| Next changeset 1:c68a35962d6e (2025-04-11) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 3be367228b531c346c10700f07d57ae44394be36-dirty |
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added:
macros.xml panaroo.xml test-data/10_small.gff test-data/11_small.gff test-data/combined_DNA_CDS.fasta test-data/combined_protein_CDS.fasta test-data/combined_protein_cdhit_out.txt test-data/combined_protein_cdhit_out.txt.clstr test-data/final_graph.gml test-data/gene_data.csv test-data/gene_presence_absence.Rtab test-data/gene_presence_absence.csv test-data/gene_presence_absence_roary.csv test-data/pan_genome_reference.fa test-data/pre_filt_graph.gml test-data/struct_presence_absence.Rtab test-data/summary_statistics.txt |
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| diff -r 000000000000 -r 01864c78c5a5 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Aug 27 05:51:12 2024 +0000 |
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| @@ -0,0 +1,68 @@ +<macros> + <token name="@TOOL_VERSION@">1.5.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.05</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0194</edam_topic> + </edam_topics> + </xml> + <xml name="biotools"> + <xrefs> + <xref type="bio.tools">panaroo</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">panaroo</requirement> + <requirement type="package" version="170427">prank</requirement> + </requirements> + </xml> + <xml name="clean_mode"> + <option value="strict">strict</option> + <option value="moderate">moderate</option> + <option value="sensitive">sensitive</option> + </xml> + <xml name="genetic_code"> + <option value="1">1. Standard</option> + <option value="2">2. Vertebrate Mitochondrial</option> + <option value="3">3. Yeast Mitochondrial</option> + <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> + <option value="5">5. Invertebrate Mitochondrial</option> + <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> + <option value="9">9. Echinoderm Mitochondrial</option> + <option value="10">10. Euplotid Nuclear</option> + <option value="11" selected="True">11. Bacteria and Archaea</option> + <option value="12">12. Alternative Yeast Nuclear</option> + <option value="13">13. Ascidian Mitochondrial</option> + <option value="14">14. Flatworm Mitochondrial</option> + <option value="15">15. Blepharisma Macronuclear</option> + <option value="16">16. Chlorophycean Mitochondrial</option> + <option value="21">21. Trematode Mitochondrial</option> + <option value="22">22. Scenedesmus obliquus mitochondrial</option> + <option value="23">23. Thraustochytrium Mitochondrial</option> + <option value="24">24. Pterobranchia mitochondrial</option> + <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option> + <option value="26">26. Pachysolen tannophilus Nuclear Code</option> + <option value="27">27. Karyorelict Nuclear Code</option> + <option value="28">28. Condylostoma Nuclear Code</option> + <option value="29">29. Mesodinium Nuclear Code</option> + <option value="30">30. Peritrich Nuclear Code</option> + <option value="31">31. Blastocrithidia Nuclear Code</option> + <option value="33">33. Cephalodiscidae Mitochondrial UAA-Tyr Code</option> + </xml> + <xml name="refind_mode_option"> + <option value="default" selected="True">default</option> + <option value="strict">strict</option> + <option value="off">off</option> + </xml> + <xml name="gene_alignment"> + <option value="None" selected="True">None</option> + <option value="core">core</option> + <option value="pan">pan</option> + </xml> + <xml name="gene_aligner"> + <option value="mafft" selected="True">mafft</option> + <option value="prank">prank</option> + </xml> +</macros> |
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| diff -r 000000000000 -r 01864c78c5a5 panaroo.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/panaroo.xml Tue Aug 27 05:51:12 2024 +0000 |
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| b'@@ -0,0 +1,281 @@\n+<tool id="panaroo" name="Panaroo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>A Bacterial Pangenome Analysis Pipeline</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="edam_ontology"/>\n+ <expand macro="biotools"/>\n+ <expand macro="requirements"/>\n+ <stdio>\n+ <exit_code range="1:" />\n+ <regex match="System..*Exception"\n+ source="both"\n+ level="fatal"\n+ description="Error encountered" />\n+ </stdio>\n+ <command><![CDATA[\n+\n+ mkdir outdir &&\n+\t \n+\t #import re\n+\t #set input_directory = \'input_directory\'\n+\t mkdir $input_directory &&\n+\t #for $gff in $gff_input_collection:\n+\t #set identifier = re.sub(\'[^\\s\\w\\-\\\\.]\',\'_\',str($gff.element_identifier))\n+\t ln -fs \'$gff\' \'$input_directory/$identifier\' &&\n+\t #end for\n+\n+\t panaroo \n+\t -t \\${GALAXY_SLOTS:-2}\n+ #if str($gen_code) != \'None\':\n+ --codon-table $gen_code\n+\t #end if\n+ #if str($advanced.adv_options_selector) == "set":\n+\t #if $advanced.remove_invalid_gene\n+\t\t $advanced.remove_invalid_gene\n+\t #end if\n+\t -c \'$advanced.matching_option.seq_threshold\'\n+\t -f \'$advanced.matching_option.peptide_threshold\'\n+\t --len_dif_percent \'$advanced.matching_option.length_diff_cutoff\'\n+\t $advanced.matching_option.merge_paralogs\n+\t --search_radius \'$advanced.refind_option.search_radius\'\n+\t --refind_prop_match \'$advanced.refind_option.refind_prop_match\'\n+\t --refind-mode \'$advanced.refind_option.refind_mode\'\n+\t --min_trailing_support \'$advanced.graph_correction_option.min_trailing_support\'\n+\t --trailing_recursive \'$advanced.graph_correction_option.trailing_recursive\'\n+\t --edge_support_threshold \'$advanced.graph_correction_option.edge_support_threshold\'\n+\t --remove_by_consensus \'$advanced.graph_correction_option.remove_by_consensus\'\n+\t --high_var_flag \'$advanced.graph_correction_option.high_var_flag\'\n+\t --min_edge_support_sv \'$advanced.graph_correction_option.min_edge_support_sv\'\n+\t $advanced.graph_correction_option.all_seq_in_graph\n+\t $advanced.graph_correction_option.no_clean_edges\n+\t\n+\t #if $advanced.gene_alignment_option.a != \'None\'\n+\t\t-a \'$advanced.gene_alignment_option.a\'\n+\t #end if\n+\n+\t #if \'$advanced.gene_alignment_option.aligner\' == \'mafft\'\n+ --aligner mafft\n+\t #else\n+ --aligner \'$advanced.gene_alignment_option.aligner\'\n+\t #end if\n+\t #if $advanced.gene_alignment_option.core_subset != \'\'\n+\t\t--core_subset $advanced.gene_alignment_option.core_subset\n+\t #end if\n+ #end if\n+\t -i $input_directory/*.gff \n+\t -o outdir \n+\t --clean-mode $mode \n+\t > \'$log\' &&\n+\t mv outdir/gene_presence_absence.Rtab outdir/gene_presence_absence_rtab.Rtab &&\n+\t 2>&1 \n+\n+ ]]></command>\n+ <inputs>\n+\t<param name="gff_input_collection" type="data_collection" format="gff" collection_type="list" label="GFF Input Collection" help="A list of gff files (i.e prokka)"/>\n+\t<param name="mode" type="select" label="The stringency mode at which to run panaroo" help="--clean-mode">\n+ <expand macro="clean_mode"/>\n+ \t</param>\n+\t<param name="gen_code" type="select" label="the codon table user for translation" help="default: 11">\n+ <expand macro="genetic_code"/>\n+ \t</param>\n+ <conditional name="advanced">\n+ <param name="adv_options_selector" type="select" label="Set advanced options?" help="Provides additional controls">\n+ <option value="set">Set</option>\n+ <option value="do_not_set" selected="True">Do not set</option>\n+ </param>\n+\t <when value="set">\n+\t\t <param name="remove_invalid_gene" argument="--remove-invalid-genes" type="boolean" truevalue="--remove-invalid-genes" falsevalue="" label="removes annotations that do not conform to the expected Prokka format such as those including premature stop codons" help="-'..b't \\-\\-clean-mode strict \\-\\-remove-invalid-genes) -->\n+ <test expect_num_outputs="2">\n+ <param name="gen_code" value="11"/>\n+ <param name="mode" value="strict"/>\n+ <param name="adv_options_selector" value="do_not_set"/>\n+ <param name="gff_input_collection">\n+ <collection type="list">\n+ <element name="gff10.gff" value="10_small.gff"/>\n+ <element name="gff11.gff" value="11_small.gff"/>\n+ </collection>\n+ </param>\n+ <output_collection name="output" count="13"/>\n+ <output name="log">\n+ <assert_contents>\n+ <has_text text="pre-processing gff3 files..."/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+\t <test expect_num_outputs="2">\n+\t <param name="gen_code" value="11"/>\n+\t <param name="mode" value="strict"/>\n+\t <param name="adv_options_selector" value="set"/>\n+\t <param name="a" value="None"/>\n+\t <param name="gff_input_collection">\n+\t\t<collection type="list">\n+\t\t <element name="gff10.gff" value="10_small.gff"/>\n+\t\t <element name="gff11.gff" value="11_small.gff"/>\n+\t\t</collection>\n+\t </param>\n+\t <output_collection name="output_advance" count="13"/>\n+\t <output name="log">\n+\t\t <assert_contents>\n+\t\t <has_text text="pre-processing gff3 files..."/>\n+\t\t </assert_contents>\n+ </output>\n+ \t</test>\n+\t<test expect_num_outputs="3">\n+\t <param name="gen_code" value="11"/>\n+\t <param name="mode" value="strict"/>\n+\t <param name="adv_options_selector" value="set"/>\n+\t <param name="a" value="core"/>\n+\t <param name="gff_input_collection">\n+\t\t<collection type="list">\n+\t\t <element name="gff10.gff" value="10_small.gff"/>\n+\t\t <element name="gff11.gff" value="11_small.gff"/>\n+\t </collection>\n+ </param>\n+\t <output_collection name="output_pangenome" count="18"/>\n+\t <output_collection name="output_pangenome_fasta" count="251"/>\n+\t <output name="log">\n+\t\t <assert_contents>\n+\t\t <has_text text="pre-processing gff3 files..."/>\n+\t\t </assert_contents>\n+\t </output>\n+\t</test>\n+ </tests>\n+ <help><![CDATA[\n+Panaroo_ is A Bacterial Pangenome Analysis Pipeline.\n+\n+**INPUTS**\n+Panaroo now supports multiple input formats. To use non-standard GFF3 files you must profile the input file as a list in a text file (one per line). Separate GFF and FASTA files can be provided per isolate by providing each file delimited by a space or a tab. Genbank file formats are also supported with extensions \'.gbk\', \'.gb\' or \'.gbff\'. These must compliant with Genbank/ENA/DDJB. This can be forced in Prokka by specifying the --compliance parameter.\n+\n+ - a list of gff format in a collection\n+\n+**OUTPUTS**\n+\n+ - combined_protein_cdhit_out.txt\n+ - combined_protein_cdhit_out.txt.clstr\n+ - pre_filt_graph.gml\n+ - gene_data.csv\n+ - combined_protein_CDS.fasta\n+ - combined_DNA_CDS.fasta\n+ - gene_presence_absence_rtab.Rtab\n+ - gene_presence_absence_roary.csv\n+ - gene_presence_absence.csv\n+ - summary_statistics.txt\n+ - pan_genome_reference.fa\n+ - struct_presence_absence.Rtab\n+ - final_graph.gml\n+\n+**OUTPUTS with Advance parameters**\n+\n+ - combined_protein_cdhit_out.txt\n+ - combined_protein_cdhit_out.txt.clstr\n+ - pre_filt_graph.gml\n+ - gene_data.csv\n+ - combined_protein_CDS.fasta\n+ - combined_DNA_CDS.fasta\n+ - gene_presence_absence_rtab.Rtab\n+ - gene_presence_absence_roary.csv\n+ - gene_presence_absence.csv\n+ - summary_statistics.txt\n+ - pan_genome_reference.fa\n+ - struct_presence_absence.Rtab\n+ - final_graph.gml\n+ - core_gene_alignment\n+ - core_gene_alignment_filtered\n+ - core_alignment_filtered_header\n+ - core_alignment_header\n+ - a collection of fasta files\n+\n+.. _Panaroo: https://gthlab.au/panaroo/#/gettingstarted/quickstart\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1186/s13059-020-02090-4</citation>\n+ </citations>\n+</tool>\n+ \n' |
