGGTATCCGGTGAGGTGGCGGAAAGGCTTCATTATGCCTATCCGGAGTATGATAGGAATATAACAAAATATACCAGGGACATGTATAAAAAATACACTGGTAAAACCGGCTGCCTGGATAGCACATATGCCGCTGATATAGAAGAGAGGCGGGAACAGTGA", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Gene": "aph(3\')-III", "Predicted Phenotype": "kanamycin,amikacin", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "795/795", "Contig": "contig00046", "Start": 3229, "End": 2435, "Accession": "M26832", "Sequence": "ATGGCTAAAATGAGAATATCACCGGAATTGAAAAAACTGATCGAAAAATACCGCTGCGTAAAAGATACGGAAGGAATGTCTCCTGCTAAGGTATATAAGCTGGTGGGAGAAAATGAAAACCTATATTTAAAAATGACGGACAGCCGGTATAAAGGGACCACCTATGATGTGGAACGGGAAAAGGACATGATGCTATGGCTGGAAGGAAAGCTGCCTGTTCCAAAGGTCCTGCACTTTGAACGGCATGATGGCTGGAGCAATCTGCTCATGAGTGAGGCCGATGGCGTCCTTTGCTCGGAAGAGTATGAAGATGAACAAAGCCCTGAAAAGATTATCGAGCTGTATGCGGAGTGCATCAGGCTCTTTCACTCCATCGACATATCGGATTGTCCCTATACGAATAGCTTAGACAGCCGCTTAGCCGAATTGGATTACTTACTGAATAACGATCTGGCCGATGTGGATTGCGAAAACTGGGAAGAAGACACTCCATTTAAAGATCCGCGCGAGCTGTATGATTTTTTAAAGACGGAAAAGCCCGAAGAGGAACTTGTCTTTTCCCACGGCGACCTGGGAGACAGCAACATCTTTGTGAAAGATGGCAAAGTAAGTGGCTTTATTGATCTTGGGAGAAGCGGCAGGGCGGACAAGTGGTATGACATTGCCTTCTGCGTCCGGTCGATCAGGGAGGATATCGGGGAAGAACAGTATGTCGAGCTATTTTTTGACTTACTGGGGATCAAGCCTGATTGGGAGAAAATAAAATATTATATTTTACTGGATGAATTGTTTTAG", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Gene": "cat(pC221)", "Predicted Phenotype": "chloramphenicol", "Identity": 97.69, "Overlap": 100.0, "HSP Length/Total Length": "648/648", "Contig": "contig00048", "Start": 4344, "End": 4991, "Accession": "X02529", "Sequence": "ATGACTTTTAATATTATTGAATTAGAAAATTGGGATAGAAAAGAATATTTTGAACACTATTTTAATCAGCAAACTACTTATAGCATTACTAAAGAAATTGATATTACTTTGTTTAAAGATATGATAAAAAAGAAAGGATATGAAATTTATCCCTCTTTAATTTATGCAATTATGGAAGTTGTAAATAAAAATAAAGTGTTTAGAACAGGAATTAATAGTGAGAATAAATTAGGTTATTGGGATAAGTTAAATCCTTTGTATACAGTTTTTAATAAGCAAACTGAAAAATTTACTAACATTTGGACTGAATCTGATAAAAACTTCATTTCTTTTTATAATAATTATAAAAATGACTTGCTTGAATATAAAGATAAAGAAGAAATGTTTCCTAAAAAACCGATACCTGAAAACACCATACCGATTTCAATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAATATTGGTAACAATAGCAGCTTTTTATTGCCTATTATTACGATAGGTAAATTTTATAGTGAGAATAATAAAATTTATATACCAGTTGCTCTGCAACTTCATCATTCTGTATGTGATGGTTACCATGCTTCACTATTTATGAATGAATTTCAAGATATAATTCATAGGGTAGATGATTGGATTTAG", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Gene": "dfrG", "Predicted Phenotype": "trimethoprim", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "498/498", "Contig": "contig00049", "Start": 275, "End": 772, "Accession": "AB205645", "Sequence": "ATGAAAGTTTCTTTGATTGCTGCGATGGATAAGAATAGAGTGATTGGCAAAGAGAATGACATTCCTTGGAGGATTCCCAAGGACTGGGAATATGTTAAAAATACTACAAAGGGACATCCGATAATATTAGGTAGGAAGAACCTTGAATCAATCGGAAGAGCCTTACCTGACAGAAGAAATATTAT'..b'idfinder", "file_path": "tests/data/dummy/staramr/plasmidfinder.tsv", "hid": "12345", "content": [{"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Plasmid": "rep7a", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "939/939", "Contig": "contig00048", "Start": 3276, "End": 4214, "Accession": "X92945", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Plasmid": "rep9b", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "1014/1014", "Contig": "contig00023", "Start": 3630, "End": 4643, "Accession": "CP002494", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Plasmid": "repUS12", "Identity": 99.75, "Overlap": 99.62, "HSP Length/Total Length": "792/795", "Contig": "contig00051", "Start": 918, "End": 127, "Accession": "AF181950", "coverage_ratio": 