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| diff -r 000000000000 -r 01864c78c5a5 test-data/10_small.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/10_small.gff Tue Aug 27 05:51:12 2024 +0000 |
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| b'@@ -0,0 +1,8854 @@\n+##gff-version 3\n+##sequence-region .10665_7_10.1 1 504764\n+.10665_7_10.1\tProdigal:2.6\tCDS\t134\t499\t.\t-\t0\tID=KPLBOJCC_00001;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WLQ5;locus_tag=KPLBOJCC_00001;product=putative protein\n+.10665_7_10.1\tProdigal:2.6\tCDS\t653\t2044\t.\t+\t0\tID=KPLBOJCC_00002;inference=ab initio prediction:Prodigal:2.6;locus_tag=KPLBOJCC_00002;product=hypothetical protein\n+.10665_7_10.1\tProdigal:2.6\tCDS\t2063\t2932\t.\t+\t0\tID=KPLBOJCC_00003;eC_number=1.-.-.-;db_xref=COG:COG2175;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WG83;locus_tag=KPLBOJCC_00003;product=Putative dioxygenase\n+.10665_7_10.1\tProdigal:2.6\tCDS\t2929\t3480\t.\t+\t0\tID=KPLBOJCC_00004;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WM67;locus_tag=KPLBOJCC_00004;product=putative protein\n+.10665_7_10.1\tProdigal:2.6\tCDS\t3509\t5107\t.\t+\t0\tID=KPLBOJCC_00005;eC_number=6.2.1.-;db_xref=COG:COG0318;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WQ55;locus_tag=KPLBOJCC_00005;product=Putative fatty-acid--CoA ligase FadD10\n+.10665_7_10.1\tProdigal:2.6\tCDS\t5100\t5348\t.\t+\t0\tID=KPLBOJCC_00006;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WM65;locus_tag=KPLBOJCC_00006;product=putative protein\n+.10665_7_10.1\tProdigal:2.6\tCDS\t5330\t12868\t.\t+\t0\tID=KPLBOJCC_00007;eC_number=6.1.1.13;Name=dltA;gene=dltA;inference=ab initio prediction:Prodigal:2.6,protein motif:HAMAP:MF_00593;locus_tag=KPLBOJCC_00007;product=D-alanine--poly(phosphoribitol) ligase subunit 1\n+.10665_7_10.1\tProdigal:2.6\tCDS\t13106\t15028\t.\t+\t0\tID=KPLBOJCC_00008;db_xref=COG:COG3336;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WM63;locus_tag=KPLBOJCC_00008;product=putative protein\n+.10665_7_10.1\tProdigal:2.6\tCDS\t15244\t17502\t.\t-\t0\tID=KPLBOJCC_00009;eC_number=3.6.3.-;Name=ctpB;db_xref=COG:COG2217;gene=ctpB;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WPT9;locus_tag=KPLBOJCC_00009;product=Cation-transporting P-type ATPase B\n+.10665_7_10.1\tProdigal:2.6\tCDS\t17646\t19160\t.\t+\t0\tID=KPLBOJCC_00010;inference=ab initio prediction:Prodigal:2.6;locus_tag=KPLBOJCC_00010;product=hypothetical protein\n+.10665_7_10.1\tProdigal:2.6\tCDS\t19309\t19593\t.\t-\t0\tID=KPLBOJCC_00011;Name=rpmB_1;gene=rpmB_1;inference=ab initio prediction:Prodigal:2.6,protein motif:HAMAP:MF_00373;locus_tag=KPLBOJCC_00011;product=50S ribosomal protein L28\n+.10665_7_10.1\tProdigal:2.6\tCDS\t19703\t20899\t.\t+\t0\tID=KPLBOJCC_00012;db_xref=COG:COG0523;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WPI5;locus_tag=KPLBOJCC_00012;product=putative protein\n+.10665_7_10.1\tProdigal:2.6\tCDS\t20994\t25871\t.\t-\t0\tID=KPLBOJCC_00013;eC_number=3.6.3.-;Name=ctpI_1;db_xref=COG:COG0474;gene=ctpI_1;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WPS5;locus_tag=KPLBOJCC_00013;product=putative cation-transporting ATPase I\n+.10665_7_10.1\tProdigal:2.6\tCDS\t26225\t26467\t.\t-\t0\tID=KPLBOJCC_00014;inference=ab initio prediction:Prodigal:2.6;locus_tag=KPLBOJCC_00014;product=hypothetical protein\n+.10665_7_10.1\tProdigal:2.6\tCDS\t26713\t28203\t.\t+\t0\tID=KPLBOJCC_00015;inference=ab initio prediction:Prodigal:2.6;locus_tag=KPLBOJCC_00015;product=hypothetical protein\n+.10665_7_10.1\tProdigal:2.6\tCDS\t28351\t29100\t.\t+\t0\tID=KPLBOJCC_00016;eC_number=3.4.21.105;Name=glpG;gene=glpG;inference=ab initio prediction:Prodigal:2.6,protein motif:HAMAP:MF_01594;locus_tag=KPLBOJCC_00016;product=Rhomboid protease GlpG\n+.10665_7_10.1\tProdigal:2.6\tCDS\t29281\t31338\t.\t+\t0\tID=KPLBOJCC_00017;inference=ab initio prediction:Prodigal:2.6;locus_tag=KPLBOJCC_00017;product=hypothetical protein\n+.10665_7_10.1\tProdigal:2.6\tCDS\t31620\t32576\t.\t+\t0\tID=KPLBOJCC_00018;eC_number=1.1.1.281;Name=rmd;gene=rmd;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:Q6T1X6;locus_tag=KPLBOJCC_00018;product=GDP-6-deoxy-D-mannose reductase\n+.10665_'..b'CGCCGCGGAGCTGTTCGAGCTGGGCGCCCGGGAGCTGATGTGGGGA\n+GTGCGGCATTAGCCCGCATGAAGAAGTGACTGGGAGTGACAATCATGACGCGAGGGCGTA\n+AGCCGAGACCGGGCCGCATCGTTTTCGTGGGCTCCGGTCCGGGCGACCCCGGCTTGCTTA\n+CGACACGGGCTGCCGCGGTGCTGGCCAACGCCGCGCTGGTGTTCACCGATCCCGACGTAC\n+CGGAGCCGGTGGTGGCGCTGATCGGCACGGATCTGCCCCCCGTGTCCGGCCCGGCGCCCG\n+CCGAGCCGGTTGCCGGGAACGGCGATGCGGCCGGCGGAGGAAGTGCGCAGGAACACGGCC\n+GGGCCGCGTCCGCGGTAGTCTCCGGTGGTCCTGACATCCGCCCGGCGCTGGGCGATCCCG\n+CCGATGTGGCCAAGACGCTGACCGCCGAGGCCCGTTCGGGTGTCGACGTGGTGCGGCTGG\n+TGGCGGGCGATCCGCTCACGGTGGATGCGGTAATCAGCGAGGTGAACGCCGTCGCACGCA\n+CCCACCTGCACATCGAAATCGTGCCCGGCCTGGCCGCCAGCAGCGCGGTCCCGACCTATG\n+CCGGGTTGCCGCTGGGTTCGTCGCACACCGTCGCCGACGTGCGTATCGACCCCGAAAACA\n+CCGACTGGGACGCGCTGGCTGCCGCACCCGGGCCGCTGATCCTGCAGGCCACCGCATCGC\n+ATCTAGCCGAATCGGCCCGCAGCCTGATCGATCACCAGCTGGCCGAGTCCACTCCGTGCG\n+TGGTGACCGCACACGGCACCACCTGTCAGCAGCGTTCGGTCGAGACCACACTTCAGGGAT\n+TGACCGACCCGGCCGTCCTGGGCGCTACCGACCCCGCGTGCTCCGCAAACGGGAGGGACT\n+CCCAGGCCGGACCGCTGATAGTGACCATCGGCAAGACGGTGACCAGTCGGGCAAAGCTGA\n+ACTGGTGGGAGAGCCGCGCCCTCTACGGCTGGACGGTGTTGGTGCCGCGCACCAAGGACC\n+AGGCCGGCGAGATGAGCGAGCGGCTCACGTCGTACGGCGCGCTGCCGGTGGAGGTGCCGA\n+CCATCGCCGTCGAGCCGCCGCGCAGCCCCGCGCAGATGGAGCGCGCCGTCAAGGGCCTGG\n+TCGATGGCCGATTCCAGTGGATCGTGTTCACCTCCACCAACGCGGTGCGTGCGGTGTGGG\n+AGAAGTTCGGCGAGTTCGGTCTGGATGCCCGCGCGTTCTCCGGGGTGAAGATCGCCTGTG\n+TCGGCGAGTCGACGGCCGACCGGGTGCGCGCCTTCGGAATCAGTCCCGAGCTGGTGCCCT\n+CCGGGGAGCAGTCCTCGCTTGGCTTGCTAGACGACTTCCCGCCCTACGACAGCGTTTTCG\n+ACCCGGTGAACCGGGTTTTGCTGCCGCGCGCCGACATCGCCACCGAAACGCTGGCCGAGG\n+GACTGCGAGAGCGTGGCTGGGAGATCGAGGACGTCACCGCCTACCGGACCGTGCGGGCCG\n+CGCCGCCGCCGGCCACTACCCGGGAAATGATCAAGACGGGCGGGTTTGACGCGGTATGTT\n+TCACCTCCAGCTCGACGGTGCGAAACCTGGTCGGCATCGCCGGCAAGCCGCACGCGCGGA\n+CGATCATCGCCTGCATAGGGCCAAAGACCGCCGAGACCGCAGCCGAGTTCGGCTTGCGGG\n+TCGATGTCCAGCCGGACACCGCCGCCATCGGCCCGCTGGTCGATGCGCTGGCCGAGCATG\n+CCGCCCGGTTGCGCGCTGAGGGTGCGCTGCCCCCGCCGCGCAAGAAGAGCCGCAGGCGCT\n+AGTGGCCCACCCTCGTCAGGTGAGCGTGCGTGTCTGTACACCGACACGCCGACCGAGCTG\n+GCATTTTGCGTACGCTCGCGGCTACGAATGAGCATGAGTTCCTATCCGCGGCAGCGACCG\n+CGCCGGCTCCGCTCCACCGTCGCGATGCGCCGTCTGGTTGCGCAAACCTCGTTGGAGCCA\n+AGGCATTTGGTGCTGCCGATGTTCGTTGCCGACGGCATTGACGAGCCGCGGCCGATTACC\n+TCCATGCCGGGCGTGGTACAGCACACCCGGGATTCGCTACGTAGGGCCGCGGCAGCCGCG\n+GTGGCCGCCGGCGTGGGTGGGCTGATGCTTTTCGGCGTGCCGCGCGACCAGGACAAGGAC\n+GGTGTCGGTTCGGCGGGCATCGACCCCGACGGGATCCTCAACGTCGCCCTTCGCGATCTG\n+GCCAAGGACCTGGGTGAGGCCACGGTGTTGATGGCCGACACCTGTCTGGACGAGTTCACC\n+GACCACGGGCACTGCGGTGTGCTCGATGACCGGGGCCGGGTCGATAACGACGCCACCGTG\n+GCCCGCTATGTGGAACTGGCTGTGGCGCAAGCGGAATCGGGCGCCCACGTGGTCGGACCC\n+AGTGGGATGATGGATGGCCAGGTAGCCGCGATCCGGGACGGTTTGGACGCCGCCGGCTAC\n+ATCGATGTGGTGATCTTGGCCTACGCCGCGAAGTTTGCTTCGGCGTTCTACGGCCCGTTC\n+CGCGAGGCGGTGAGCTCTAGCCTGTCCGGGGATCGGCGCACCTACCAGCAGGAGCCGGGC\n+AACGCCGCCGAGGCGCTGCGTGAGATCGAGCTCGATCTCGACGAAGGCGCCGACATTGTG\n+ATGGTCAAACCCGCGATGGGCTACCTCGATGTGGTGGCGGCCGCGGCGGACGTCTCGCCG\n+GTCCCGGTGGCCGCCTATCAGGTCTCGGGAGAGTACGCGATGATTCGTGCGGCGGCGGCC\n+AATAATTGGATCGATGAGCGTGCCGCGGTGCTAGAGTCGCTGACCGGTATCCGGCGTGCC\n+GGCGCCGACATCGTGCTCACCTACTGGGCGGTAGACGCGGCGGGCTGGCTTACGTGACGG\n+AGGCCTGACATGACACCAACCGGGGATACCAAGCCCAAGTTGTTGTTCTACGAACCCGGC\n+GCGAGCTGGTACTGGGTGCTGACTGGTCCGCTTGCGGCGGTGTCGGTGCTCCTCCTCGAG\n+ATATCCAGCGGCGCCGGGGTTGGGTTGATAACGCCGGCGATCTTTCTGGTGATGGTGTCG\n+GCGTTCGTGGCATTGCAGGTGAAGGCGGCGCGGATTCACACGTCGGTCGAGCTGACGCAT\n+GATGCCTTGCGCCAAGGCACCGAGACCATCAGGCTGGCCGAAATCGTCAAAATCTATCCG\n+GAGGCAGACGGCCGCGAGACGTCCGGGGAAGAGCCGGCAAAGTGGCAGTCGGCGCGGACC\n+CTGGGCGAGCTCGTCGGCGTACCGCGCGGCCGGGTGGGAATCGGGCTGAAGCTGACCGGA\n+GGCCGCACCGCCCAGGCCTGGGCGCGTCGTCATCAACAGCTGCGGGCGGCGCTGACTCCG\n+CTGGTTCAGGAGCGGCTCGGGCCCGTGGATTCTGATGTCGCCGACGTCAACGGTGACGAC\n+GCCGGGCCAGCGCGGTGATCGCCCGCTACCGGGCCGGGGCCGAACTGTTCCTGGCTTGTG\n+CCGCGCTTGCCGGATCTGCGGCGAGCTGGTCGCGGACCCGCTCCACCGTGGCCGTCGCGC\n+CCGTCATCGACGGCCAGCCGGTCACCCTGTCGGTGGTCTATCACCCGCAACCGTTGGTGC\n+TGACCCTGCTGCTGGCGACGATCGCCGGCGTGTTGTCGGTGGTGGGGACGGCCAGGTTGC\n+GGCGCGCGCGAGCTGGCTTGAACGCACATCCGGACGGCTTGAACCAGCGTCCGCCCGGCG\n+GTTGGTGTCATTGAGCCGTTTGCGTGGATCACTTCCGCTGCTGCTTGATCGGGCCCTGGT\n+CTGTGTCGGCAGCGGCTGGTAGTATCGAAAGTATGTTCGATCAGGTGCGGGGGCGCATGC\n+CTTCACCGGAGGCGATCGCTCATTTTGATGAGCGGTTTGAATGC\n' |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/11_small.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/11_small.gff Tue Aug 27 05:51:12 2024 +0000 |
| b |
| b'@@ -0,0 +1,10248 @@\n+##gff-version 3\n+##sequence-region .10665_7_11.1 1 581686\n+.10665_7_11.1\tProdigal:2.6\tCDS\t136\t501\t.\t-\t0\tID=NCFNLLIC_00001;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WLQ5;locus_tag=NCFNLLIC_00001;product=putative protein\n+.10665_7_11.1\tProdigal:2.6\tCDS\t655\t2046\t.\t+\t0\tID=NCFNLLIC_00002;inference=ab initio prediction:Prodigal:2.6;locus_tag=NCFNLLIC_00002;product=hypothetical protein\n+.10665_7_11.1\tProdigal:2.6\tCDS\t2065\t2934\t.\t+\t0\tID=NCFNLLIC_00003;eC_number=1.-.-.-;db_xref=COG:COG2175;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WG83;locus_tag=NCFNLLIC_00003;product=Putative dioxygenase\n+.10665_7_11.1\tProdigal:2.6\tCDS\t2931\t3482\t.\t+\t0\tID=NCFNLLIC_00004;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WM67;locus_tag=NCFNLLIC_00004;product=putative protein\n+.10665_7_11.1\tProdigal:2.6\tCDS\t3511\t5109\t.\t+\t0\tID=NCFNLLIC_00005;eC_number=6.2.1.-;db_xref=COG:COG0318;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WQ55;locus_tag=NCFNLLIC_00005;product=Putative fatty-acid--CoA ligase FadD10\n+.10665_7_11.1\tProdigal:2.6\tCDS\t5102\t5350\t.\t+\t0\tID=NCFNLLIC_00006;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WM65;locus_tag=NCFNLLIC_00006;product=putative protein\n+.10665_7_11.1\tProdigal:2.6\tCDS\t5332\t12870\t.\t+\t0\tID=NCFNLLIC_00007;eC_number=6.1.1.13;Name=dltA;gene=dltA;inference=ab initio prediction:Prodigal:2.6,protein motif:HAMAP:MF_00593;locus_tag=NCFNLLIC_00007;product=D-alanine--poly(phosphoribitol) ligase subunit 1\n+.10665_7_11.1\tProdigal:2.6\tCDS\t13108\t15030\t.\t+\t0\tID=NCFNLLIC_00008;db_xref=COG:COG3336;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WM63;locus_tag=NCFNLLIC_00008;product=putative protein\n+.10665_7_11.1\tProdigal:2.6\tCDS\t15246\t17504\t.\t-\t0\tID=NCFNLLIC_00009;eC_number=3.6.3.-;Name=ctpB;db_xref=COG:COG2217;gene=ctpB;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WPT9;locus_tag=NCFNLLIC_00009;product=Cation-transporting P-type ATPase B\n+.10665_7_11.1\tProdigal:2.6\tCDS\t17648\t19162\t.\t+\t0\tID=NCFNLLIC_00010;inference=ab initio prediction:Prodigal:2.6;locus_tag=NCFNLLIC_00010;product=hypothetical protein\n+.10665_7_11.1\tProdigal:2.6\tCDS\t19311\t19595\t.\t-\t0\tID=NCFNLLIC_00011;Name=rpmB_1;gene=rpmB_1;inference=ab initio prediction:Prodigal:2.6,protein motif:HAMAP:MF_00373;locus_tag=NCFNLLIC_00011;product=50S ribosomal protein L28\n+.10665_7_11.1\tProdigal:2.6\tCDS\t19705\t20901\t.\t+\t0\tID=NCFNLLIC_00012;db_xref=COG:COG0523;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WPI5;locus_tag=NCFNLLIC_00012;product=putative protein\n+.10665_7_11.1\tProdigal:2.6\tCDS\t20996\t25873\t.\t-\t0\tID=NCFNLLIC_00013;eC_number=3.6.3.-;Name=ctpI_1;db_xref=COG:COG0474;gene=ctpI_1;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P9WPS5;locus_tag=NCFNLLIC_00013;product=putative cation-transporting ATPase I\n+.10665_7_11.1\tProdigal:2.6\tCDS\t26227\t26469\t.\t-\t0\tID=NCFNLLIC_00014;inference=ab initio prediction:Prodigal:2.6;locus_tag=NCFNLLIC_00014;product=hypothetical protein\n+.10665_7_11.1\tProdigal:2.6\tCDS\t26715\t28205\t.\t+\t0\tID=NCFNLLIC_00015;inference=ab initio prediction:Prodigal:2.6;locus_tag=NCFNLLIC_00015;product=hypothetical protein\n+.10665_7_11.1\tProdigal:2.6\tCDS\t28353\t29102\t.\t+\t0\tID=NCFNLLIC_00016;eC_number=3.4.21.105;Name=glpG;gene=glpG;inference=ab initio prediction:Prodigal:2.6,protein motif:HAMAP:MF_01594;locus_tag=NCFNLLIC_00016;product=Rhomboid protease GlpG\n+.10665_7_11.1\tProdigal:2.6\tCDS\t29283\t31340\t.\t+\t0\tID=NCFNLLIC_00017;inference=ab initio prediction:Prodigal:2.6;locus_tag=NCFNLLIC_00017;product=hypothetical protein\n+.10665_7_11.1\tProdigal:2.6\tCDS\t31622\t32578\t.\t+\t0\tID=NCFNLLIC_00018;eC_number=1.1.1.281;Name=rmd;gene=rmd;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:Q6T1X6;locus_tag=NCFNLLIC_00018;product=GDP-6-deoxy-D-mannose reductase\n+.10665'..b'TGGCGCCGTCCAAGGTGTAAAACCGGCCGGCGTAGGTGGGGTTT\n+GGCTCGGTCCACACGGCCTTGATGACCTGCAGCGACTCGGCAAGCGCGGAGACTCGGTCG\n+CCAACCGGCGGGAACGGGATGCCGTAGGCTTGCGACTCGCGCCGAAACCAGCCGGCGCCC\n+AATCCCAGATCGAGACGTCCCTGGGAAATGACGTCCAGCGTCGCAGCCATCTTGGCCAGC\n+ACGGAAGGATGACGGTAGGAATTGCACAGCACGCTGGTGCCCAACCGCAGCTTCGTGGTG\n+TCGCGGGACAATGCCGCAAGTGCGGTCCAGCACTCGAGCAGGGGCAGCGACCTCGAAGGG\n+GCGCACTGGCCCGCCCCGCCGGTTTCGGTGCCGGTCGCGGAGCCGGTGTCGGCGGCGATG\n+CCGGCGACCTTCGCATACTCGCCGGGGCTTATCGTCAGGAAGTGGTCGCATAACCACACT\n+GAATCGAATCCGTATTCTTCCGCCGTCTGCGAGACGACAACCATTTCGCGGTAACTGCCG\n+ACCGCCAGGCCATTAACCGTCGCAGCCAACATGAGTCCGAAGTGCGGGTCGTCTTTGGCG\n+TTCATGCGAAATCTCGTTTCTCGATAATTCCGGCACCTGATCCGGGCAACGTTCGGGGTA\n+ACGTGACGGAGAACTGGTACCGCTCGGGGCGATGGTGGAACACGACCACTTCAAGGGGCT\n+TGCCGTCATTGGTGTAGCTGGTGCGGTCGACGACCAGTACCGGCGAACCCACCGCCAGAC\n+CCAACGCGTCGGCTACGTCGGGGGAGGCCCCGGCGGCATGGATTTCGTGGGTAGCCTGTG\n+CAATGCGTACACCCAGTCGCCGCTCCCACATCGCATATGTGGTTTCGGTGTCCGCGCTGC\n+CCGATAGCAACGGCTCGACGGCTGGGCCCACGCCGGGCGGAAGATAGGCCGTGACCAGGG\n+CCAAGGGTTGATCGCCAGTGCGGATGCGCCGGCGAATACAGAGGACCTCAACCAAACCCA\n+GCGTCTCGGAAATCCGTTGCGGCGCCGGTCCGGTCTGGTGTGACAGCACGTCGACCTGCG\n+GGGTAACACCACAGCTCAACAACACCTCTGTGATGATGCGCACGCCGCAACTGAGCTCCT\n+GTTCCACCGGATCGGCGACGAAGGTACCCAAGCCTTGCCGGCGCACTAGCCATCCCTGAC\n+GTTGCAGCATGCCGACCGCCGCGCGCACGGTCACGCGGCTCAAACCGGAACGGTCGATCA\n+ATTCTCGTTCGCTGGGCAAGCGCCCGCCGCGCGGCAGCCGCTGCTGGATGATCTGGGCCT\n+TTAGCGCCTCGGCAAGCTGGGTACTCGCCGGCACGCTGCCACGCGATATCCGCAGATCGG\n+CAGCGTCCAGGTCCAGCTTGACAGATGTCATAAGACGTATTAAAACGTCTTATACTCACC\n+ACGTCAAGCGTGCGTGCGCGGTAGCAGCGGAAGAAGGTCAGCCATGACGTCACCCGTCGC\n+GGTCATCGCCCGGTTCATGCCACGGCCTGACGCTAGGTCGGCCCTGCGCGCTCTCTTGGA\n+CGCAATGATTACCCCGACACGGGCCGAGGACGGATGCCGTAGCTACGACCTCTACGAGAG\n+CGCCGACGGCGGCGAGCTGGTGCTTTTCGAACGGTACCGCAGCCGCATCGCGCTCGACGA\n+GCACCGCGGTTCGCCGCACTATCTGAACTACCGGGCACAGGTCGGTGAATTGCTGACCCG\n+GCCCGTCGCGGTGACTGTGCTCGCGCCGCTCGACGAGGCTTCTGCTTAGAGCGGGTAGCA\n+CCCAGGCAGCTTGATCCACGCCCGGCACCGGCCGAGCGCTCGGGAACCGCCGCAGACCAC\n+CGCAGTCCCCCCGTGGGTTCAGCGGCGCGGCGGCGGGTTGGCTATACCAGCAGGTAAAAC\n+GAATCTCGGTAGGATTCAAGAAGTCTCAGCCACAGTTCGCTGATGGTCGGGAAGCACGGA\n+ACGGCGTGCCACAACCGATCGATTGGCACCTGGCCGGCGACGGCGACGGTGGCCGAATGC\n+AACAGCTCGGCGGCGCCCGGGCCAACCATGGTCACGCCCAGCAGATGGCCCCGATCGACG\n+TCGACCACCATGCGCGCCCTGCCGGTGTATCCGTCGGCAAAGAGCTTGGCTCCCATAACG\n+ACATCGCCGATTTCGACATCGATCGCTTTGATCCGGTGACCAGCCTGTGCGGCCTGATCA\n+GCTGTCAGGCCGACCGCTGCGGCTTCGGGGTCGGTAAAGAATGCCTGCGGCACCGCGTGA\n+TGGTCGGCGGTGGTCGCGTGCATGCCCCACGACGTGGTGTCTAGCGGTCGTCCGGCGGCA\n+CGGGCGCCGATCGCGGTGCCGGCGATCCGCGCCTGGTATTTGCCTTGGTGGGTCAGCAAC\n+GCGCGATGGTTGACGTCGCCGGCGGCATAGAGCCAGCCGTCGTCAACAGCCCGCACTCGG\n+CAGGTGTCATCGACGTCCAGCCAGCTGCCCGGCGTCAGTCCTATTGTCTCCAAGCCGATG\n+TCGTCGGTTCGCGGTGCTCGGCCGGTGGCGAAGAGTACCTCGTCGACCCGCAGCTCGGTA\n+CCGTCGTCCAGCTCGAGGACCACTGGGCCAGTTGGGTTGGGGCGGCCCAGCGCGCGTACC\n+GATACTCCCACGCGCACGTCAACGCCGGCGTCGGCCAGTCCGCGACCGATGAGTTCCCCC\n+ACAAACGGTTCCATTCGGGGCAGCAGGCCAGATCCCCGAGCCAGCAGGGTCACCGAGGCG\n+CCCAGTCCCTGCCAGGCGGTCGCCATCTCCACACCGACGCCGCCGGCGCCGACGATCGCA\n+AGCCGGTCGGGGACCGTACTGTTGTCGGTGGCTTGGCGATTGGTCCATGGCCGGGCTTCG\n+GTGATGCCAGGAAGGTCGGGGAGTGCTGGCCGGCTTCCGGTGCAGATGACAACGGCATGC\n+CGGGCGGTCAGCGCCACGCTTTCGCCGCTCGACTTGGTGACGACGACGCGGCGCGGACCG\n+TCCAATCGCCCGTCACCGCGTATCAGCGTCGCGCCGATTCCACTCACCCAGTCGGCCTGG\n+CCGGTGTCGTCCCAGTGGGCCACATAGCGGTTGCGGCGGCCAAAGACGCCGGCTGTGTTG\n+ATCGAGCCGTCGACTGCTTCGCGCGCGCCGTCGACCCGTCGGGCGTCAGAGATCGCGATG\n+ACCGGACGCAGCAAGGCTTTGCTGGGCACACAGGCCCAATAGGAGCATTCACCCCCGACG\n+AGTTCGCGCTCCACCACCGCGACACGCAGGCCCCCCGCGCGGGCACGATCGGCGACGTTC\n+TGTCCAACGGGTCCCGCGCCGAGCACGACGACGTCATACGTTTCACCCTCACGGCAGCCG\n+GGTGTTGCCATTGGCGCCTGGTCCTGTTGGGCCGCGGTCATAATCAAAGATCCTTTCGTC\n+GGACTCTGCCAGCGACGCTACGCGCGCCTAGCGCCGGTGAGCCGTGCCGGCCTATCGCCC\n+ACCAGACGCAAAAGCTCTCGACACGCCGTGCGAAAAGGGACCTTTATGTCTCAGTGTCGG\n+TGTTGTGTGTGCCGCGAGGTGGGTGTGTCGGTGTGACAGACGCCGTGTCGCGGTGGTTTG\n+TTCCGGATCACCTGGTGTCTGGCTCACTTTGCGTCTGCCGTCCTCTTGGGGTTGGCGTTG\n+AGCAGTATTGCCGGCACTAGGTGAGAAGGACCGGCCGGCGTGACTTGATAGGAGCGTGGC\n+TTTCGCCCCGACTGAGATGTGTCCGCCGACCGGCCCAACCTCAACACCCCCTCAAGTGAA\n+GGAGGTGAACCGCCCCGGCATGTCCGGAGACTCCAGTTCTTGGAAAGGATGGGGTCATGT\n+CAGGTGGTTCATCGAGGAGGTACCCGCCGGAGCTGCGTGAGCGGGC\n' |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/combined_DNA_CDS.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combined_DNA_CDS.fasta Tue Aug 27 05:51:12 2024 +0000 |
| b |
| b'@@ -0,0 +1,18206 @@\n+>0_0_0\n+TTGTGTCACTTCAGTTTCACGGTTATCAGCGGGGCGCTCTTTGTCAGTGCCCGACGTTAT\n+GATTCGAACATGTTAGCGAATAGCCGGGAGGAGCTTGTCGAGGTCTTCGACGCGCTGGAT\n+GCCGACCTGGACCGCTTGGACGAGGTGTCCTTTGAGGTGCTGAGCACCCCGGAACGGCTG\n+CGGTCTCTGGAACGTCTGGAATGCTTGGCGCGCCGGCTACCGGCGGCCCAGCACACGTTG\n+ATCAACCAACTCGACACCCAAGCCAGCGAGGAAGAACTGGGCGGCACGCTGTGCTGCGCG\n+CTGGCCAACCGGCTGCGCATCACCAAGCCCGAAGCCGGCCGACGCAGCGCCGAAGCCAAG\n+CCTTAG\n+>0_0_1\n+ATGGCTATACCACCGGAGGTGCACTCGGGCCTGTTGAGCGCCGGGTGCGGTCCGGGATCA\n+TTGCTTGTTGCCGCGCAGCAGTGGCAAGAACTTAGTGATCAGTACGCACTCGCATGCGCC\n+GAGTTGGGCCAATTGTTGGGCGAGGTTCAGGCCAGCAGCTGGCAGGGAACCGCCGCCACC\n+CAGTACGTGGCTGCCCATGGCCCCTATCTGGCCTGGCTTGAGCAAACCGCGATCAACAGC\n+GCCGTCACCGCCGCACAGCACGTAGCGGCTGCCGCTGCCTACTGCAGCGCCCTGGCCGCG\n+ATGCCCACCCCAGCAGAGCTGGCCGCCAACCACGCCATTCATGGCGTTCTGATCGCCACC\n+AACTTCTTCGGGATCAACACCGTTCCGATCGCGCTCAACGAAGCCGATTATGTCCGCATG\n+TGGCTGCAAGCCGCCGACACCATGGCCGCCTACCAGGCCGTCGCCGATGCGGCCACGGTG\n+GCCGTACCGTCCACCCAACCGGCGCCACCGATCCGCGCGCCCGGCGGCGATGCCGCAGAT\n+ACCCGGCTAGACGTATTGAGTTCAATTGGTCAGCTCATCCGGGATATCTTGGATTTCATT\n+GCCAACCCGTACAAGTATTTTCTGGAGTTTTTCGAGCAATTCGGCTTCAGCCCGGCCGTA\n+ACGGTCGTCCTTGCCCTTGTTGCCCTGCAGCTGTACGACTTTCTTTGGTATCCCTATTAC\n+GCCTCGTACGGCCTGCTCCTGCTTCCGTTCTTCACTCCCACCTTGAGCGCGTTGACCGCC\n+CTAAGCGCGCTGATCCATTTGCTGAACCTGCCCCCGGCTGGACTGCTTCCTATCGCCGCA\n+GCGCTCGGTCCCGGCGACCAATGGGGCGCAAACTTGGCTGTGGCTGTCACGCCGGCCACG\n+GCGGCCGTGCCCGGCGGAAGCCCGCCCACCAGCAACCCCGCGCCCGCCGCTCCCAGCTCG\n+AACTCGGTTGGCAGCGCTTCGGCTGCACCCGGCATCAGCTATGCCGTGCCCGGCCTGGCG\n+CCACCCGGGGTTAGCTCTGGCCCTAAAGCCGGCACCAAATCACCTGACACCGCCGCCGAC\n+ACCCTTGCAACCGCGGGCGCAGCACGACCGGGCCTCGCCCGAGCCCACCGAAGAAAGCGC\n+AGCGAAAGCGGCGTCGGGATACGCGGTTACCGCGACGAATTTTTGGACGCGACCGCCACG\n+GTGGACGCCGCTACGGATGTGCCCGCTCCCGCCAACGCGGCTGGCAGTCAAGGTGCCGGC\n+ACTCTCGGCTTTGCCGGTACCGCACCGACAACCAGCGGCGCCGCGGCCGGAATGGTTCAA\n+CTGTCGTCGCACAGCACAAGCACTACAGTCCCGTTGCTGCCCACTACCTGGACAACCGAC\n+GCCGAACAATGA\n+>0_0_2\n+ATGACGCTTAAGGTCAAAGGCGAGGGACTCGGTGCGCAGGTCACAGGGGTCGATCCCAAG\n+AATCTGGACGATATAACCACCGACGAGATCCGGGATATCGTTTACACGAACAAGCTCGTT\n+GTGCTAAAAGACGTCCATCCGTCTCCGCGGGAGTTCATCAAACTCGGCAGGATAATTGGA\n+CAAATCGTTCCGTATTACGAACCCATGTACCATCACGAAGACCACCCGGAGATCTTTGTC\n+TCCTCCACTGAGGAAGGTCAGGGGGTCCCAAAAACCGGCGCGTTCTGGCATATCGACTAT\n+ATGTTTATGCCGGAACCTTTCGCGTTTTCCATGGTGCTGCCGCTGGCGGTGCCTGGACAC\n+GACCGCGGGACCTATTTCATCGATCTCGCCAGGGTCTGGCAGTCGCTGCCCGCCGCCAAG\n+CGAGACCCGGCCCGCGGAACCGTCAGCACCCACGACCCTCGACGCCACATCAAGATCCGA\n+CCCAGCGACGTCTACCGGCCCATCGGAGAGGTATGGGACGAGATCAACCGGACCACGCCC\n+CCAATAAAGTGGCCTACGGTCATCCGGCACCCAAAGACCGGCCAAGAGATCCTCTACATC\n+TGCGCGACGGGCACCACCAAGATCGAGGACAAGGACGGCAATCCGGTTGATCCGGAGGTG\n+CTGCAAGAACTCATGGCCGCGACCGGACAGCTCGATCCTGAGTACCAGTCGCCGTTCATA\n+CATACTCAGCACTACCAGGTTGGCGACATCATCTTGTGGGACAACCGGGTTCTCATGCAC\n+CGAGCGAAGCACGGCAGCGCCGCGGGCACTCTGACGACCTACCGCCTGACCATGCTTGAT\n+GGCCTCAAGACGCCGGGATACGCGGCATGA\n+>0_0_3\n+ATGAGCCACACCGACTTGACGCCCTGCACACGGGTGCTGGCATCCAGCGGCACGGTTCCG\n+ATCGCAGAGGAACTGCTGGCCAGAGTGCTCGAGCCCTACTCCTGCAAAGGATGTCGCTAC\n+CTCATCGACGCACAGTACAGCGCCACCGAGGATTCGGTTCTTGCCTATGGCAACTTCACG\n+ATCGGTGAGTCCGCCTATATTCGAAGCACGGGGCACTTCAACGCGGTCGAACTGATTCTG\n+TGTTTCAATCAGCTCGCCTACAGCGCCTTCGCTCCGGCCGTCCTCAACGAGGAAATCCGG\n+GTGCTTCGCGGCTGGTCGATCGACGACTACTGCCAACACCAGCTCTCTAGCATGCTGATC\n+AGGAAGGCATCATCGCGGTTCAGAAAACCGCTGAACCCGCAAAAGTTCTCTGCCCGCCTC\n+CTGTGTCGAGATCTGCAGGTCATCGAACGAACCTGGCGCTATCTCAAGGTCCCGTGCGTC\n+ATCGAGTTCTGGGACGAGAACGGCGGGGCGGCGTCCGGTGAGATCGAACTAGCGGCCCTC\n+AACATTCCGTAA\n+>0_0_4\n+ATGCCTCAGTTGCCATCTACCGTGCTGGACCGGGTCTTCGAGCAGGCACGGCAGCAGCCG\n+GAAGCAATCGCCTTGCGTCGCTGCGACGGCACTAGCGCACTGCGGTACCGTGAACTCGTC\n+GCCGAAGTTGGTGGCCTTGCCGCGGATTTGCGTGCCCAGTCGGTTAGCCGGGGTTCTAGG\n+GTGCTGGTCATTTCCGACAATGGACCCGAGACGTACCTGTCGGTGCTGGCGTGTGCAAAG\n+CTCGGGGCGATCGCCGTCATGGCCGACGGCAATCTTCCGATCGCAGCCATCGAACGATTC\n+TGTCAGATCACCGACCCCGCAGCGGCTCTCGTCGCACCAGGGAGCAAGATGGCATCTTCC\n+GCCGTTCCCGAGGCGCTGCACTCGATACCAGTGATCGCGGTCGACATAGCCGCTGTTACA\n+CGGGAATCCGAGCATTCCTTGGATGCAGCCAGCCTCGCCGGGAACGCGGACCAGGGGAGC\n+GAGGATCCGCTGGCGATGATCTTCACCAGCGGTACCACGGGCGAGCCCAAGGCTGTGCTA\n+CTGGCCAACCGCACCTTCTTCGCCGTCCCGGACATCTTGCAAAAAGAGGGTTTGAACTGG\n+GTCACTTGGGTCGTCGGCGAAACCAC'..b'CAGCTACGCCGACTATCCCAGCGCGGTCGCGCAATGG\n+TACGAACGAATCGCTCAGTCGGTCCTGAAGGCGTTGCAGTCCACCGAAGTACACGCCTTG\n+GTAGCCGCTGACGAGGAACTGTGGACCGGCCCCCCGGTTGAATTGGCCGACGCAACCCAC\n+CGACTGTGA\n+>1_0_539\n+ATGAACGCCAAAGACGACCCGCACTTCGGACTCATGTTGGCTGCGACGGTTAATGGCCTG\n+GCGGTCGGCAGTTACCGCGAAATGGTTGTCGTCTCGCAGACGGCGGAAGAATACGGATTC\n+GATTCAGTGTGGTTATGCGACCACTTCCTGACGATAAGCCCCGGCGAGTATGCGAAGGTC\n+GCCGGCATCGCCGCCGACACCGGCTCCGCGACCGGCACCGAAACCGGCGGGGCGGGCCAG\n+TGCGCCCCTTCGAGGTCGCTGCCCCTGCTCGAGTGCTGGACCGCACTTGCGGCATTGTCC\n+CGCGACACCACGAAGCTGCGGTTGGGCACCAGCGTGCTGTGCAATTCCTACCGTCATCCT\n+TCCGTGCTGGCCAAGATGGCTGCGACGCTGGACGTCATTTCCCAGGGACGTCTCGATCTG\n+GGATTGGGCGCCGGCTGGTTTCGGCGCGAGTCGCAAGCCTACGGCATCCCGTTCCCGCCG\n+GTTGGCGACCGAGTCTCCGCGCTTGCCGAGTCGCTGCAGGTCATCAAGGCCGTGTGGACC\n+GAGCCAAACCCCACCTACGCCGGCCGGTTTTACACCTTGGACGGCGCCACCTGCGATCCG\n+CCGCCGGTGCAACGGCCACATCCTCCGTTGTGGATCGGCGGGGAAGGCGACCGGGTCCAG\n+CGCATCGCCGCTAAGCATGCCCAGGGCCTGAACGTGCGCTGGTGGTCGCCGCAGCAAGTC\n+ACCCAACGCCGCGGATTTCTCACCCAGGCGTCGGAGGCGGCCGGGCGTGACCCCGACACG\n+CTGCGACTGTCGGTCACGCTGCTGCTGGCACCCACCCAGTCCGGCGAGGAAGAAGTCCGG\n+ATCCGCGAAGAATTCGCGTCCATCCCCGAGCCGGGGCTCATCGTCGGGACACCCGACAGG\n+TGTGTCGAGCGCATTCGTGAATACCAGGACCGCGGTGTCGGCCATTTTCTCTTCACGATT\n+CCACACGTCGTGAAGTCCGATTATCTGCACATCATCGGCAGTGACATCATTCCGCGGGTC\n+AAAACTGAGGTCACGATTCCATGA\n+>1_0_540\n+ATGACATCTGTCAAGCTGGACCTGGACGCTGCCGATCTGCGGATATCGCGTGGCAGCGTG\n+CCGGCGAGTACCCAGCTTGCCGAGGCGCTAAAGGCCCAGATCATCCAGCAGCGGCTGCCG\n+CGCGGCGGGCGCTTGCCCAGCGAACGAGAATTGATCGACCGTTCCGGTTTGAGCCGCGTG\n+ACCGTGCGCGCGGCGGTCGGCATGCTGCAACGTCAGGGATGGCTAGTGCGCCGGCAAGGC\n+TTGGGTACCTTCGTCGCCGATCCGGTGGAACAGGAGCTCAGTTGCGGCGTGCGCATCATC\n+ACAGAGGTGTTGTTGAGCTGTGGTGTTACCCCGCAGGTCGACGTGCTGTCACACCAGACC\n+GGACCGGCGCCGCAACGGATTTCCGAGACGCTGGGTTTGGTTGAGGTCCTCTGTATTCGC\n+CGGCGCATCCGCACTGGCGATCAACCCTTGGCCCTGGTCACGGCCTATCTTCCGCCCGGC\n+GTGGGCCCAGCCGTCGAGCCGTTGCTATCGGGCAGCGCGGACACCGAAACCACATATGCG\n+ATGTGGGAGCGGCGACTGGGTGTACGCATTGCACAGGCTACCCACGAAATCCATGCCGCC\n+GGGGCCTCCCCCGACGTAGCCGACGCGTTGGGTCTGGCGGTGGGTTCGCCGGTACTGGTC\n+GTCGACCGCACCAGCTACACCAATGACGGCAAGCCCCTTGAAGTGGTCGTGTTCCACCAT\n+CGCCCCGAGCGGTACCAGTTCTCCGTCACGTTACCCCGAACGTTGCCCGGATCAGGTGCC\n+GGAATTATCGAGAAACGAGATTTCGCATGA\n+>1_0_541\n+ATGACGTCACCCGTCGCGGTCATCGCCCGGTTCATGCCACGGCCTGACGCTAGGTCGGCC\n+CTGCGCGCTCTCTTGGACGCAATGATTACCCCGACACGGGCCGAGGACGGATGCCGTAGC\n+TACGACCTCTACGAGAGCGCCGACGGCGGCGAGCTGGTGCTTTTCGAACGGTACCGCAGC\n+CGCATCGCGCTCGACGAGCACCGCGGTTCGCCGCACTATCTGAACTACCGGGCACAGGTC\n+GGTGAATTGCTGACCCGGCCCGTCGCGGTGACTGTGCTCGCGCCGCTCGACGAGGCTTCT\n+GCTTAG\n+>1_0_542\n+ATGACCGCGGCCCAACAGGACCAGGCGCCAATGGCAACACCCGGCTGCCGTGAGGGTGAA\n+ACGTATGACGTCGTCGTGCTCGGCGCGGGACCCGTTGGACAGAACGTCGCCGATCGTGCC\n+CGCGCGGGGGGCCTGCGTGTCGCGGTGGTGGAGCGCGAACTCGTCGGGGGTGAATGCTCC\n+TATTGGGCCTGTGTGCCCAGCAAAGCCTTGCTGCGTCCGGTCATCGCGATCTCTGACGCC\n+CGACGGGTCGACGGCGCGCGCGAAGCAGTCGACGGCTCGATCAACACAGCCGGCGTCTTT\n+GGCCGCCGCAACCGCTATGTGGCCCACTGGGACGACACCGGCCAGGCCGACTGGGTGAGT\n+GGAATCGGCGCGACGCTGATACGCGGTGACGGGCGATTGGACGGTCCGCGCCGCGTCGTC\n+GTCACCAAGTCGAGCGGCGAAAGCGTGGCGCTGACCGCCCGGCATGCCGTTGTCATCTGC\n+ACCGGAAGCCGGCCAGCACTCCCCGACCTTCCTGGCATCACCGAAGCCCGGCCATGGACC\n+AATCGCCAAGCCACCGACAACAGTACGGTCCCCGACCGGCTTGCGATCGTCGGCGCCGGC\n+GGCGTCGGTGTGGAGATGGCGACCGCCTGGCAGGGACTGGGCGCCTCGGTGACCCTGCTG\n+GCTCGGGGATCTGGCCTGCTGCCCCGAATGGAACCGTTTGTGGGGGAACTCATCGGTCGC\n+GGACTGGCCGACGCCGGCGTTGACGTGCGCGTGGGAGTATCGGTACGCGCGCTGGGCCGC\n+CCCAACCCAACTGGCCCAGTGGTCCTCGAGCTGGACGACGGTACCGAGCTGCGGGTCGAC\n+GAGGTACTCTTCGCCACCGGCCGAGCACCGCGAACCGACGACATCGGCTTGGAGACAATA\n+GGACTGACGCCGGGCAGCTGGCTGGACGTCGATGACACCTGCCGAGTGCGGGCTGTTGAC\n+GACGGCTGGCTCTATGCCGCCGGCGACGTCAACCATCGCGCGTTGCTGACCCACCAAGGC\n+AAATACCAGGCGCGGATCGCCGGCACCGCGATCGGCGCCCGTGCCGCCGGACGACCGCTA\n+GACACCACGTCGTGGGGCATGCACGCGACCACCGCCGACCATCACGCGGTGCCGCAGGCA\n+TTCTTTACCGACCCCGAAGCCGCAGCGGTCGGCCTGACAGCTGATCAGGCCGCACAGGCT\n+GGTCACCGGATCAAAGCGATCGATGTCGAAATCGGCGATGTCGTTATGGGAGCCAAGCTC\n+TTTGCCGACGGATACACCGGCAGGGCGCGCATGGTGGTCGACGTCGATCGGGGCCATCTG\n+CTGGGCGTGACCATGGTTGGCCCGGGCGCCGCCGAGCTGTTGCATTCGGCCACCGTCGCC\n+GTCGCCGGCCAGGTGCCAATCGATCGGTTGTGGCACGCCGTTCCGTGCTTCCCGACCATC\n+AGCGAACTGTGGCTGAGACTTCTTGAATCCTACCGAGATTCGTTTTACCTGCTGGTATAG\n' |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/combined_protein_CDS.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combined_protein_CDS.fasta Tue Aug 27 05:51:12 2024 +0000 |
| b |
| b'@@ -0,0 +1,7048 @@\n+>0_0_0\n+MCHFSFTVISGALFVSARRYDSNMLANSREELVEVFDALDADLDRLDEVSFEVLSTPERL\n+RSLERLECLARRLPAAQHTLINQLDTQASEEELGGTLCCALANRLRITKPEAGRRSAEAK\n+P\n+>0_0_1\n+MAIPPEVHSGLLSAGCGPGSLLVAAQQWQELSDQYALACAELGQLLGEVQASSWQGTAAT\n+QYVAAHGPYLAWLEQTAINSAVTAAQHVAAAAAYCSALAAMPTPAELAANHAIHGVLIAT\n+NFFGINTVPIALNEADYVRMWLQAADTMAAYQAVADAATVAVPSTQPAPPIRAPGGDAAD\n+TRLDVLSSIGQLIRDILDFIANPYKYFLEFFEQFGFSPAVTVVLALVALQLYDFLWYPYY\n+ASYGLLLLPFFTPTLSALTALSALIHLLNLPPAGLLPIAAALGPGDQWGANLAVAVTPAT\n+AAVPGGSPPTSNPAPAAPSSNSVGSASAAPGISYAVPGLAPPGVSSGPKAGTKSPDTAAD\n+TLATAGAARPGLARAHRRKRSESGVGIRGYRDEFLDATATVDAATDVPAPANAAGSQGAG\n+TLGFAGTAPTTSGAAAGMVQLSSHSTSTTVPLLPTTWTTDAEQ\n+>0_0_2\n+MTLKVKGEGLGAQVTGVDPKNLDDITTDEIRDIVYTNKLVVLKDVHPSPREFIKLGRIIG\n+QIVPYYEPMYHHEDHPEIFVSSTEEGQGVPKTGAFWHIDYMFMPEPFAFSMVLPLAVPGH\n+DRGTYFIDLARVWQSLPAAKRDPARGTVSTHDPRRHIKIRPSDVYRPIGEVWDEINRTTP\n+PIKWPTVIRHPKTGQEILYICATGTTKIEDKDGNPVDPEVLQELMAATGQLDPEYQSPFI\n+HTQHYQVGDIILWDNRVLMHRAKHGSAAGTLTTYRLTMLDGLKTPGYAA\n+>0_0_3\n+MSHTDLTPCTRVLASSGTVPIAEELLARVLEPYSCKGCRYLIDAQYSATEDSVLAYGNFT\n+IGESAYIRSTGHFNAVELILCFNQLAYSAFAPAVLNEEIRVLRGWSIDDYCQHQLSSMLI\n+RKASSRFRKPLNPQKFSARLLCRDLQVIERTWRYLKVPCVIEFWDENGGAASGEIELAAL\n+NIP\n+>0_0_4\n+MPQLPSTVLDRVFEQARQQPEAIALRRCDGTSALRYRELVAEVGGLAADLRAQSVSRGSR\n+VLVISDNGPETYLSVLACAKLGAIAVMADGNLPIAAIERFCQITDPAAALVAPGSKMASS\n+AVPEALHSIPVIAVDIAAVTRESEHSLDAASLAGNADQGSEDPLAMIFTSGTTGEPKAVL\n+LANRTFFAVPDILQKEGLNWVTWVVGETTYSPLPATHIGGLWWILTCLMHGGLCVTGGEN\n+TTSLLEILTTNAVATTCLVPTLLSKLVSELKSANATVPSLRLVGYGGSRAIAADVRFIEA\n+TGVRTAQVYGLSETGCTALCLPTDDGSIVKIEAGAVGRPYPGVDVYLAATDGIGPTAPGA\n+GPSASFGTLWIKSPANMLGYWNNPERTAEVLIDGWVNTGDLLERREDGFFYIKGRSSEMI\n+ICGGVNIAPDEVDRIAEGVSGVREAACYEIPDEEFGALVGLAVVASAELDESAARALKHT\n+IAARFRRESEPMARPSTIVIVTDIPRTQSGKVMRASLAAAATADKARVVVRG\n+>0_0_5\n+MAEPVRDRILAAVCDVLYIDEADLIDGDETDLRDLGLDSVRFVLLMKQLGVNRQSELPSR\n+LAANPSIAGWLRELEAVCTEFG\n+>0_0_6\n+MHRVRLSRSQRNLYNGVRQDNNPALYLIGKSYRFRRLELARFLAALHATVLDNPVQLCVL\n+ENSGADYPDLVPRLRFGDIVRVGSADEHLQSTWCSGILGKPLVRHTVHTDPNGYVTGLDV\n+HTHHILLDGGATGTIEADLARYLTTDPAGETPSVGAGLAKLREAHRRETAKVEESRGRLS\n+AVVQRELADEAYHGGHGHSVSDAPGTAAKGVLHESATICGNAFDAILTLSEAQRVPLNVL\n+VAAAAVAVDASLRQNTETLLVHTVDNRFGDSDLNVATCLVNSVAQTVRFPPFASVSDVVR\n+TLDRGYVKAVRRRWLREEHYRRMYLAINRTSHVEALTLNFIREPCAPGLRPFLSEVPIAT\n+DIGPVEGMTVASVLDEEQRTLNLAIWNRADLPACKTHPKVAERIAAALESMAAMWDRPIA\n+MIVNDWFGIGPDGTRCQGDWPARQPSTPAWFLDSARGVHQFLGRRRFVYPWVAWLVQRGA\n+APGDVLVFTDDDTDKTIDLLIACHLAGCGYSVCDTADEISVRTNAITEHGDGILVTVVDV\n+AATQLAVVGHDELRKVVDERVTQVTHDALLATKTAYIMPTSGTTGQPKLVRISHGSLAVF\n+CDAISRAYGWGAHDTVLQCAPLTSDISVEEIFGGAACGARLVRSAAMKTGDLAALVDDLV\n+ARETTIVDLPTAVWQLLCADGDAIDAIGRSRLRQIVIGGEAIRCSAVDKWLESAASQGIS\n+LLSSYGPTEATVVATFLPIVCDQTTMDGALLRLGRPILPNTVFLAFGEVVIVGDLVADGY\n+LGIDGDGFGTVTAADGSRRRAFATGDRVTVDAEGFPVFSGRKDAVVKISGKRVDIAEVTR\n+RIAEDPAVSDVAVELHSGSLGVWFKSQRTREGEQDAAAATRIRLVLVSLGVSSFFVVGVP\n+NIPRKPNGKIDSDNLPRLPQWSAAGLNTAETGQRAAGLSQIWSRQLGRAIGPDSSLLGEG\n+IGSLDLIRILPETRRYLGWRLSLLDLIGADTAANLADYAPTPDAPTGEDRFRPLVAAQRP\n+AAIPLSFAQRRLWFLDQLQRPAPVYNMAVALRLRGYLDTEALGAAVADVVGRHESLRTVF\n+PAVDGVPRQLVIEARRADLGCDIVDATAWPADRLQRAIEEAARHSFDLATEIPLRTWLFR\n+IADDEHVLVAVAHHIAADGWSVAPLTADLSAAYASRCAGRAPDWAPLPVQYVDYTLWQRE\n+ILGDLDDSDSPIAAQLAYWENALAGMPERLRLPTARPYPPVADQRGASLVVDWPASVQQQ\n+VRRIARQHNATSFMVVAAGLAVLLSKLSGSPDVAVGFPIAGRSDPALDNLVGFFVNTLVL\n+RVNLAGDPSFAELLGQVRARSLAAYENQDVPFEVLVDRLKPTRALTHHPLIQVMLAWQDN\n+PVGQLNLGDLQATPMPIDTRTARMDLVFSLAERFSEGSEPAGIGGAVEYRTDVFEAQAID\n+VLIERLRKVLVAVAAAPERTVSSIDALDGTERARLDEWGNRAVLTAPAPTPVSIPQMLAA\n+QVARIPEAEAVCCGDASMTYRELDEASNRLAHRLAGCGAGPGECVALLFERCAPAVVAMV\n+AVLKTGAAYLPIDPANPPPRVAFMLGDAVPVAAVTTAGLRSRLAGHDLPIIDVVDALAAY\n+PGTPPPMPAAVNLAYILYTSGTTGEPKGVGITHRNVTRLFASLPARLSAAQVWSQCHSYG\n+FDASAWEIWGALLGGGRLVIVPESVAASPNDFHGLLVAEHVSVLTQTPAAVAMLPTQGLE\n+SVALVVAGEACPAALVDRWAPGRVMLNAYGPTETTICAAISAPLRPGSGMPPIGVPVSGA\n+ALFVLDSWLRPVPAGVAGELYIAGAGVGVGYWRRAGLTASRFVACPFGGSGARMYRTGDL\n+VCWRADGQLEFLGRTDDQVKIRGYRIELGEVATALAELAGVGQAVVIAREDRPGDKRLVG\n+YATEIAPGAVDPAGLRAQLAQRLPGYLVPAAVVVIDALPLTVNGKLDHRALPAPEYGDTN\n+GYRAPAGPVEKTVAGIFARVLGLERVGVDDSFFELGGDSLAAMRVIAAINTTLNADLPVR\n+ALLHASSTRGLSQLLGRDARPTSDPRLVSVHGDNPTEVHASDLTLDRFIDADTLATAVNL\n+PGPSPELRTVLLTGATGFLGR'..b'DTRMAAAVCSLALMLAMFGANVYASRMADPTGYAGAAPSRSFPWPPP\n+>1_0_530\n+MLGNAMVEACPAEGDAPVPITPAGRPRSGQRSYPDRLDVGLLRTAGVCVLASVMAHVDVT\n+VVSVAQRTFVADFGSTQAVVAWTMTGYMLALATVIPTAGWAADRFGTRRLFMGSVLAFTL\n+GSLLCAVAPNILLLIIFRVVQGFGGGMLTPVSFAILAREAGPKRLGRVMAVVGIPMLLGP\n+VGGPILGGWLIGAYGWRWIFLVNLPVGLSALVLAAIVFPRDRPAASENFDYMGLLLLSPG\n+LATFLFGVSSSPARGTMADRHVLIPAITGLALIAAFVAHSWYRTEHPLIDMRLFQNRAVA\n+QANMTMTVLSLGLFGSFLLLPSYLQQVLHQSPMQSGVHIIPQGLGAMLAMPIAGAMMDRR\n+GPAKIVLVGIMLIAAGLGTFAFGVARQADYLPILPTGLAIMGMGMGCSMMPLSGAAVQTL\n+APHQIARGSTLISVNQQVGGSIGTALMSVLLTYQFNHSEIIATAKKVALTPESGAGRGAA\n+VDPSSLPRQTNFAAQLLHDLSHAYAVVFVIATALVVSTLIPAAFLPKQQASHRRAPLLSA\n+>1_0_531\n+MSVSGIGESTLADVDAFCAEMDARSVPVSLLVAPRMRDDYRLDRDPRTVDWLTGRRAAGD\n+ALVLHGYDEAATKRRRGEFAMLRAHEANLRLMAADRVLEHLGLRTRLFAAPGWLVSPGVR\n+TALPANGFRLLADLHGITDLVRLTTVRARVLGIGEGFLAEPWWCRMVVMSAERIARRGGV\n+VRIAVAARHLRKSGPLQAMLDAVDLAMLQGCTPMVYRWRADAAVLDAA\n+>1_0_532\n+MALTCTDMSDAVAGSDAEGLTADAIVVGAGLAGLVAACELADRGLRVLILDQENRANVGG\n+QAFWSFGGLFLVNSPEQRRLGIRDSHELALQDWLGTAAFDRPEDYWPEQWAHAYVDFAAG\n+EKRSWLRARGLKIFPLVGWAERGGYDAQGHGNSVPRFHITWGTGPALVDIFVRQLRDRPT\n+VRFAHRHQVDKLIVEGNAVTGVRGTVLEPSDEPRGAPSSRKSVGKFEFRASAVIVASGGI\n+GGNHELVRKNWPRRMGRIPKQLLSGVPAHVDGRMIGIAQKAGAAVINPDRMWHYTEGITN\n+YDPIWPRHGIRIIPGPSSLWLDAAGKRLPVPLFPGFDTLGTLEYITKSGHDYTWFVLNAK\n+IIEKEFALSGQEQNPDLTGRRLGQLLRSRAHAGPPGPVQAFIDRGVDFVHANSLRELVAA\n+MNELPDVVPLDYETVAAAVTARDREVVNKYSKDGQITAIRAARRYRGDRFGRVVAPHRLT\n+DPKAGPLIAVKLHILTRKTLGGIETDLDARVLKADGTPLAGLYAAGEVAGFGGGGVHGYR\n+ALEGTFLGGCIFSGRAAGRGAAEDIR\n+>1_0_533\n+MQLTHFGHSCLLAEFGQTRLLFDPGTFSHGFEGITGLSAILITHQHPDHIDVTRLPTLLE\n+DNPAAELYADPQTAAQLGEPWRAVHVGDELPLAELTVRAVGGCHAVIHPEIPVIENISYL\n+VGDSKHRARLMHPGDALFVPGEQVDVLATPAAAPWMKISEAVDYLRAVAPARAVPIHQAI\n+VAPDARGIYYGRLTEMTTTDFQVLPEESAVTF\n+>1_0_534\n+MRLILATMLVAGRLLATLMAAPSAQAEPETCPPICDQIPATAWISTHAVPLNSQYRWPAM\n+AGAAVAVTRATPRFGFEQVCATPAFPHDSRDWAVAGRVTVVHPDGQWQLQAQVLHWRGDT\n+ARGGQIAASVFGTAVAALRACQLGAPLQSPSVTDDEPTRMAAVISGPVIMHTYLVAHVSS\n+STISELTLWSSGPPQVPWPTVADSAVLDALTAPLCEAYIGSCP\n+>1_0_535\n+MARVVVHVMPKAEILDPQGQAIVGALGRLGHLGISDVRQGKRFELEVDDTVDDTTLAEIA\n+ESLLANTVIEDWTISRDPQ\n+>1_0_536\n+MTARIGVVTFPGTLDDVDAARAARQVGAEVVSLWHADADLKGVDAVVVPGGFSYGDYLRA\n+GAIARFAPVMDEVVAAADRGMPVLGICNGFQVLCEAGLLPGALTRNVGLHFICRDVWLRV\n+ASTSTAWTSRFEPDADLLVPLKSGEGRYVAPEKVLDELEGEGRVVFRYHDNVNGSLRDIA\n+GICSANGRVVGLMPHPEHAIEALTGPSDDGLGLFYSALDAVLTG\n+>1_0_537\n+MTESIGEPLSTNLIERYLRARGRRYFRGHHDAEFFFVANAHLRLHVHLEISPAYRDVFTI\n+RVSPAYFFPATDHTRLAEIVNAWNLQNHEVTAIVHGSSDPHRIGVAAERSLIRDRIRFDD\n+FATFVDNAVSAATELFGQLTAAGLPPTATPPLLRDAG\n+>1_0_538\n+MTLANNGTGMDHFLTPTEYLDAGHPLVRTTAATLIRDAVSDTERVRRIYYYVRDVPYDVL\n+ASFRYLAQGHHRASDVIGHGVAFCMGKASSFVALCRAAGVPARIAFQTIDAPDKEFLSPQ\n+VRALWGGRTGRPFPWHSLGEAYLGRRWVKLDATIDAPTAARLGKPYRQEFDGATPIPTVE\n+GTILRENGSYADYPSAVAQWYERIAQSVLKALQSTEVHALVAADEELWTGPPVELADATH\n+RL\n+>1_0_539\n+MNAKDDPHFGLMLAATVNGLAVGSYREMVVVSQTAEEYGFDSVWLCDHFLTISPGEYAKV\n+AGIAADTGSATGTETGGAGQCAPSRSLPLLECWTALAALSRDTTKLRLGTSVLCNSYRHP\n+SVLAKMAATLDVISQGRLDLGLGAGWFRRESQAYGIPFPPVGDRVSALAESLQVIKAVWT\n+EPNPTYAGRFYTLDGATCDPPPVQRPHPPLWIGGEGDRVQRIAAKHAQGLNVRWWSPQQV\n+TQRRGFLTQASEAAGRDPDTLRLSVTLLLAPTQSGEEEVRIREEFASIPEPGLIVGTPDR\n+CVERIREYQDRGVGHFLFTIPHVVKSDYLHIIGSDIIPRVKTEVTIP\n+>1_0_540\n+MTSVKLDLDAADLRISRGSVPASTQLAEALKAQIIQQRLPRGGRLPSERELIDRSGLSRV\n+TVRAAVGMLQRQGWLVRRQGLGTFVADPVEQELSCGVRIITEVLLSCGVTPQVDVLSHQT\n+GPAPQRISETLGLVEVLCIRRRIRTGDQPLALVTAYLPPGVGPAVEPLLSGSADTETTYA\n+MWERRLGVRIAQATHEIHAAGASPDVADALGLAVGSPVLVVDRTSYTNDGKPLEVVVFHH\n+RPERYQFSVTLPRTLPGSGAGIIEKRDFA\n+>1_0_541\n+MTSPVAVIARFMPRPDARSALRALLDAMITPTRAEDGCRSYDLYESADGGELVLFERYRS\n+RIALDEHRGSPHYLNYRAQVGELLTRPVAVTVLAPLDEASA\n+>1_0_542\n+MTAAQQDQAPMATPGCREGETYDVVVLGAGPVGQNVADRARAGGLRVAVVERELVGGECS\n+YWACVPSKALLRPVIAISDARRVDGAREAVDGSINTAGVFGRRNRYVAHWDDTGQADWVS\n+GIGATLIRGDGRLDGPRRVVVTKSSGESVALTARHAVVICTGSRPALPDLPGITEARPWT\n+NRQATDNSTVPDRLAIVGAGGVGVEMATAWQGLGASVTLLARGSGLLPRMEPFVGELIGR\n+GLADAGVDVRVGVSVRALGRPNPTGPVVLELDDGTELRVDEVLFATGRAPRTDDIGLETI\n+GLTPGSWLDVDDTCRVRAVDDGWLYAAGDVNHRALLTHQGKYQARIAGTAIGARAAGRPL\n+DTTSWGMHATTADHHAVPQAFFTDPEAAAVGLTADQAAQAGHRIKAIDVEIGDVVMGAKL\n+FADGYTGRARMVVDVDRGHLLGVTMVGPGAAELLHSATVAVAGQVPIDRLWHAVPCFPTI\n+SELWLRLLESYRDSFYLLV\n' |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/combined_protein_cdhit_out.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combined_protein_cdhit_out.txt Tue Aug 27 05:51:12 2024 +0000 |
| b |