1.0037878788}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Plasmid": "repUS40", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "1158/1158", "Contig": "contig00026", "Start": 21156, "End": 22313, "Accession": "KP399637", "coverage_ratio": 1.0}, {"Isolate ID": "10_Enterococcus_faecalis_S17_L001", "Plasmid": "repUS43", "Identity": 100.0, "Overlap": 100.0, "HSP Length/Total Length": "1206/1206", "Contig": "contig00040", "Start": 9430, "End": 8225, "Accession": "CP003584", "coverage_ratio": 1.0}]}, {"name": "pointfinder", "file_path": "tests/data/dummy/staramr/pointfinder.tsv", "hid": "12345", "content": [{"Isolate ID": "SRR1952908", "Gene": "gyrA(S83Y)", "Predicted Phenotype": "ciprofloxacinI/R,nalidixicacid", "Type": "codon", "Position": 83, "Mutation": "TCC->TAC(S->Y)", "Identity": 99.96, "Overlap": 100.0, "HSP Length/Total Length": "2637/2637", "Contig": "contig00008", "Start": 22801, "End": 20165, "coverage_ratio": 1.0}]}, {"name": "settings", "file_path": "tests/data/dummy/staramr/settings.txt", "hid": "12345", "content": {"command_line": "/home/piemari/apps/conda/envs/amr/bin/staramrsearch--nprocs4--no-exclude-genes--pid-threshold95--percent-length-overlap-resfinder90--percent-length-overlap-pointfinder90--percent-length-overlap-plasmidfinder90--output-dir/storage/scratch/piemari/60579242/staramr/staramr_10_Enterococcus_faecalis_S17_L001/storage/scratch/piemari/60579242/staramr/10_Enterococcus_faecalis_S17_L001.fasta", "version": "0.9.1", "start_time": "2023-02-1314:26:11", "end_time": "2023-02-1314:26:13", "total_minutes": "0.04", "resfinder_db_dir": "/home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/resfinder", "resfinder_db_url": "https://bitbucket.org/genomicepidemiology/resfinder_db.git", "resfinder_db_commit": "23661dbb58797b302464855611223b7ba4a21f75", "resfinder_db_date": "Fri,02Dec202211:36", "pointfinder_db_dir": "/home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/pointfinder", "pointfinder_db_url": "https://bitbucket.org/genomicepidemiology/pointfinder_db.git", "pointfinder_db_commit": "a25ac32c7a7a904dff14ffbd17e3b3f7cd732954", "pointfinder_db_date": "Fri,28Oct202210:19", "pointfinder_organisms_all": "campylobacter,enterococcus_faecalis,enterococcus_faecium,escherichia_coli,helicobacter_pylori,klebsiella,mycobacterium_tuberculosis,neisseria_gonorrhoeae,plasmodium_falciparum,salmonella,staphylococcus_aureus", "pointfinder_organisms_valid": "campylobacter,enterococcus_faecalis,enterococcus_faecium,escherichia_coli,helicobacter_pylori,salmonella", "plasmidfinder_db_dir": "/home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/plasmidfinder", "plasmidfinder_db_url": "https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git", "plasmidfinder_db_commit": "b1c9ddac0e618e07630a94452293d84f296a6de5", "plasmidfinder_db_date": "Thu,12Jan202312:51", "mlst_version": "2.23.0", "pointfinder_organism": "None", "pointfinder_gene_drug_version": "072621.1", "resfinder_gene_drug_version": "072621"}}], "tool_has_database": false}]\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/summarize.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/summarize.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"analysis_software_version": "1.0", "reference_database_version": "1.0", "analysis_software_name": "abricate", "results": [{"name": "abricate_report", "file_path": "tests/data/dummy/abricate/report.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00002", "START": 142975, "END": 143985, "STRAND": "+", "GENE": "bopD", "COVERAGE": "1-1011/1011", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 98.91, "DATABASE": "vfdb", "ACCESSION": "NP_814691", "PRODUCT": "(bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00003", "START": 7884, "END": 11111, "STRAND": "-", "GENE": "fss3", "COVERAGE": "1-3228/3228", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.38, "DATABASE": "vfdb", "ACCESSION": "NP_815578", "PRODUCT": "(fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00003", "START": 162314, "END": 163240, "STRAND": "+", "GENE": "efaA", "COVERAGE": "1-927/927", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.89, "DATABASE": "vfdb", "ACCESSION": "NP_815739", "PRODUCT": "(efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00006", "START": 33703, "END": 37014, "STRAND": "+", "GENE": "ebpA", "COVERAGE": "1-3312/3312", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.49, "DATABASE": "vfdb", "ACCESSION": "NP_814821", "PRODUCT": "(ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00006", "START": 37018, "END": 38448, "STRAND": "+", "GENE": "ebpB", "COVERAGE": "1-1431/1431", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.3, "DATABASE": "vfdb", "ACCESSION": "NP_814822", "PRODUCT": "(ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00006", "START": 38445, "END": 40328, "STRAND": "+", "GENE": "ebpC", "COVERAGE": "1-1878/1878", "GAPS": "1/6", "%COVERAGE": 100.0, "%IDENTITY": 98.99, "DATABASE": "vfdb", "ACCESSION": "NP_814823", "PRODUCT": "(ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00006", "START": 40422, "END": 41276, "STRAND": "+", "GENE": "srtC", "COVERAGE": "1-855/855", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.3, "DATABASE": "vfdb", "ACCESSION": "NP_814824", "PRODUCT": "(srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00006", "START": 44356, "END": 46374, "STRAND": "+", "GENE": "ace", "COVERAGE": "1-2025/2025", "GAPS": "2/6", "%COVERAGE": 99.7, "%IDENTITY": 96.74, "DATABASE": "vfdb", "ACCESSION": "NP_814829", "PRODUCT": "(ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]", "RESISTANCE": null}, {"FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00010", "START": 49447, "END": 50301'..b'AAAAATAAAAAAAGGAAACCGAATTGGTTCGATTCAGTTCCATATTACGAAAAAACAAATTGCTCCTAATCCTTCTTACAAAATTGGCGATTCTGTGTATGAAGCGCAACAAGCAGAAAAAGAACAAAATCAAATTACTTTATTTGCGCAGGCAATGCAAAGTCAATACACTACCATTTTGATGGAAAATATGTTGATTGGGTACAAAGATATGCAAGATATTGAATTAATGGCAAGCTTGCAAGAAATGGTTTATCCCTTGTATGACGAGTTGAAAACTCTTAGAGGATTAGACGGTGTGAGAAATCACTTAGAATACGTTTCAAGAAAACAAATAGGCTATTCTAAAACTAATATTGTCAAGTATTTAAAAACAGCTATCACACAATATTTGCCAACGGTAAAAATGATGGATATGGATAATAGAGTGTAA"}, "contig00023": {"sequence_informations": {"len": "45935", "cov": "46.6", "corr": "0"}, "nucleotide_sequence": "ATGAACGATTTTCAATTTATTTCAGCTAATGAAACCTATAGAAATTTGTATTACCAATTACCTAAAGTACTTTTTACATCAGAATTTTATAAGACTATGTCTAATGATAGTAAAATAGCTTACGCAATGTTGCAAGACCGATGTGAATATTCAATACAAAATAATTGGATTGATCAAGATGGGCATATATATTTTATCTTTACACGAAATGAACTGATGGATATTTTAGGGTGTAAAGAAAATAAAATTGCAAAAATAAAAAAAGAATTAAAAGACAAAAATTTACTTTATGAAAAACGTATTCCTCCGAAAAAACTCTCTACTGGTGAATTCAAAAACTATCCAAACAGATTGTATTTAGGTAAGCTGGAAGTTTCAGCAACAGATGTTTACGCCATCAGTAATGCTAGCTATACAAATGAGTTTCCCGAAAGTGGGAAAAACCAACCTTCGGATAAACATGATAAAATCGGCATTTCTTTCGAAAGTGGGAAAAACCAACGTCCAGAAGAATCCAATAATACCAGTACTTTGTTCGAAAGTGGGAAAAACCAACCCAATCTATATCTAACTAATTCTTTAGATACAATAGATACAATAGATACTGAAAAAGAACGATTGCAACAACAATTATTGCTCGATCAATTTTCAGAAGTTCAAGAGCATACATTTCTTAGCAAAAATAGCTTAAAATTTATTGCTGCCTTTTCTGATACTATTCAAGAAGCACATGAAATGGTTGGAACAATTATTCGTGCTAAAACTAAAGTAGAAAAAGAATACAATATCGTTCTAATTGGTGAAGATTATCAAGAAGAAATAGACAAATGTTTGCGTCGTGTGATGCATAAAATCAAGACAGATTCTACTGTAAAAAGTCCAAAAGGCCTATTCTACAAGTCGTTTTACAATTTATTTGTTGAATGTACAATAGAGAAAAAAAGTCATTTAAATAAAAATAGTACGGACAACACCCCAGAAATAACTACACATAACTGGATTGAGTATCAATAA"}, "contig00048": {"sequence_informations": {"len": "5336", "cov": "19.5", "corr": "0"}, "nucleotide_sequence": "ATGAAGAAAATTGATGAAAAATTAGCTGCAGAAATCTCACTAAAAAAACCGGCCGTCTCTAATAGCCGGTTAAGTAATAGCCGGTTAAGTGGTCAAACTTTGGGAAAATCTCAACCCGCATTAAGTTTTGATGCCATGACAATCGTTGGAAATTTGAACAAAACTAATGCTAAAAAGCTATCTGACTTTATGAGTGTAGAGCCACAAATACGACTTTGGGATATACTTCAAACAAAGTTTAAAGCTAAGGCACTTCAAGAAAAAGTTTATATCGAATATGACAAAGTAAAAGCAGATACTTGGGATAGACGTAATATGCGTGTTGAATTTAATCCCAATAAACTCACACATGAAGAAATGATTTGGTTAAAACAAAATATTATCGACTACATGGAAGATGACGGTTTTACAAGATTAGACTTAGCTTTTGATTTTGAAGATGATTTGAGCGATTACTATGCAATGACTGATAAAGCAGTTAAGAAAACTGTTTTTTATGGTCGTAATGGCAAGCCAGAAACAAAATATTTTGGTGTCCGTGATAGTGATAGATTTATTAGAATTTATAATAAAAAACAAGAACGTAAAGATAACGCAGATGTTGAAGTTGTGTCTGAACATTTATGGCGTGTAGAAGTTGAATTAAAAAGAGATATGGTTGATTACTGGAATGATTGTTTTAATGATTTACACATCTTGAAACCTGCGTGGGCTACTTTAGAAAAAATTAATGAGCAAGCTATGGTTTATACTTTGTTGCATGAAGAAAGTATGTGGGGAAAGCTAAGTAAGAATACTAAGACTAAATTTAAAAAATTGATTAGAGAAATATCTCCAATTGATTTAACGGAATTAATGAAATCGACTTTAAAAGCGAACGAAAAACAATTGCAAAAGCAGATTGATTTTTGGCAACGTGAATTTAGGTTTTGGAAGTAA"}, "contig00040": {"sequence_informations": {"len": "12074", "cov": "69.2", "corr": "0"}, "nucleotide_sequence": "TTGGAGGGATTTTTACTGAATGAACAAACTTGGTTACAGCATTTAAAAGAAAAACGCTTGGCTTATGGACTATCTCAAAACCGTTTAGCTGTTGCGACTGGTATTACAAGGCAGTATCTAAGCGATATTGAAACAGGAAAAGTCAAGCCATCAGAGGATTTACAGCAGTCCCTTTGGGAAGCTCTGGAACGCTTCAATCCCGACGCTCCCCTTGAAATGCTGTTTGATTATGTAAGAATTCGCTTTCCGACAACAGACGTACAGCAGGTGGTCGAAAACATCTTACAACTGAAACTGTCCTATTTTCTTCATGAGGACTATGGTTTCTATTCTTATTCAGAGCATTATGCTTTAGGCGACATATTCGTCCTTTGCTCCCATGAACTGGACAAAGGAGTTCTGGTGGAATTGAAAGGTCGTGGGTGCAGACAATTTGAAAGCTATCTTCTGGCACAACAAAGAAGCTGGTATGAGTTCTTTATGGACGTTTTGGTGGCTGGCGGTGTGATGAAACGCCTTGACCTTGCCATTAACGATAAGACAGGGATTTTAAATATCCCTGTACTCACTGAAAAGTGCCAACAGGAAGAATGTATCTCCGTCTTCCGCAGTTTTAAAAGCTATCGCAGTGGCGAACTGGTACGCAAAGAGGAAAAGGAATGTATGGGAAACACCCTCTATATCGGTTCATTACAAAGTGAAGTTTATTTCTGTATCTATGAAAAGGACTACGAGCAGTACAAGAAAAATGATATTCCCATTGAAGACGCAGAAGTAAAAAACCGTTTTGAGATTCGATTGAAAAATGAGCGTGCCTATTATGCAGTCCGTGATTTACTCGTCTATGACAATCCAGAGCATACCGCCTTTAAAATTATCAATCGGTATATCCGTTTTGTAGATAAAGACGATTCCAAACCTCGTTCTGATTGGAAACTGAATGAAGAATGGGCTTGGTTTATTGGGAACAATCGTGAACGATTAAAACTAACCACAAAACCAGAGCCTTACTCCTTCCAAAGGACGCTGAACTGGCTATCTCATCAAGTTGCCCCGACCTTAAAGGTTGCGATTAAACTTGATGAAATCAACCAGACGCAGGTTGTAAAAGACATTCTCGACCATGCGAAACTGACAGACCGACACAAGCAGATTTTGAAGCAACAGTCAGTAAAAGAACAGGACGTGATAACAACAAAAAAATAA"}}}], "tool_has_database": true}]\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/summarize/tabular_file_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/tabular_file_output.json Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[{"analysis_software_name": "tabular_file", "reference_database_version": "", "analysis_software_version": "", "results": [{"name": "tabular_file_report", "file_path": "tests/data/dummy/tabular_file/report.tsv", "hid": "12345", "galaxy_hid": "", "content": [{"#FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00002", "START": 