| b'@@ -0,0 +1,5119 @@\n+>0_0_0\n+MCHFSFTVISGALFVSARRYDSNMLANSREELVEVFDALDADLDRLDEVSFEVLSTPERL\n+RSLERLECLARRLPAAQHTLINQLDTQASEEELGGTLCCALANRLRITKPEAGRRSAEAK\n+P\n+>0_0_1\n+MAIPPEVHSGLLSAGCGPGSLLVAAQQWQELSDQYALACAELGQLLGEVQASSWQGTAAT\n+QYVAAHGPYLAWLEQTAINSAVTAAQHVAAAAAYCSALAAMPTPAELAANHAIHGVLIAT\n+NFFGINTVPIALNEADYVRMWLQAADTMAAYQAVADAATVAVPSTQPAPPIRAPGGDAAD\n+TRLDVLSSIGQLIRDILDFIANPYKYFLEFFEQFGFSPAVTVVLALVALQLYDFLWYPYY\n+ASYGLLLLPFFTPTLSALTALSALIHLLNLPPAGLLPIAAALGPGDQWGANLAVAVTPAT\n+AAVPGGSPPTSNPAPAAPSSNSVGSASAAPGISYAVPGLAPPGVSSGPKAGTKSPDTAAD\n+TLATAGAARPGLARAHRRKRSESGVGIRGYRDEFLDATATVDAATDVPAPANAAGSQGAG\n+TLGFAGTAPTTSGAAAGMVQLSSHSTSTTVPLLPTTWTTDAEQ\n+>0_0_2\n+MTLKVKGEGLGAQVTGVDPKNLDDITTDEIRDIVYTNKLVVLKDVHPSPREFIKLGRIIG\n+QIVPYYEPMYHHEDHPEIFVSSTEEGQGVPKTGAFWHIDYMFMPEPFAFSMVLPLAVPGH\n+DRGTYFIDLARVWQSLPAAKRDPARGTVSTHDPRRHIKIRPSDVYRPIGEVWDEINRTTP\n+PIKWPTVIRHPKTGQEILYICATGTTKIEDKDGNPVDPEVLQELMAATGQLDPEYQSPFI\n+HTQHYQVGDIILWDNRVLMHRAKHGSAAGTLTTYRLTMLDGLKTPGYAA\n+>0_0_3\n+MSHTDLTPCTRVLASSGTVPIAEELLARVLEPYSCKGCRYLIDAQYSATEDSVLAYGNFT\n+IGESAYIRSTGHFNAVELILCFNQLAYSAFAPAVLNEEIRVLRGWSIDDYCQHQLSSMLI\n+RKASSRFRKPLNPQKFSARLLCRDLQVIERTWRYLKVPCVIEFWDENGGAASGEIELAAL\n+NIP\n+>0_0_4\n+MPQLPSTVLDRVFEQARQQPEAIALRRCDGTSALRYRELVAEVGGLAADLRAQSVSRGSR\n+VLVISDNGPETYLSVLACAKLGAIAVMADGNLPIAAIERFCQITDPAAALVAPGSKMASS\n+AVPEALHSIPVIAVDIAAVTRESEHSLDAASLAGNADQGSEDPLAMIFTSGTTGEPKAVL\n+LANRTFFAVPDILQKEGLNWVTWVVGETTYSPLPATHIGGLWWILTCLMHGGLCVTGGEN\n+TTSLLEILTTNAVATTCLVPTLLSKLVSELKSANATVPSLRLVGYGGSRAIAADVRFIEA\n+TGVRTAQVYGLSETGCTALCLPTDDGSIVKIEAGAVGRPYPGVDVYLAATDGIGPTAPGA\n+GPSASFGTLWIKSPANMLGYWNNPERTAEVLIDGWVNTGDLLERREDGFFYIKGRSSEMI\n+ICGGVNIAPDEVDRIAEGVSGVREAACYEIPDEEFGALVGLAVVASAELDESAARALKHT\n+IAARFRRESEPMARPSTIVIVTDIPRTQSGKVMRASLAAAATADKARVVVRG\n+>0_0_5\n+MAEPVRDRILAAVCDVLYIDEADLIDGDETDLRDLGLDSVRFVLLMKQLGVNRQSELPSR\n+LAANPSIAGWLRELEAVCTEFG\n+>0_0_6\n+MHRVRLSRSQRNLYNGVRQDNNPALYLIGKSYRFRRLELARFLAALHATVLDNPVQLCVL\n+ENSGADYPDLVPRLRFGDIVRVGSADEHLQSTWCSGILGKPLVRHTVHTDPNGYVTGLDV\n+HTHHILLDGGATGTIEADLARYLTTDPAGETPSVGAGLAKLREAHRRETAKVEESRGRLS\n+AVVQRELADEAYHGGHGHSVSDAPGTAAKGVLHESATICGNAFDAILTLSEAQRVPLNVL\n+VAAAAVAVDASLRQNTETLLVHTVDNRFGDSDLNVATCLVNSVAQTVRFPPFASVSDVVR\n+TLDRGYVKAVRRRWLREEHYRRMYLAINRTSHVEALTLNFIREPCAPGLRPFLSEVPIAT\n+DIGPVEGMTVASVLDEEQRTLNLAIWNRADLPACKTHPKVAERIAAALESMAAMWDRPIA\n+MIVNDWFGIGPDGTRCQGDWPARQPSTPAWFLDSARGVHQFLGRRRFVYPWVAWLVQRGA\n+APGDVLVFTDDDTDKTIDLLIACHLAGCGYSVCDTADEISVRTNAITEHGDGILVTVVDV\n+AATQLAVVGHDELRKVVDERVTQVTHDALLATKTAYIMPTSGTTGQPKLVRISHGSLAVF\n+CDAISRAYGWGAHDTVLQCAPLTSDISVEEIFGGAACGARLVRSAAMKTGDLAALVDDLV\n+ARETTIVDLPTAVWQLLCADGDAIDAIGRSRLRQIVIGGEAIRCSAVDKWLESAASQGIS\n+LLSSYGPTEATVVATFLPIVCDQTTMDGALLRLGRPILPNTVFLAFGEVVIVGDLVADGY\n+LGIDGDGFGTVTAADGSRRRAFATGDRVTVDAEGFPVFSGRKDAVVKISGKRVDIAEVTR\n+RIAEDPAVSDVAVELHSGSLGVWFKSQRTREGEQDAAAATRIRLVLVSLGVSSFFVVGVP\n+NIPRKPNGKIDSDNLPRLPQWSAAGLNTAETGQRAAGLSQIWSRQLGRAIGPDSSLLGEG\n+IGSLDLIRILPETRRYLGWRLSLLDLIGADTAANLADYAPTPDAPTGEDRFRPLVAAQRP\n+AAIPLSFAQRRLWFLDQLQRPAPVYNMAVALRLRGYLDTEALGAAVADVVGRHESLRTVF\n+PAVDGVPRQLVIEARRADLGCDIVDATAWPADRLQRAIEEAARHSFDLATEIPLRTWLFR\n+IADDEHVLVAVAHHIAADGWSVAPLTADLSAAYASRCAGRAPDWAPLPVQYVDYTLWQRE\n+ILGDLDDSDSPIAAQLAYWENALAGMPERLRLPTARPYPPVADQRGASLVVDWPASVQQQ\n+VRRIARQHNATSFMVVAAGLAVLLSKLSGSPDVAVGFPIAGRSDPALDNLVGFFVNTLVL\n+RVNLAGDPSFAELLGQVRARSLAAYENQDVPFEVLVDRLKPTRALTHHPLIQVMLAWQDN\n+PVGQLNLGDLQATPMPIDTRTARMDLVFSLAERFSEGSEPAGIGGAVEYRTDVFEAQAID\n+VLIERLRKVLVAVAAAPERTVSSIDALDGTERARLDEWGNRAVLTAPAPTPVSIPQMLAA\n+QVARIPEAEAVCCGDASMTYRELDEASNRLAHRLAGCGAGPGECVALLFERCAPAVVAMV\n+AVLKTGAAYLPIDPANPPPRVAFMLGDAVPVAAVTTAGLRSRLAGHDLPIIDVVDALAAY\n+PGTPPPMPAAVNLAYILYTSGTTGEPKGVGITHRNVTRLFASLPARLSAAQVWSQCHSYG\n+FDASAWEIWGALLGGGRLVIVPESVAASPNDFHGLLVAEHVSVLTQTPAAVAMLPTQGLE\n+SVALVVAGEACPAALVDRWAPGRVMLNAYGPTETTICAAISAPLRPGSGMPPIGVPVSGA\n+ALFVLDSWLRPVPAGVAGELYIAGAGVGVGYWRRAGLTASRFVACPFGGSGARMYRTGDL\n+VCWRADGQLEFLGRTDDQVKIRGYRIELGEVATALAELAGVGQAVVIAREDRPGDKRLVG\n+YATEIAPGAVDPAGLRAQLAQRLPGYLVPAAVVVIDALPLTVNGKLDHRALPAPEYGDTN\n+GYRAPAGPVEKTVAGIFARVLGLERVGVDDSFFELGGDSLAAMRVIAAINTTLNADLPVR\n+ALLHASSTRGLSQLLGRDARPTSDPRLVSVHGDNPTEVHASDLTLDRFIDADTLATAVNL\n+PGPSPELRTVLLTGATGFLGR'..b'DTRMAAAVCSLALMLAMFGANVYASRMADPTGYAGAAPSRSFPWPPP\n+>1_0_530\n+MLGNAMVEACPAEGDAPVPITPAGRPRSGQRSYPDRLDVGLLRTAGVCVLASVMAHVDVT\n+VVSVAQRTFVADFGSTQAVVAWTMTGYMLALATVIPTAGWAADRFGTRRLFMGSVLAFTL\n+GSLLCAVAPNILLLIIFRVVQGFGGGMLTPVSFAILAREAGPKRLGRVMAVVGIPMLLGP\n+VGGPILGGWLIGAYGWRWIFLVNLPVGLSALVLAAIVFPRDRPAASENFDYMGLLLLSPG\n+LATFLFGVSSSPARGTMADRHVLIPAITGLALIAAFVAHSWYRTEHPLIDMRLFQNRAVA\n+QANMTMTVLSLGLFGSFLLLPSYLQQVLHQSPMQSGVHIIPQGLGAMLAMPIAGAMMDRR\n+GPAKIVLVGIMLIAAGLGTFAFGVARQADYLPILPTGLAIMGMGMGCSMMPLSGAAVQTL\n+APHQIARGSTLISVNQQVGGSIGTALMSVLLTYQFNHSEIIATAKKVALTPESGAGRGAA\n+VDPSSLPRQTNFAAQLLHDLSHAYAVVFVIATALVVSTLIPAAFLPKQQASHRRAPLLSA\n+>1_0_531\n+MSVSGIGESTLADVDAFCAEMDARSVPVSLLVAPRMRDDYRLDRDPRTVDWLTGRRAAGD\n+ALVLHGYDEAATKRRRGEFAMLRAHEANLRLMAADRVLEHLGLRTRLFAAPGWLVSPGVR\n+TALPANGFRLLADLHGITDLVRLTTVRARVLGIGEGFLAEPWWCRMVVMSAERIARRGGV\n+VRIAVAARHLRKSGPLQAMLDAVDLAMLQGCTPMVYRWRADAAVLDAA\n+>1_0_532\n+MALTCTDMSDAVAGSDAEGLTADAIVVGAGLAGLVAACELADRGLRVLILDQENRANVGG\n+QAFWSFGGLFLVNSPEQRRLGIRDSHELALQDWLGTAAFDRPEDYWPEQWAHAYVDFAAG\n+EKRSWLRARGLKIFPLVGWAERGGYDAQGHGNSVPRFHITWGTGPALVDIFVRQLRDRPT\n+VRFAHRHQVDKLIVEGNAVTGVRGTVLEPSDEPRGAPSSRKSVGKFEFRASAVIVASGGI\n+GGNHELVRKNWPRRMGRIPKQLLSGVPAHVDGRMIGIAQKAGAAVINPDRMWHYTEGITN\n+YDPIWPRHGIRIIPGPSSLWLDAAGKRLPVPLFPGFDTLGTLEYITKSGHDYTWFVLNAK\n+IIEKEFALSGQEQNPDLTGRRLGQLLRSRAHAGPPGPVQAFIDRGVDFVHANSLRELVAA\n+MNELPDVVPLDYETVAAAVTARDREVVNKYSKDGQITAIRAARRYRGDRFGRVVAPHRLT\n+DPKAGPLIAVKLHILTRKTLGGIETDLDARVLKADGTPLAGLYAAGEVAGFGGGGVHGYR\n+ALEGTFLGGCIFSGRAAGRGAAEDIR\n+>1_0_533\n+MQLTHFGHSCLLAEFGQTRLLFDPGTFSHGFEGITGLSAILITHQHPDHIDVTRLPTLLE\n+DNPAAELYADPQTAAQLGEPWRAVHVGDELPLAELTVRAVGGCHAVIHPEIPVIENISYL\n+VGDSKHRARLMHPGDALFVPGEQVDVLATPAAAPWMKISEAVDYLRAVAPARAVPIHQAI\n+VAPDARGIYYGRLTEMTTTDFQVLPEESAVTF\n+>1_0_534\n+MRLILATMLVAGRLLATLMAAPSAQAEPETCPPICDQIPATAWISTHAVPLNSQYRWPAM\n+AGAAVAVTRATPRFGFEQVCATPAFPHDSRDWAVAGRVTVVHPDGQWQLQAQVLHWRGDT\n+ARGGQIAASVFGTAVAALRACQLGAPLQSPSVTDDEPTRMAAVISGPVIMHTYLVAHVSS\n+STISELTLWSSGPPQVPWPTVADSAVLDALTAPLCEAYIGSCP\n+>1_0_535\n+MARVVVHVMPKAEILDPQGQAIVGALGRLGHLGISDVRQGKRFELEVDDTVDDTTLAEIA\n+ESLLANTVIEDWTISRDPQ\n+>1_0_536\n+MTARIGVVTFPGTLDDVDAARAARQVGAEVVSLWHADADLKGVDAVVVPGGFSYGDYLRA\n+GAIARFAPVMDEVVAAADRGMPVLGICNGFQVLCEAGLLPGALTRNVGLHFICRDVWLRV\n+ASTSTAWTSRFEPDADLLVPLKSGEGRYVAPEKVLDELEGEGRVVFRYHDNVNGSLRDIA\n+GICSANGRVVGLMPHPEHAIEALTGPSDDGLGLFYSALDAVLTG\n+>1_0_537\n+MTESIGEPLSTNLIERYLRARGRRYFRGHHDAEFFFVANAHLRLHVHLEISPAYRDVFTI\n+RVSPAYFFPATDHTRLAEIVNAWNLQNHEVTAIVHGSSDPHRIGVAAERSLIRDRIRFDD\n+FATFVDNAVSAATELFGQLTAAGLPPTATPPLLRDAG\n+>1_0_538\n+MTLANNGTGMDHFLTPTEYLDAGHPLVRTTAATLIRDAVSDTERVRRIYYYVRDVPYDVL\n+ASFRYLAQGHHRASDVIGHGVAFCMGKASSFVALCRAAGVPARIAFQTIDAPDKEFLSPQ\n+VRALWGGRTGRPFPWHSLGEAYLGRRWVKLDATIDAPTAARLGKPYRQEFDGATPIPTVE\n+GTILRENGSYADYPSAVAQWYERIAQSVLKALQSTEVHALVAADEELWTGPPVELADATH\n+RL\n+>1_0_539\n+MNAKDDPHFGLMLAATVNGLAVGSYREMVVVSQTAEEYGFDSVWLCDHFLTISPGEYAKV\n+AGIAADTGSATGTETGGAGQCAPSRSLPLLECWTALAALSRDTTKLRLGTSVLCNSYRHP\n+SVLAKMAATLDVISQGRLDLGLGAGWFRRESQAYGIPFPPVGDRVSALAESLQVIKAVWT\n+EPNPTYAGRFYTLDGATCDPPPVQRPHPPLWIGGEGDRVQRIAAKHAQGLNVRWWSPQQV\n+TQRRGFLTQASEAAGRDPDTLRLSVTLLLAPTQSGEEEVRIREEFASIPEPGLIVGTPDR\n+CVERIREYQDRGVGHFLFTIPHVVKSDYLHIIGSDIIPRVKTEVTIP\n+>1_0_540\n+MTSVKLDLDAADLRISRGSVPASTQLAEALKAQIIQQRLPRGGRLPSERELIDRSGLSRV\n+TVRAAVGMLQRQGWLVRRQGLGTFVADPVEQELSCGVRIITEVLLSCGVTPQVDVLSHQT\n+GPAPQRISETLGLVEVLCIRRRIRTGDQPLALVTAYLPPGVGPAVEPLLSGSADTETTYA\n+MWERRLGVRIAQATHEIHAAGASPDVADALGLAVGSPVLVVDRTSYTNDGKPLEVVVFHH\n+RPERYQFSVTLPRTLPGSGAGIIEKRDFA\n+>1_0_541\n+MTSPVAVIARFMPRPDARSALRALLDAMITPTRAEDGCRSYDLYESADGGELVLFERYRS\n+RIALDEHRGSPHYLNYRAQVGELLTRPVAVTVLAPLDEASA\n+>1_0_542\n+MTAAQQDQAPMATPGCREGETYDVVVLGAGPVGQNVADRARAGGLRVAVVERELVGGECS\n+YWACVPSKALLRPVIAISDARRVDGAREAVDGSINTAGVFGRRNRYVAHWDDTGQADWVS\n+GIGATLIRGDGRLDGPRRVVVTKSSGESVALTARHAVVICTGSRPALPDLPGITEARPWT\n+NRQATDNSTVPDRLAIVGAGGVGVEMATAWQGLGASVTLLARGSGLLPRMEPFVGELIGR\n+GLADAGVDVRVGVSVRALGRPNPTGPVVLELDDGTELRVDEVLFATGRAPRTDDIGLETI\n+GLTPGSWLDVDDTCRVRAVDDGWLYAAGDVNHRALLTHQGKYQARIAGTAIGARAAGRPL\n+DTTSWGMHATTADHHAVPQAFFTDPEAAAVGLTADQAAQAGHRIKAIDVEIGDVVMGAKL\n+FADGYTGRARMVVDVDRGHLLGVTMVGPGAAELLHSATVAVAGQVPIDRLWHAVPCFPTI\n+SELWLRLLESYRDSFYLLV\n' |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/combined_protein_cdhit_out.txt.clstr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combined_protein_cdhit_out.txt.clstr Tue Aug 27 05:51:12 2024 +0000 |
| b |
| b'@@ -0,0 +1,1709 @@\n+>Cluster 0\n+0\t3295aa, >0_0_269... *\n+>Cluster 1\n+0\t3186aa, >0_0_219... *\n+1\t3182aa, >1_0_219... at 99.97%\n+>Cluster 2\n+0\t2512aa, >0_0_6... *\n+1\t2512aa, >1_0_6... at 100.00%\n+>Cluster 3\n+0\t1625aa, >0_0_12... *\n+1\t1625aa, >1_0_12... at 100.00%\n+>Cluster 4\n+0\t1539aa, >0_0_340... *\n+>Cluster 5\n+0\t1400aa, >0_0_148... *\n+1\t1400aa, >1_0_148... at 100.00%\n+>Cluster 6\n+0\t1398aa, >1_0_392... *\n+>Cluster 7\n+0\t1330aa, >0_0_199... *\n+1\t1330aa, >1_0_199... at 100.00%\n+>Cluster 8\n+0\t1316aa, >1_0_412... *\n+>Cluster 9\n+0\t1306aa, >1_0_317... *\n+>Cluster 10\n+0\t1209aa, >0_0_178... *\n+1\t1209aa, >1_0_178... at 100.00%\n+>Cluster 11\n+0\t1194aa, >0_0_105... *\n+1\t1194aa, >1_0_105... at 100.00%\n+>Cluster 12\n+0\t1172aa, >1_0_411... *\n+>Cluster 13\n+0\t1097aa, >1_0_373... *\n+>Cluster 14\n+0\t1094aa, >1_0_372... *\n+>Cluster 15\n+0\t1085aa, >0_0_300... *\n+>Cluster 16\n+0\t967aa, >0_0_365... *\n+>Cluster 17\n+0\t965aa, >0_0_113... *\n+1\t965aa, >1_0_113... at 100.00%\n+>Cluster 18\n+0\t964aa, >1_0_421... *\n+>Cluster 19\n+0\t958aa, >0_0_316... *\n+>Cluster 20\n+0\t944aa, >0_0_117... *\n+1\t944aa, >1_0_117... at 100.00%\n+>Cluster 21\n+0\t935aa, >0_0_191... *\n+1\t935aa, >1_0_191... at 100.00%\n+>Cluster 22\n+0\t899aa, >0_0_192... *\n+1\t899aa, >1_0_192... at 100.00%\n+>Cluster 23\n+0\t882aa, >0_0_252... *\n+>Cluster 24\n+0\t877aa, >1_0_323... *\n+>Cluster 25\n+0\t855aa, >1_0_355... *\n+>Cluster 26\n+0\t848aa, >0_0_298... *\n+>Cluster 27\n+0\t837aa, >0_0_193... *\n+1\t837aa, >1_0_193... at 100.00%\n+>Cluster 28\n+0\t836aa, >0_0_165... *\n+1\t836aa, >1_0_165... at 100.00%\n+>Cluster 29\n+0\t816aa, >0_0_253... *\n+>Cluster 30\n+0\t801aa, >1_0_492... *\n+>Cluster 31\n+0\t799aa, >0_0_287... *\n+>Cluster 32\n+0\t795aa, >1_0_324... *\n+>Cluster 33\n+0\t787aa, >1_0_456... *\n+>Cluster 34\n+0\t783aa, >0_0_320... *\n+>Cluster 35\n+0\t783aa, >1_0_491... *\n+>Cluster 36\n+0\t752aa, >0_0_8... *\n+1\t752aa, >1_0_8... at 100.00%\n+>Cluster 37\n+0\t750aa, >0_0_325... *\n+>Cluster 38\n+0\t748aa, >0_0_108... *\n+1\t748aa, >1_0_108... at 100.00%\n+>Cluster 39\n+0\t731aa, >0_0_183... *\n+1\t731aa, >1_0_183... at 100.00%\n+>Cluster 40\n+0\t728aa, >0_0_350... *\n+>Cluster 41\n+0\t719aa, >1_0_528... *\n+>Cluster 42\n+0\t714aa, >0_0_26... *\n+1\t714aa, >1_0_26... at 100.00%\n+>Cluster 43\n+0\t701aa, >1_0_429... *\n+>Cluster 44\n+0\t693aa, >0_0_427... *\n+>Cluster 45\n+0\t691aa, >0_0_94... *\n+1\t691aa, >1_0_94... at 100.00%\n+>Cluster 46\n+0\t690aa, >0_0_323... *\n+>Cluster 47\n+0\t685aa, >0_0_16... *\n+1\t685aa, >1_0_16... at 100.00%\n+>Cluster 48\n+0\t676aa, >0_0_373... *\n+>Cluster 49\n+0\t676aa, >1_0_307... *\n+>Cluster 50\n+0\t663aa, >0_0_109... *\n+1\t663aa, >1_0_109... at 100.00%\n+>Cluster 51\n+0\t646aa, >0_0_161... *\n+1\t646aa, >1_0_161... at 100.00%\n+>Cluster 52\n+0\t645aa, >1_0_501... *\n+>Cluster 53\n+0\t640aa, >0_0_7... *\n+1\t640aa, >1_0_7... at 100.00%\n+>Cluster 54\n+0\t640aa, >0_0_256... *\n+>Cluster 55\n+0\t637aa, >1_0_414... *\n+>Cluster 56\n+0\t631aa, >0_0_197... *\n+1\t631aa, >1_0_197... at 100.00%\n+>Cluster 57\n+0\t629aa, >0_0_409... *\n+>Cluster 58\n+0\t625aa, >0_0_264... *\n+>Cluster 59\n+0\t623aa, >1_0_469... *\n+>Cluster 60\n+0\t620aa, >0_0_226... *\n+1\t620aa, >1_0_226... at 100.00%\n+>Cluster 61\n+0\t615aa, >0_0_103... *\n+1\t615aa, >1_0_103... at 100.00%\n+>Cluster 62\n+0\t611aa, >0_0_157... *\n+1\t611aa, >1_0_157... at 100.00%\n+>Cluster 63\n+0\t606aa, >0_0_122... *\n+1\t606aa, >1_0_122... at 100.00%\n+>Cluster 64\n+0\t601aa, >0_0_32... *\n+1\t601aa, >1_0_32... at 100.00%\n+>Cluster 65\n+0\t594aa, >1_0_269... *\n+>Cluster 66\n+0\t591aa, >0_0_212... *\n+1\t591aa, >1_0_212... at 100.00%\n+>Cluster 67\n+0\t588aa, >0_0_57... *\n+1\t588aa, >1_0_57... at 100.00%\n+>Cluster 68\n+0\t584aa, >1_0_500... *\n+>Cluster 69\n+0\t582aa, >0_0_24... *\n+1\t582aa, >1_0_24... at 100.00%\n+>Cluster 70\n+0\t581aa, >0_0_319... *\n+>Cluster 71\n+0\t576aa, >0_0_137... *\n+1\t576aa, >1_0_137... at 100.00%\n+>Cluster 72\n+0\t575aa, >0_0_98... *\n+1\t575aa, >1_0_98... at 100.00%\n+>Cluster 73\n+0\t575aa, >1_0_371... *\n+>Cluster 74\n+0\t568aa, >0_0_143... *\n+1\t568aa, >1_0_143... at 100.00%\n+>Cluster 75\n+0\t566aa, >1_0_532... *\n+>Cluster 76\n+0\t565aa, >0_0_432... *\n+>Cluster 77\n+0\t560aa, >0'..b'er 643\n+0\t101aa, >1_0_257... *\n+>Cluster 644\n+0\t101aa, >1_0_445... *\n+>Cluster 645\n+0\t101aa, >1_0_541... *\n+>Cluster 646\n+0\t100aa, >0_0_101... *\n+1\t100aa, >1_0_101... at 100.00%\n+>Cluster 647\n+0\t100aa, >0_0_214... *\n+1\t100aa, >1_0_214... at 100.00%\n+>Cluster 648\n+0\t100aa, >1_0_280... *\n+>Cluster 649\n+0\t100aa, >1_0_448... *\n+>Cluster 650\n+0\t99aa, >0_0_435... *\n+>Cluster 651\n+0\t97aa, >0_0_163... *\n+1\t97aa, >1_0_163... at 100.00%\n+>Cluster 652\n+0\t97aa, >0_0_202... *\n+1\t97aa, >1_0_202... at 100.00%\n+>Cluster 653\n+0\t97aa, >0_0_379... *\n+>Cluster 654\n+0\t96aa, >0_0_99... *\n+1\t96aa, >1_0_99... at 100.00%\n+>Cluster 655\n+0\t96aa, >0_0_203... *\n+1\t96aa, >1_0_203... at 100.00%\n+>Cluster 656\n+0\t95aa, >0_0_56... *\n+1\t95aa, >1_0_56... at 100.00%\n+>Cluster 657\n+0\t94aa, >0_0_10... *\n+1\t94aa, >1_0_10... at 100.00%\n+>Cluster 658\n+0\t94aa, >0_0_387... *\n+>Cluster 659\n+0\t93aa, >1_0_450... *\n+>Cluster 660\n+0\t92aa, >0_0_376... *\n+>Cluster 661\n+0\t92aa, >0_0_429... *\n+>Cluster 662\n+0\t92aa, >1_0_281... *\n+>Cluster 663\n+0\t91aa, >0_0_339... *\n+>Cluster 664\n+0\t90aa, >1_0_408... *\n+>Cluster 665\n+0\t89aa, >1_0_496... *\n+>Cluster 666\n+0\t88aa, >1_0_306... *\n+>Cluster 667\n+0\t87aa, >0_0_393... *\n+>Cluster 668\n+0\t86aa, >0_0_194... *\n+1\t86aa, >1_0_194... at 100.00%\n+>Cluster 669\n+0\t86aa, >1_0_368... *\n+>Cluster 670\n+0\t85aa, >0_0_180... *\n+1\t85aa, >1_0_180... at 100.00%\n+>Cluster 671\n+0\t85aa, >1_0_336... *\n+>Cluster 672\n+0\t85aa, >1_0_493... *\n+>Cluster 673\n+0\t84aa, >1_0_330... *\n+>Cluster 674\n+0\t84aa, >1_0_365... *\n+>Cluster 675\n+0\t84aa, >1_0_406... *\n+>Cluster 676\n+0\t83aa, >1_0_400... *\n+>Cluster 677\n+0\t83aa, >1_0_404... *\n+>Cluster 678\n+0\t82aa, >0_0_5... *\n+1\t82aa, >1_0_5... at 100.00%\n+>Cluster 679\n+0\t82aa, >1_0_434... *\n+>Cluster 680\n+0\t81aa, >1_0_349... *\n+>Cluster 681\n+0\t80aa, >0_0_13... *\n+1\t80aa, >1_0_13... at 100.00%\n+>Cluster 682\n+0\t79aa, >1_0_357... *\n+>Cluster 683\n+0\t79aa, >1_0_535... *\n+>Cluster 684\n+0\t78aa, >0_0_419... *\n+>Cluster 685\n+0\t77aa, >0_0_152... *\n+1\t77aa, >1_0_152... at 100.00%\n+>Cluster 686\n+0\t77aa, >1_0_403... *\n+>Cluster 687\n+0\t77aa, >1_0_454... *\n+>Cluster 688\n+0\t76aa, >0_0_370... *\n+>Cluster 689\n+0\t76aa, >1_0_410... *\n+>Cluster 690\n+0\t75aa, >0_0_213... *\n+1\t75aa, >1_0_213... at 100.00%\n+>Cluster 691\n+0\t75aa, >1_0_358... *\n+>Cluster 692\n+0\t74aa, >0_0_59... *\n+1\t74aa, >1_0_59... at 100.00%\n+>Cluster 693\n+0\t74aa, >0_0_239... *\n+1\t74aa, >1_0_239... at 100.00%\n+>Cluster 694\n+0\t74aa, >0_0_292... *\n+>Cluster 695\n+0\t74aa, >1_0_340... *\n+>Cluster 696\n+0\t73aa, >0_0_215... *\n+1\t73aa, >1_0_215... at 100.00%\n+>Cluster 697\n+0\t73aa, >1_0_353... *\n+>Cluster 698\n+0\t72aa, >1_0_287... *\n+>Cluster 699\n+0\t71aa, >0_0_187... *\n+1\t71aa, >1_0_187... at 100.00%\n+>Cluster 700\n+0\t71aa, >1_0_320... *\n+>Cluster 701\n+0\t70aa, >1_0_377... *\n+>Cluster 702\n+0\t68aa, >0_0_331... *\n+>Cluster 703\n+0\t68aa, >1_0_510... *\n+>Cluster 704\n+0\t66aa, >0_0_293... *\n+>Cluster 705\n+0\t65aa, >1_0_351... *\n+>Cluster 706\n+0\t65aa, >1_0_467... *\n+>Cluster 707\n+0\t64aa, >0_0_141... *\n+1\t64aa, >1_0_141... at 100.00%\n+>Cluster 708\n+0\t63aa, >0_0_306... *\n+>Cluster 709\n+0\t62aa, >0_0_21... *\n+1\t62aa, >1_0_21... at 100.00%\n+>Cluster 710\n+0\t61aa, >1_0_462... *\n+>Cluster 711\n+0\t60aa, >0_0_28... *\n+1\t60aa, >1_0_28... at 100.00%\n+>Cluster 712\n+0\t57aa, >0_0_149... *\n+1\t57aa, >1_0_149... at 100.00%\n+>Cluster 713\n+0\t57aa, >1_0_338... *\n+>Cluster 714\n+0\t56aa, >1_0_502... *\n+>Cluster 715\n+0\t55aa, >1_0_311... *\n+>Cluster 716\n+0\t55aa, >1_0_378... *\n+>Cluster 717\n+0\t53aa, >1_0_267... *\n+>Cluster 718\n+0\t53aa, >1_0_529... *\n+>Cluster 719\n+0\t51aa, >1_0_401... *\n+>Cluster 720\n+0\t48aa, >0_0_95... *\n+1\t48aa, >1_0_95... at 100.00%\n+>Cluster 721\n+0\t48aa, >1_0_490... *\n+>Cluster 722\n+0\t45aa, >1_0_495... *\n+>Cluster 723\n+0\t41aa, >0_0_65... *\n+1\t41aa, >1_0_65... at 100.00%\n+>Cluster 724\n+0\t40aa, >1_0_309... *\n+>Cluster 725\n+0\t39aa, >0_0_104... *\n+1\t39aa, >1_0_104... at 100.00%\n+>Cluster 726\n+0\t38aa, >1_0_254... *\n+>Cluster 727\n+0\t37aa, >1_0_413... *\n+>Cluster 728\n+0\t33aa, >0_0_420... *\n+>Cluster 729\n+0\t29aa, >1_0_437... *\n' |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/final_graph.gml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/final_graph.gml Tue Aug 27 05:51:12 2024 +0000 |
| [ |
| b'@@ -0,0 +1,8530 @@\n+graph [\n+ isolateNames "10_small"\n+ isolateNames "11_small"\n+ node [\n+ id 0\n+ label "625"\n+ size 2\n+ centroid "0_0_0"\n+ maxLenId 0\n+ members 0\n+ members 1\n+ seqIDs "0_0_0"\n+ seqIDs "1_0_0"\n+ hasEnd 1\n+ protein "MCHFSFTVISGALFVSARRYDSNMLANSREELVEVFDALDADLDRLDEVSFEVLSTPERLRSLERLECLARRLPAAQHTLINQLDTQASEEELGGTLCCALANRLRITKPEAGRRSAEAKP"\n+ dna "TTGTGTCACTTCAGTTTCACGGTTATCAGCGGGGCGCTCTTTGTCAGTGCCCGACGTTATGATTCGAACATGTTAGCGAATAGCCGGGAGGAGCTTGTCGAGGTCTTCGACGCGCTGGATGCCGACCTGGACCGCTTGGACGAGGTGTCCTTTGAGGTGCTGAGCACCCCGGAACGGCTGCGGTCTCTGGAACGTCTGGAATGCTTGGCGCGCCGGCTACCGGCGGCCCAGCACACGTTGATCAACCAACTCGACACCCAAGCCAGCGAGGAAGAACTGGGCGGCACGCTGTGCTGCGCGCTGGCCAACCGGCTGCGCATCACCAAGCCCGAAGCCGGCCGACGCAGCGCCGAAGCCAAGCCTTAG"\n+ annotation ""\n+ description "putative protein"\n+ lengths 366\n+ lengths 366\n+ longCentroidID 366\n+ longCentroidID "0_0_0"\n+ paralog 0\n+ mergedDNA 0\n+ genomeIDs "0;1"\n+ geneIDs "0_0_0;1_0_0"\n+ degrees 1\n+ name "group_50"\n+ ]\n+ node [\n+ id 1\n+ label "145"\n+ size 2\n+ centroid "0_0_1"\n+ maxLenId 0\n+ members 0\n+ members 1\n+ seqIDs "0_0_1"\n+ seqIDs "1_0_1"\n+ hasEnd 0\n+ protein "MAIPPEVHSGLLSAGCGPGSLLVAAQQWQELSDQYALACAELGQLLGEVQASSWQGTAATQYVAAHGPYLAWLEQTAINSAVTAAQHVAAAAAYCSALAAMPTPAELAANHAIHGVLIATNFFGINTVPIALNEADYVRMWLQAADTMAAYQAVADAATVAVPSTQPAPPIRAPGGDAADTRLDVLSSIGQLIRDILDFIANPYKYFLEFFEQFGFSPAVTVVLALVALQLYDFLWYPYYASYGLLLLPFFTPTLSALTALSALIHLLNLPPAGLLPIAAALGPGDQWGANLAVAVTPATAAVPGGSPPTSNPAPAAPSSNSVGSASAAPGISYAVPGLAPPGVSSGPKAGTKSPDTAADTLATAGAARPGLARAHRRKRSESGVGIRGYRDEFLDATATVDAATDVPAPANAAGSQGAGTLGFAGTAPTTSGAAAGMVQLSSHSTSTTVPLLPTTWTTDAEQ"\n+ dna "ATGGCTATACCACCGGAGGTGCACTCGGGCCTGTTGAGCGCCGGGTGCGGTCCGGGATCATTGCTTGTTGCCGCGCAGCAGTGGCAAGAACTTAGTGATCAGTACGCACTCGCATGCGCCGAGTTGGGCCAATTGTTGGGCGAGGTTCAGGCCAGCAGCTGGCAGGGAACCGCCGCCACCCAGTACGTGGCTGCCCATGGCCCCTATCTGGCCTGGCTTGAGCAAACCGCGATCAACAGCGCCGTCACCGCCGCACAGCACGTAGCGGCTGCCGCTGCCTACTGCAGCGCCCTGGCCGCGATGCCCACCCCAGCAGAGCTGGCCGCCAACCACGCCATTCATGGCGTTCTGATCGCCACCAACTTCTTCGGGATCAACACCGTTCCGATCGCGCTCAACGAAGCCGATTATGTCCGCATGTGGCTGCAAGCCGCCGACACCATGGCCGCCTACCAGGCCGTCGCCGATGCGGCCACGGTGGCCGTACCGTCCACCCAACCGGCGCCACCGATCCGCGCGCCCGGCGGCGATGCCGCAGATACCCGGCTAGACGTATTGAGTTCAATTGGTCAGCTCATCCGGGATATCTTGGATTTCATTGCCAACCCGTACAAGTATTTTCTGGAGTTTTTCGAGCAATTCGGCTTCAGCCCGGCCGTAACGGTCGTCCTTGCCCTTGTTGCCCTGCAGCTGTACGACTTTCTTTGGTATCCCTATTACGCCTCGTACGGCCTGCTCCTGCTTCCGTTCTTCACTCCCACCTTGAGCGCGTTGACCGCCCTAAGCGCGCTGATCCATTTGCTGAACCTGCCCCCGGCTGGACTGCTTCCTATCGCCGCAGCGCTCGGTCCCGGCGACCAATGGGGCGCAAACTTGGCTGTGGCTGTCACGCCGGCCACGGCGGCCGTGCCCGGCGGAAGCCCGCCCACCAGCAACCCCGCGCCCGCCGCTCCCAGCTCGAACTCGGTTGGCAGCGCTTCGGCTGCACCCGGCATCAGCTATGCCGTGCCCGGCCTGGCGCCACCCGGGGTTAGCTCTGGCCCTAAAGCCGGCACCAAATCACCTGACACCGCCGCCGACACCCTTGCAACCGCGGGCGCAGCACGACCGGGCCTCGCCCGAGCCCACCGAAGAAAGCGCAGCGAAAGCGGCGTCGGGATACGCGGTTACCGCGACGAATTTTTGGACGCGACCGCCACGGTGGACGCCGCTACGGATGTGCCCGCTCCCGCCAACGCGGCTGGCAGTCAAGGTGCCGGCACTCTCGGCTTTGCCGGTACCGCACCGACAACCAGCGGCGCCGCGGCCGGAATGGTTCAACTGTCGTCGCACAGCACAAGCACTACAGTCCCGTTGCTGCCCACTACCTGGACAACCGACGCCGAACAATGA"\n+ annotation ""\n+ description "hypothetical protein"\n+ lengths 1392\n+ lengths 1392\n+ longCentroidID 1392\n+ longCentroidID "0_0_1"\n+ paralog 0\n+ mergedDNA 0\n+ genomeIDs "0;1"\n+ geneIDs "0_0_1;1_0_1"\n+ degrees 2\n+ name "group_61"\n+ ]\n+ node [\n+ id 2\n+ label "325"\n+ size 2\n+ centroid "0_0_2"\n+ maxLenId 0\n+ members 0\n+ members 1\n+ seqIDs "0_0_2"\n+ seqIDs "1_0_2"\n+ hasEnd 0\n+ protein "MTLKVKGEGLGAQVTGVDPKNLDDITTDEIRDIVYTNKLVVLKDVHPSPREFIKLGRIIGQIVPYYEPMYHHEDHPEIFVSSTEEGQGVPKTGAFWHIDYMFMPEPFAFSMVLPLAVPGHDRGTYFIDLARVWQSLPAAKRDPARGTVSTHDPRRHIKIRPSDVYRPIGEVWDEINRTTPPIKWPTVIRHPKTGQEILYICATGTTKIEDKDGNPVDPEVLQELMAATGQLDPEYQSPFIHTQHYQVGDIILWDNRVLMHRAKHGSAAGTLTTYRLTMLDGLKTPGYAA"\n+ dna "ATGACGCTTAAGGTCAAAGGCGAGGGACTCGGTGCGCAGGTCACAGGGGTCGATCCCAAGAATCTGGACGATATAACCACCGACGAGATCCGGGATATCGTTTACACGAACAAGCTCGTTGTGCTAAAAGACGTCCATCCGTCTCCGCGGGAGTTCATCA'..b'members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 212\n+ target 213\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 213\n+ target 214\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 214\n+ target 215\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 215\n+ target 216\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 216\n+ target 217\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 217\n+ target 218\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 218\n+ target 219\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 219\n+ target 220\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 220\n+ target 221\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 221\n+ target 222\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 222\n+ target 223\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 223\n+ target 224\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 224\n+ target 225\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 225\n+ target 226\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 226\n+ target 227\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 227\n+ target 228\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 228\n+ target 229\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 229\n+ target 230\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 230\n+ target 231\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 231\n+ target 232\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 232\n+ target 233\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 233\n+ target 234\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 234\n+ target 235\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 235\n+ target 236\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 236\n+ target 237\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 237\n+ target 238\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 238\n+ target 239\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 239\n+ target 240\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 240\n+ target 241\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 241\n+ target 242\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 242\n+ target 243\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 243\n+ target 244\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 244\n+ target 245\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 245\n+ target 246\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 246\n+ target 247\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+ edge [\n+ source 247\n+ target 248\n+ size 2\n+ members 0\n+ members 1\n+ genomeIDs "0;1"\n+ ]\n+]\n' |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/gene_data.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_data.csv Tue Aug 27 05:51:12 2024 +0000 |