142975, "END": 143985, "STRAND": "+", "GENE": "bopD", "COVERAGE": "1-1011/1011", "COVERAGE_MAP": "===============", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 98.91, "DATABASE": "vfdb", "ACCESSION": "NP_814691", "PRODUCT": "(bopD)sugar-bindingtranscriptionalregulatorLacIfamily[BopD(VF0362)][EnterococcusfaecalisV583]", "RESISTANCE": null}, {"#FILE": "/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta", "SEQUENCE": "contig00003", "START": 7884, "END": 11111, "STRAND": "-", "GENE": "fss3", "COVERAGE": "1-3228/3228", "COVERAGE_MAP": "===============", "GAPS": "0/0", "%COVERAGE": 100.0, "%IDENTITY": 99.38, "DATABASE": "vfdb", "ACCESSION": "NP_815578", "PRODUCT": "(fss3)EnterococcusfaecalissurfaceproteinFss3fibrinogenbindingprotein[Fibrinogenbindingprotein(AI273)][EnterococcusfaecalisV583]", "RESISTANCE": null}]}], "tool_has_database": false}] \ No newline at end of file |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 test-data/tabular_file/report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tabular_file/report.tsv Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,3 @@ +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00002 142975 143985 + bopD 1-1011/1011 =============== 0/0 100.00 98.91 vfdb NP_814691 (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583] +/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta contig00003 7884 11111 - fss3 1-3228/3228 =============== 0/0 100.00 99.38 vfdb NP_815578 (fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583] |
| b |
| diff -r 000000000000 -r 05c1bcba20c9 tooldistillator_summarize.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tooldistillator_summarize.xml Tue Apr 30 08:41:54 2024 +0000 |
| [ |
| @@ -0,0 +1,50 @@ +<tool id="tooldistillator_summarize" name="ToolDistillator Summarize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description> + Aggregate several JSON reports from ToolDistillator + </description> + <macros> + <import>macro.xml</import> + </macros> + <expand macro="biotools"/> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="aggressive"><![CDATA[ +tooldistillator --version && +mkdir -p input_files && +#for $file in $summarize_data +cp '$file' ./input_files/ && +#end for +tooldistillator + summarize + input_files/* + -o summary.json +]]> + </command> + <inputs> + <param name="summarize_data" type="data" multiple="true" format="json" label="Results in Json format" help="Summarize results from tooldistillator in json format"/> + </inputs> + <outputs> + <data name="summary_json" format="json" from_work_dir="summary.json" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test expect_num_outputs="1"> <!-- TEST_1 sumarize json results --> + <param name="summarize_data" ftype="json" value="summarize/abricate_output.json,summarize/bracken_full_output.json,summarize/plasmidfinder_output.json"/> + <output name="summary_json" ftype="json" value="summarize/summarize.json" compare="sim_size"> + <assert_contents> + <has_text_matching expression="Enterococcus.*faecalis" /> + <has_json_property_with_text property="name" text="plasmid_hit" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools. + + + +This tool here summarize JSON output file from ToolDistillator to only one JSON file + ]]></help> + <expand macro="citations"/> +</tool> |