| b |
| b'@@ -0,0 +1,980 @@\n+gff_file,scaffold_name,clustering_id,annotation_id,prot_sequence,dna_sequence,gene_name,description\n+10_small,.10665_7_10.1,0_0_0,KPLBOJCC_00001,MCHFSFTVISGALFVSARRYDSNMLANSREELVEVFDALDADLDRLDEVSFEVLSTPERLRSLERLECLARRLPAAQHTLINQLDTQASEEELGGTLCCALANRLRITKPEAGRRSAEAKP,TTGTGTCACTTCAGTTTCACGGTTATCAGCGGGGCGCTCTTTGTCAGTGCCCGACGTTATGATTCGAACATGTTAGCGAATAGCCGGGAGGAGCTTGTCGAGGTCTTCGACGCGCTGGATGCCGACCTGGACCGCTTGGACGAGGTGTCCTTTGAGGTGCTGAGCACCCCGGAACGGCTGCGGTCTCTGGAACGTCTGGAATGCTTGGCGCGCCGGCTACCGGCGGCCCAGCACACGTTGATCAACCAACTCGACACCCAAGCCAGCGAGGAAGAACTGGGCGGCACGCTGTGCTGCGCGCTGGCCAACCGGCTGCGCATCACCAAGCCCGAAGCCGGCCGACGCAGCGCCGAAGCCAAGCCTTAG,,putative protein\n+10_small,.10665_7_10.1,0_0_1,KPLBOJCC_00002,MAIPPEVHSGLLSAGCGPGSLLVAAQQWQELSDQYALACAELGQLLGEVQASSWQGTAATQYVAAHGPYLAWLEQTAINSAVTAAQHVAAAAAYCSALAAMPTPAELAANHAIHGVLIATNFFGINTVPIALNEADYVRMWLQAADTMAAYQAVADAATVAVPSTQPAPPIRAPGGDAADTRLDVLSSIGQLIRDILDFIANPYKYFLEFFEQFGFSPAVTVVLALVALQLYDFLWYPYYASYGLLLLPFFTPTLSALTALSALIHLLNLPPAGLLPIAAALGPGDQWGANLAVAVTPATAAVPGGSPPTSNPAPAAPSSNSVGSASAAPGISYAVPGLAPPGVSSGPKAGTKSPDTAADTLATAGAARPGLARAHRRKRSESGVGIRGYRDEFLDATATVDAATDVPAPANAAGSQGAGTLGFAGTAPTTSGAAAGMVQLSSHSTSTTVPLLPTTWTTDAEQ,ATGGCTATACCACCGGAGGTGCACTCGGGCCTGTTGAGCGCCGGGTGCGGTCCGGGATCATTGCTTGTTGCCGCGCAGCAGTGGCAAGAACTTAGTGATCAGTACGCACTCGCATGCGCCGAGTTGGGCCAATTGTTGGGCGAGGTTCAGGCCAGCAGCTGGCAGGGAACCGCCGCCACCCAGTACGTGGCTGCCCATGGCCCCTATCTGGCCTGGCTTGAGCAAACCGCGATCAACAGCGCCGTCACCGCCGCACAGCACGTAGCGGCTGCCGCTGCCTACTGCAGCGCCCTGGCCGCGATGCCCACCCCAGCAGAGCTGGCCGCCAACCACGCCATTCATGGCGTTCTGATCGCCACCAACTTCTTCGGGATCAACACCGTTCCGATCGCGCTCAACGAAGCCGATTATGTCCGCATGTGGCTGCAAGCCGCCGACACCATGGCCGCCTACCAGGCCGTCGCCGATGCGGCCACGGTGGCCGTACCGTCCACCCAACCGGCGCCACCGATCCGCGCGCCCGGCGGCGATGCCGCAGATACCCGGCTAGACGTATTGAGTTCAATTGGTCAGCTCATCCGGGATATCTTGGATTTCATTGCCAACCCGTACAAGTATTTTCTGGAGTTTTTCGAGCAATTCGGCTTCAGCCCGGCCGTAACGGTCGTCCTTGCCCTTGTTGCCCTGCAGCTGTACGACTTTCTTTGGTATCCCTATTACGCCTCGTACGGCCTGCTCCTGCTTCCGTTCTTCACTCCCACCTTGAGCGCGTTGACCGCCCTAAGCGCGCTGATCCATTTGCTGAACCTGCCCCCGGCTGGACTGCTTCCTATCGCCGCAGCGCTCGGTCCCGGCGACCAATGGGGCGCAAACTTGGCTGTGGCTGTCACGCCGGCCACGGCGGCCGTGCCCGGCGGAAGCCCGCCCACCAGCAACCCCGCGCCCGCCGCTCCCAGCTCGAACTCGGTTGGCAGCGCTTCGGCTGCACCCGGCATCAGCTATGCCGTGCCCGGCCTGGCGCCACCCGGGGTTAGCTCTGGCCCTAAAGCCGGCACCAAATCACCTGACACCGCCGCCGACACCCTTGCAACCGCGGGCGCAGCACGACCGGGCCTCGCCCGAGCCCACCGAAGAAAGCGCAGCGAAAGCGGCGTCGGGATACGCGGTTACCGCGACGAATTTTTGGACGCGACCGCCACGGTGGACGCCGCTACGGATGTGCCCGCTCCCGCCAACGCGGCTGGCAGTCAAGGTGCCGGCACTCTCGGCTTTGCCGGTACCGCACCGACAACCAGCGGCGCCGCGGCCGGAATGGTTCAACTGTCGTCGCACAGCACAAGCACTACAGTCCCGTTGCTGCCCACTACCTGGACAACCGACGCCGAACAATGA,,hypothetical protein\n+10_small,.10665_7_10.1,0_0_2,KPLBOJCC_00003,MTLKVKGEGLGAQVTGVDPKNLDDITTDEIRDIVYTNKLVVLKDVHPSPREFIKLGRIIGQIVPYYEPMYHHEDHPEIFVSSTEEGQGVPKTGAFWHIDYMFMPEPFAFSMVLPLAVPGHDRGTYFIDLARVWQSLPAAKRDPARGTVSTHDPRRHIKIRPSDVYRPIGEVWDEINRTTPPIKWPTVIRHPKTGQEILYICATGTTKIEDKDGNPVDPEVLQELMAATGQLDPEYQSPFIHTQHYQVGDIILWDNRVLMHRAKHGSAAGTLTTYRLTMLDGLKTPGYAA,ATGACGCTTAAGGTCAAAGGCGAGGGACTCGGTGCGCAGGTCACAGGGGTCGATCCCAAGAATCTGGACGATATAACCACCGACGAGATCCGGGATATCGTTTACACGAACAAGCTCGTTGTGCTAAAAGACGTCCATCCGTCTCCGCGGGAGTTCATCAAACTCGGCAGGATAATTGGACAAATCGTTCCGTATTACGAACCCATGTACCATCACGAAGACCACCCGGAGATCTTTGTCTCCTCCACTGAGGAAGGTCAGGGGGTCCCAAAAACCGGCGCGTTCTGGCATATCGACTATATGTTTATGCCGGAACCTTTCGCGTTTTCCATGGTGCTGCCGCTGGCGGTGCCTGGACACGACCGCGGGACCTATTTCATCGATCTCGCCAGGGTCTGGCAGTCGCTGCCCGCCGCCAAGCGAGACCCGGCCCGCGGAACCGTCAGCACCCACGACCCTCGACGCCACATCAAGATCCGACCCAGCGACGTCTACCGGCCCATCGGAGAGGTATGGGACGAGATCAACCGGACCACGCCCCCAATAAAGTGGCCTACGGTCATCCGGCACCCAAAGACCGGCCAAGAGATCCTCTACATCTGCGCGACGGGCACCACCAAGATCGAGGACAAGGACGGCAATCCGGTTGATCCGGAGGTGCTGCAAGAACTCATGGCCGCGACCGGACAGCTCGATCCTGAGTACCAGTCGCCGTTCATACATACTCAGCACTACCAGGTTGGCGACATCATCTTGTGGGACAACCGGGTTCTCATGCACCGAGCGAAGCACGGCAGCGCCGCGGGCACTCTGACGACCTACCGCCTGACCATGCTTGATGGCCTCAAGACGCCGGGATACGCGGCATGA,,Putative dioxygenase\n+10_small,.10665_7_10.1,0_0_3,KPLBOJCC_00004,MSHTDLTPCTRVLASSGTVPIAEELLARVLEPYSCKGCRYLIDAQYSATEDSVLAYGNFTIGESAYIRSTGHFNAVELILCFNQLAYSAFAPAVLNEEIRVLRGWSIDDYCQHQLSSMLIRKASSRFRKPL'..b'GCTGCTGGCACCCACCCAGTCCGGCGAGGAAGAAGTCCGGATCCGCGAAGAATTCGCGTCCATCCCCGAGCCGGGGCTCATCGTCGGGACACCCGACAGGTGTGTCGAGCGCATTCGTGAATACCAGGACCGCGGTGTCGGCCATTTTCTCTTCACGATTCCACACGTCGTGAAGTCCGATTATCTGCACATCATCGGCAGTGACATCATTCCGCGGGTCAAAACTGAGGTCACGATTCCATGA,,putative protein\n+11_small,.10665_7_11.1,1_0_540,NCFNLLIC_00547,MTSVKLDLDAADLRISRGSVPASTQLAEALKAQIIQQRLPRGGRLPSERELIDRSGLSRVTVRAAVGMLQRQGWLVRRQGLGTFVADPVEQELSCGVRIITEVLLSCGVTPQVDVLSHQTGPAPQRISETLGLVEVLCIRRRIRTGDQPLALVTAYLPPGVGPAVEPLLSGSADTETTYAMWERRLGVRIAQATHEIHAAGASPDVADALGLAVGSPVLVVDRTSYTNDGKPLEVVVFHHRPERYQFSVTLPRTLPGSGAGIIEKRDFA,ATGACATCTGTCAAGCTGGACCTGGACGCTGCCGATCTGCGGATATCGCGTGGCAGCGTGCCGGCGAGTACCCAGCTTGCCGAGGCGCTAAAGGCCCAGATCATCCAGCAGCGGCTGCCGCGCGGCGGGCGCTTGCCCAGCGAACGAGAATTGATCGACCGTTCCGGTTTGAGCCGCGTGACCGTGCGCGCGGCGGTCGGCATGCTGCAACGTCAGGGATGGCTAGTGCGCCGGCAAGGCTTGGGTACCTTCGTCGCCGATCCGGTGGAACAGGAGCTCAGTTGCGGCGTGCGCATCATCACAGAGGTGTTGTTGAGCTGTGGTGTTACCCCGCAGGTCGACGTGCTGTCACACCAGACCGGACCGGCGCCGCAACGGATTTCCGAGACGCTGGGTTTGGTTGAGGTCCTCTGTATTCGCCGGCGCATCCGCACTGGCGATCAACCCTTGGCCCTGGTCACGGCCTATCTTCCGCCCGGCGTGGGCCCAGCCGTCGAGCCGTTGCTATCGGGCAGCGCGGACACCGAAACCACATATGCGATGTGGGAGCGGCGACTGGGTGTACGCATTGCACAGGCTACCCACGAAATCCATGCCGCCGGGGCCTCCCCCGACGTAGCCGACGCGTTGGGTCTGGCGGTGGGTTCGCCGGTACTGGTCGTCGACCGCACCAGCTACACCAATGACGGCAAGCCCCTTGAAGTGGTCGTGTTCCACCATCGCCCCGAGCGGTACCAGTTCTCCGTCACGTTACCCCGAACGTTGCCCGGATCAGGTGCCGGAATTATCGAGAAACGAGATTTCGCATGA,yvoA,HTH-type transcriptional repressor YvoA\n+11_small,.10665_7_11.1,1_0_541,NCFNLLIC_00548,MTSPVAVIARFMPRPDARSALRALLDAMITPTRAEDGCRSYDLYESADGGELVLFERYRSRIALDEHRGSPHYLNYRAQVGELLTRPVAVTVLAPLDEASA,ATGACGTCACCCGTCGCGGTCATCGCCCGGTTCATGCCACGGCCTGACGCTAGGTCGGCCCTGCGCGCTCTCTTGGACGCAATGATTACCCCGACACGGGCCGAGGACGGATGCCGTAGCTACGACCTCTACGAGAGCGCCGACGGCGGCGAGCTGGTGCTTTTCGAACGGTACCGCAGCCGCATCGCGCTCGACGAGCACCGCGGTTCGCCGCACTATCTGAACTACCGGGCACAGGTCGGTGAATTGCTGACCCGGCCCGTCGCGGTGACTGTGCTCGCGCCGCTCGACGAGGCTTCTGCTTAG,,Putative monooxygenase\n+11_small,.10665_7_11.1,1_0_542,NCFNLLIC_00549,MTAAQQDQAPMATPGCREGETYDVVVLGAGPVGQNVADRARAGGLRVAVVERELVGGECSYWACVPSKALLRPVIAISDARRVDGAREAVDGSINTAGVFGRRNRYVAHWDDTGQADWVSGIGATLIRGDGRLDGPRRVVVTKSSGESVALTARHAVVICTGSRPALPDLPGITEARPWTNRQATDNSTVPDRLAIVGAGGVGVEMATAWQGLGASVTLLARGSGLLPRMEPFVGELIGRGLADAGVDVRVGVSVRALGRPNPTGPVVLELDDGTELRVDEVLFATGRAPRTDDIGLETIGLTPGSWLDVDDTCRVRAVDDGWLYAAGDVNHRALLTHQGKYQARIAGTAIGARAAGRPLDTTSWGMHATTADHHAVPQAFFTDPEAAAVGLTADQAAQAGHRIKAIDVEIGDVVMGAKLFADGYTGRARMVVDVDRGHLLGVTMVGPGAAELLHSATVAVAGQVPIDRLWHAVPCFPTISELWLRLLESYRDSFYLLV,ATGACCGCGGCCCAACAGGACCAGGCGCCAATGGCAACACCCGGCTGCCGTGAGGGTGAAACGTATGACGTCGTCGTGCTCGGCGCGGGACCCGTTGGACAGAACGTCGCCGATCGTGCCCGCGCGGGGGGCCTGCGTGTCGCGGTGGTGGAGCGCGAACTCGTCGGGGGTGAATGCTCCTATTGGGCCTGTGTGCCCAGCAAAGCCTTGCTGCGTCCGGTCATCGCGATCTCTGACGCCCGACGGGTCGACGGCGCGCGCGAAGCAGTCGACGGCTCGATCAACACAGCCGGCGTCTTTGGCCGCCGCAACCGCTATGTGGCCCACTGGGACGACACCGGCCAGGCCGACTGGGTGAGTGGAATCGGCGCGACGCTGATACGCGGTGACGGGCGATTGGACGGTCCGCGCCGCGTCGTCGTCACCAAGTCGAGCGGCGAAAGCGTGGCGCTGACCGCCCGGCATGCCGTTGTCATCTGCACCGGAAGCCGGCCAGCACTCCCCGACCTTCCTGGCATCACCGAAGCCCGGCCATGGACCAATCGCCAAGCCACCGACAACAGTACGGTCCCCGACCGGCTTGCGATCGTCGGCGCCGGCGGCGTCGGTGTGGAGATGGCGACCGCCTGGCAGGGACTGGGCGCCTCGGTGACCCTGCTGGCTCGGGGATCTGGCCTGCTGCCCCGAATGGAACCGTTTGTGGGGGAACTCATCGGTCGCGGACTGGCCGACGCCGGCGTTGACGTGCGCGTGGGAGTATCGGTACGCGCGCTGGGCCGCCCCAACCCAACTGGCCCAGTGGTCCTCGAGCTGGACGACGGTACCGAGCTGCGGGTCGACGAGGTACTCTTCGCCACCGGCCGAGCACCGCGAACCGACGACATCGGCTTGGAGACAATAGGACTGACGCCGGGCAGCTGGCTGGACGTCGATGACACCTGCCGAGTGCGGGCTGTTGACGACGGCTGGCTCTATGCCGCCGGCGACGTCAACCATCGCGCGTTGCTGACCCACCAAGGCAAATACCAGGCGCGGATCGCCGGCACCGCGATCGGCGCCCGTGCCGCCGGACGACCGCTAGACACCACGTCGTGGGGCATGCACGCGACCACCGCCGACCATCACGCGGTGCCGCAGGCATTCTTTACCGACCCCGAAGCCGCAGCGGTCGGCCTGACAGCTGATCAGGCCGCACAGGCTGGTCACCGGATCAAAGCGATCGATGTCGAAATCGGCGATGTCGTTATGGGAGCCAAGCTCTTTGCCGACGGATACACCGGCAGGGCGCGCATGGTGGTCGACGTCGATCGGGGCCATCTGCTGGGCGTGACCATGGTTGGCCCGGGCGCCGCCGAGCTGTTGCATTCGGCCACCGTCGCCGTCGCCGGCCAGGTGCCAATCGATCGGTTGTGGCACGCCGTTCCGTGCTTCCCGACCATCAGCGAACTGTGGCTGAGACTTCTTGAATCCTACCGAGATTCGTTTTACCTGCTGGTATAG,lpdA_1,Dihydrolipoyl dehydrogenase\n' |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/gene_presence_absence.Rtab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_presence_absence.Rtab Tue Aug 27 05:51:12 2024 +0000 |
| b |
| @@ -0,0 +1,252 @@ +Gene 10_small 11_small +group_153 1 1 +dcd 1 1 +group_152 1 1 +trmB 1 1 +betI_1 1 1 +group_151 1 1 +group_150 1 1 +group_149 1 1 +group_148 1 1 +group_147 1 1 +gmhA 1 1 +group_146 1 1 +group_145 1 1 +kstR2_1 1 1 +ybgJ 1 1 +group_144 1 1 +pcm 1 1 +group_143 1 1 +group_142 1 1 +group_141 1 1 +pcp 1 1 +mshB_1 1 1 +group_140 1 1 +group_139 1 1 +group_138 1 1 +group_137 1 1 +group_136 1 1 +bluB 1 1 +group_135 1 1 +group_134 1 1 +group_133 1 1 +group_132 1 1 +ugpQ 1 1 +group_131 1 1 +group_130 1 1 +frdB_1 1 1 +group_129 1 1 +glpG 1 1 +ldtA 1 1 +group_128 1 1 +group_127 1 1 +group_126 1 1 +group_125 1 1 +group_124 1 1 +group_123 1 1 +tam 1 1 +caiD_1 1 1 +group_122 1 1 +group_121 1 1 +stf0 1 1 +group_120 1 1 +group_119 1 1 +group_118 1 1 +group_117 1 1 +group_116 1 1 +group_115 1 1 +rmlA 1 1 +group_114 1 1 +group_113 1 1 +espG3 1 1 +group_112 1 1 +ybgK 1 1 +group_111 1 1 +dnaK_1 1 1 +group_110 1 1 +group_109 1 1 +aes_1 1 1 +group_108 1 1 +group_107 1 1 +group_106 1 1 +nrdB 1 1 +oxyR 1 1 +group_105 1 1 +rmd 1 1 +group_104 1 1 +group_103 1 1 +nadR 1 1 +php 1 1 +group_102 1 1 +eccE3 1 1 +sigG 1 1 +mch 1 1 +auaH 1 1 +fbpC 1 1 +group_101 1 1 +group_100 1 1 +mcd 1 1 +fgd2 1 1 +group_99 1 1 +pntAA 1 1 +group_98 1 1 +group_97 1 1 +adhB_1 1 1 +group_96 1 1 +group_95 1 1 +group_94 1 1 +hisB_1 1 1 +gtf1 1 1 +hddA 1 1 +group_93 1 1 +group_92 1 1 +nagZ 1 1 +lprN_1 1 1 +group_91 1 1 +group_90 1 1 +group_89 1 1 +mymT 1 1 +group_88 1 1 +group_87 1 1 +group_86 1 1 +caiA_1 1 1 +group_85 1 1 +group_84 1 1 +group_83 1 1 +group_82 1 1 +group_81 1 1 +sotB 1 1 +group_80 1 1 +vapB2 1 1 +porA 1 1 +group_79 1 1 +group_78 1 1 +group_77 1 1 +group_76 1 1 +group_75 1 1 +group_74 1 1 +group_73 1 1 +fadI 1 1 +group_72 1 1 +group_71 1 1 +group_70 1 1 +group_69 1 1 +rkpK 1 1 +bbsG 1 1 +group_68 1 1 +group_67 1 1 +group_66 1 1 +group_65 1 1 +hcaB_1 1 1 +group_64 1 1 +mak 1 1 +gabD1 1 1 +group_63 1 1 +group_62 1 1 +mycP3 1 1 +esxH 1 1 +narK_2 1 1 +rpmB_1 1 1 +group_61 1 1 +group_60 1 1 +esxG 1 1 +ricR 1 1 +narK_1 1 1 +PE3_1 1 1 +group_59 1 1 +group_58 1 1 +group_57 1 1 +group_56 1 1 +eccD3 1 1 +pntB 1 1 +PE5_1 1 1 +group_55 1 1 +group_54 1 1 +geoB 1 1 +group_53 1 1 +nirD 1 1 +group_52 1 1 +group_51 1 1 +clcB 1 1 +cobQ_1 1 1 +group_50 1 1 +group_49 1 1 +group_48 1 1 +group_47 1 1 +PE3_2 1 1 +group_46 1 1 +group_45 1 1 +calB 1 1 +group_44 1 1 +PPE4_1 1 1 +group_43 1 1 +group_42 1 1 +group_41 1 1 +group_40 1 1 +PPE3 1 1 +eccB3_1 1 1 +group_39 1 1 +group_38 1 1 +sauT 1 1 +group_37 1 1 +group_36 1 1 +group_35 1 1 +PPE2 1 1 +lcfB_1 1 1 +vapC2 1 1 +group_34 1 1 +group_33 1 1 +ilvD 1 1 +group_32 1 1 +group_31 1 1 +oxc 1 1 +group_30 1 1 +group_29 1 1 +pckG 1 1 +group_28 1 1 +treS 1 1 +group_27 1 1 +group_26 1 1 +group_25 1 1 +group_24 1 1 +group_23 1 1 +group_22 1 1 +eccA3 1 1 +group_21 1 1 +sdhA_1 1 1 +group_20 1 1 +group_19 1 1 +group_18 1 1 +pepO 1 1 +group_17 1 1 +bglB 1 1 +group_16 1 1 +group_15 1 1 +group_14 1 1 +group_13 1 1 +hsaB_1 1 1 +napA 1 1 +ctpB 1 1 +baiE 1 1 +group_12 1 1 +group_11 1 1 +nasD 1 1 +group_10 1 1 +group_9 1 1 +group_8 1 1 +cobU 1 1 +group_7 1 1 +mmpL3_1 1 1 +group_6 1 1 +aac 1 1 +group_5 1 1 +group_4 1 1 +group_3 1 1 +msrA 1 1 +eccC3 1 1 +aftD 1 1 +group_2 1 1 +group_1 1 1 +ctpI_1 1 1 +dltA 1 1 +group_0 1 1 |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/gene_presence_absence.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_presence_absence.csv Tue Aug 27 05:51:12 2024 +0000 |
| [ |
| b'@@ -0,0 +1,252 @@\n+Gene,Non-unique Gene name,Annotation,10_small,11_small\n+group_153,,hypothetical protein,KPLBOJCC_00152,NCFNLLIC_00152\n+dcd,dcd,dCTP deaminase,KPLBOJCC_00237,NCFNLLIC_00237\n+group_152,,putative HTH-type transcriptional regulator,KPLBOJCC_00108,NCFNLLIC_00108\n+trmB,trmB,tRNA (guanine-N(7)-)-methyltransferase,KPLBOJCC_00120,NCFNLLIC_00120\n+betI_1,betI_1,HTH-type transcriptional regulator BetI,KPLBOJCC_00244,NCFNLLIC_00244\n+group_151,,hypothetical protein,KPLBOJCC_00042,NCFNLLIC_00042\n+group_150,,hypothetical protein,KPLBOJCC_00040,NCFNLLIC_00040\n+group_149,,hypothetical protein,KPLBOJCC_00251,NCFNLLIC_00251\n+group_148,,hypothetical protein,KPLBOJCC_00231,NCFNLLIC_00231\n+group_147,,hypothetical protein,KPLBOJCC_00186,NCFNLLIC_00186\n+gmhA,gmhA,Phosphoheptose isomerase,KPLBOJCC_00019,NCFNLLIC_00019\n+group_146,,hypothetical protein,KPLBOJCC_00245,NCFNLLIC_00245\n+group_145,,hypothetical protein,KPLBOJCC_00218,NCFNLLIC_00218\n+kstR2_1,kstR2_1,HTH-type transcriptional repressor KstR2,KPLBOJCC_00067,NCFNLLIC_00067\n+ybgJ,ybgJ,putative protein YbgJ,KPLBOJCC_00177,NCFNLLIC_00177\n+group_144,,hypothetical protein,KPLBOJCC_00224,NCFNLLIC_00224\n+pcm,pcm,Protein-L-isoaspartate O-methyltransferase,KPLBOJCC_00097,NCFNLLIC_00097\n+group_143,,hypothetical protein,KPLBOJCC_00111,NCFNLLIC_00111\n+group_142,,hypothetical protein,KPLBOJCC_00236,NCFNLLIC_00236\n+group_141,,hypothetical protein,KPLBOJCC_00229,NCFNLLIC_00229\n+pcp,pcp,Pyrrolidone-carboxylate peptidase,KPLBOJCC_00235,NCFNLLIC_00235\n+mshB_1,mshB_1,1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase,KPLBOJCC_00239,NCFNLLIC_00239\n+group_140,,hypothetical protein,KPLBOJCC_00240,NCFNLLIC_00240\n+group_139,,hypothetical protein,KPLBOJCC_00145,NCFNLLIC_00145\n+group_138,,hypothetical protein,KPLBOJCC_00112,NCFNLLIC_00112\n+group_137,,hypothetical protein,KPLBOJCC_00084,NCFNLLIC_00084\n+group_136,,hypothetical protein,KPLBOJCC_00223,NCFNLLIC_00223\n+bluB,bluB,56-dimethylbenzimidazole synthase,KPLBOJCC_00221,NCFNLLIC_00221\n+group_135,,hypothetical protein,KPLBOJCC_00189,NCFNLLIC_00189\n+group_134,,hypothetical protein,KPLBOJCC_00119,NCFNLLIC_00119\n+group_133,,Putative quercetin 23-dioxygenase,KPLBOJCC_00090,NCFNLLIC_00090\n+group_132,,hypothetical protein,KPLBOJCC_00087,NCFNLLIC_00087\n+ugpQ,ugpQ,Glycerophosphodiester phosphodiesterase cytoplasmic,KPLBOJCC_00232,NCFNLLIC_00232\n+group_131,,hypothetical protein,KPLBOJCC_00246,NCFNLLIC_00246\n+group_130,,hypothetical protein,KPLBOJCC_00172,NCFNLLIC_00172\n+frdB_1,frdB_1,Fumarate reductase iron-sulfur subunit,KPLBOJCC_00161,NCFNLLIC_00161\n+group_129,,hypothetical protein,KPLBOJCC_00093,NCFNLLIC_00093\n+glpG,glpG,Rhomboid protease GlpG,KPLBOJCC_00016,NCFNLLIC_00016\n+ldtA,ldtA,LD-transpeptidase 1,KPLBOJCC_00023,NCFNLLIC_00023\n+group_128,,putative methyltransferase,KPLBOJCC_00136,NCFNLLIC_00136\n+group_127,,LD-transpeptidase 4,KPLBOJCC_00103,NCFNLLIC_00103\n+group_126,,hypothetical protein,KPLBOJCC_00107,NCFNLLIC_00107\n+group_125,,hypothetical protein,KPLBOJCC_00234,NCFNLLIC_00234\n+group_124,,hypothetical protein,KPLBOJCC_00035,NCFNLLIC_00035\n+group_123,,hypothetical protein,KPLBOJCC_00248,NCFNLLIC_00248\n+tam,tam,putative trans-aconitate 2-methyltransferase,KPLBOJCC_00210,NCFNLLIC_00210\n+caiD_1,caiD_1,Carnitinyl-CoA dehydratase,KPLBOJCC_00134,NCFNLLIC_00134\n+group_122,,hypothetical protein,KPLBOJCC_00074,NCFNLLIC_00074\n+group_121,,hypothetical protein,KPLBOJCC_00076,NCFNLLIC_00076\n+stf0,stf0,Trehalose 2-sulfotransferase,KPLBOJCC_00211,NCFNLLIC_00211\n+group_120,,hypothetical protein,KPLBOJCC_00163,NCFNLLIC_00163\n+group_119,,hypothetical protein,KPLBOJCC_00061,NCFNLLIC_00061\n+group_118,,hypothetical protein,KPLBOJCC_00155,NCFNLLIC_00155\n+group_117,,hypothetical protein,KPLBOJCC_00051,NCFNLLIC_00051\n+group_116,,hypothetical protein,KPLBOJCC_00230,NCFNLLIC_00230\n+group_115,,Putative short-chain type dehydrogenase/reductase,KPLBOJCC_00055,NCFNLLIC_00055\n+rmlA,rmlA,Glucose-1-phosphate thymidylyltransferase,KPLBOJCC_00250,NCFNLLIC_00250\n+gro'..b"1,lcfB_1,Long-chain-fatty-acid--CoA ligase,KPLBOJCC_00183,NCFNLLIC_00183\n+vapC2,vapC2,Ribonuclease VapC2,KPLBOJCC_00217,NCFNLLIC_00217\n+group_34,,hypothetical protein,KPLBOJCC_00144,NCFNLLIC_00144\n+group_33,,hypothetical protein,KPLBOJCC_00249,NCFNLLIC_00249\n+ilvD,ilvD,Dihydroxy-acid dehydratase,KPLBOJCC_00099,NCFNLLIC_00099\n+group_32,,hypothetical protein,KPLBOJCC_00138,NCFNLLIC_00138\n+group_31,,hypothetical protein,KPLBOJCC_00213,NCFNLLIC_00213\n+oxc,oxc,Oxalyl-CoA decarboxylase,KPLBOJCC_00025,NCFNLLIC_00025\n+group_30,,Ribonuclease VapC25,KPLBOJCC_00191,NCFNLLIC_00191\n+group_29,,hypothetical protein,KPLBOJCC_00058,NCFNLLIC_00058\n+pckG,pckG,Phosphoenolpyruvate carboxykinase [GTP],KPLBOJCC_00123,NCFNLLIC_00123\n+group_28,,hypothetical protein,KPLBOJCC_00098,NCFNLLIC_00098\n+treS,treS,Trehalose synthase/amylase TreS,KPLBOJCC_00033,NCFNLLIC_00033\n+group_27,,hypothetical protein,KPLBOJCC_00028,NCFNLLIC_00028\n+group_26,,Butyryl-CoA dehydrogenase,KPLBOJCC_00158,NCFNLLIC_00158\n+group_25,,hypothetical protein,KPLBOJCC_00104,NCFNLLIC_00104\n+group_24,,Ribonuclease VapC24,KPLBOJCC_00154,NCFNLLIC_00154\n+group_23,,hypothetical protein,KPLBOJCC_00073,NCFNLLIC_00073\n+group_22,,hypothetical protein,KPLBOJCC_00242,NCFNLLIC_00242\n+eccA3,eccA3,ESX-3 secretion system protein EccA3,KPLBOJCC_00198,NCFNLLIC_00198\n+group_21,,hypothetical protein,KPLBOJCC_00171,NCFNLLIC_00171\n+sdhA_1,sdhA_1,Succinate dehydrogenase flavoprotein subunit,KPLBOJCC_00162,NCFNLLIC_00162\n+group_20,,putative protein,KPLBOJCC_00008,NCFNLLIC_00008\n+group_19,,hypothetical protein,KPLBOJCC_00072,NCFNLLIC_00072\n+group_18,,putative enoyl-CoA hydratase 1,KPLBOJCC_00037,NCFNLLIC_00037\n+pepO,pepO,Neutral endopeptidase,KPLBOJCC_00110,NCFNLLIC_00110\n+group_17,,hypothetical protein,KPLBOJCC_00017,NCFNLLIC_00017\n+bglB,bglB,Thermostable beta-glucosidase B,KPLBOJCC_00095,NCFNLLIC_00095\n+group_16,,hypothetical protein,KPLBOJCC_00165,NCFNLLIC_00165\n+group_15,,Elongation factor G-like protein,KPLBOJCC_00027,NCFNLLIC_00027\n+group_14,,hypothetical protein,KPLBOJCC_00222,NCFNLLIC_00222\n+group_13,,Acyl-CoA dehydrogenase FadE34,KPLBOJCC_00184,NCFNLLIC_00184\n+hsaB_1,hsaB_1,Flavin-dependent monooxygenase reductase subunit HsaB,KPLBOJCC_00159,NCFNLLIC_00159\n+napA,napA,Nitrate reductase,KPLBOJCC_00109,NCFNLLIC_00109\n+ctpB,ctpB,Cation-transporting P-type ATPase B,KPLBOJCC_00009,NCFNLLIC_00009\n+baiE,baiE,Bile acid 7-alpha dehydratase,KPLBOJCC_00225,NCFNLLIC_00225\n+group_12,,hypothetical protein,KPLBOJCC_00113,NCFNLLIC_00113\n+group_11,,hypothetical protein,KPLBOJCC_00045,NCFNLLIC_00045\n+nasD,nasD,Nitrite reductase [NAD(P)H],KPLBOJCC_00166,NCFNLLIC_00166\n+group_10,,hypothetical protein,KPLBOJCC_00194,NCFNLLIC_00194\n+group_9,,hypothetical protein,KPLBOJCC_00094,NCFNLLIC_00094\n+group_8,,hypothetical protein,KPLBOJCC_00193,NCFNLLIC_00193\n+cobU,cobU,Bifunctional adenosylcobalamin biosynthesis protein CobU,KPLBOJCC_00168,NCFNLLIC_00168\n+group_7,,hypothetical protein,KPLBOJCC_00192,NCFNLLIC_00192\n+mmpL3_1,mmpL3_1,Trehalose monomycolate exporter MmpL3,KPLBOJCC_00118,NCFNLLIC_00118\n+group_6,,Heme uptake protein MmpL11,KPLBOJCC_00114,NCFNLLIC_00114\n+aac,aac,Aminoglycoside 2'-N-acetyltransferase,KPLBOJCC_00175,NCFNLLIC_00175\n+group_5,,Multidrug efflux ATP-binding/permease protein,KPLBOJCC_00106,NCFNLLIC_00106\n+group_4,,hypothetical protein,KPLBOJCC_00179,NCFNLLIC_00179\n+group_3,,hypothetical protein,KPLBOJCC_00131,NCFNLLIC_00131\n+msrA,msrA,Peptide methionine sulfoxide reductase MsrA,KPLBOJCC_00044,NCFNLLIC_00044\n+eccC3,eccC3,ESX-3 secretion system protein EccC3,KPLBOJCC_00200,NCFNLLIC_00200\n+aftD,aftD,Alpha-(1->3)-arabinofuranosyltransferase,KPLBOJCC_00149,NCFNLLIC_00149\n+group_2,,putative protein,KPLBOJCC_00004,NCFNLLIC_00004\n+group_1,,hypothetical protein,KPLBOJCC_00086,NCFNLLIC_00086\n+ctpI_1,ctpI_1,putative cation-transporting ATPase I,KPLBOJCC_00013,NCFNLLIC_00013\n+dltA,dltA,D-alanine--poly(phosphoribitol) ligase subunit 1,KPLBOJCC_00007,NCFNLLIC_00007\n+group_0,,hypothetical protein,KPLBOJCC_00220,NCFNLLIC_00220\n" |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/gene_presence_absence_roary.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_presence_absence_roary.csv Tue Aug 27 05:51:12 2024 +0000 |
| [ |
| b'@@ -0,0 +1,252 @@\n+Gene,Non-unique Gene name,Annotation,No. isolates,No. sequences,Avg sequences per isolate,Genome Fragment,Order within Fragment,Accessory Fragment,Accessory Order with Fragment,QC,Min group size nuc,Max group size nuc,Avg group size nuc,10_small,11_small\n+group_153,,hypothetical protein,2,2,1.0,1,251,,,,567,567,567.0,KPLBOJCC_00152,NCFNLLIC_00152\n+dcd,dcd,dCTP deaminase,2,2,1.0,1,250,,,,573,573,573.0,KPLBOJCC_00237,NCFNLLIC_00237\n+group_152,,putative HTH-type transcriptional regulator,2,2,1.0,1,249,,,,585,585,585.0,KPLBOJCC_00108,NCFNLLIC_00108\n+trmB,trmB,tRNA (guanine-N(7)-)-methyltransferase,2,2,1.0,1,248,,,,594,594,594.0,KPLBOJCC_00120,NCFNLLIC_00120\n+betI_1,betI_1,HTH-type transcriptional regulator BetI,2,2,1.0,1,247,,,,603,603,603.0,KPLBOJCC_00244,NCFNLLIC_00244\n+group_151,,hypothetical protein,2,2,1.0,1,246,,,,606,606,606.0,KPLBOJCC_00042,NCFNLLIC_00042\n+group_150,,hypothetical protein,2,2,1.0,1,245,,,,606,606,606.0,KPLBOJCC_00040,NCFNLLIC_00040\n+group_149,,hypothetical protein,2,2,1.0,1,244,,,,612,612,612.0,KPLBOJCC_00251,NCFNLLIC_00251\n+group_148,,hypothetical protein,2,2,1.0,1,243,,,,615,615,615.0,KPLBOJCC_00231,NCFNLLIC_00231\n+group_147,,hypothetical protein,2,2,1.0,1,242,,,,621,621,621.0,KPLBOJCC_00186,NCFNLLIC_00186\n+gmhA,gmhA,Phosphoheptose isomerase,2,2,1.0,1,241,,,,624,624,624.0,KPLBOJCC_00019,NCFNLLIC_00019\n+group_146,,hypothetical protein,2,2,1.0,1,240,,,,627,627,627.0,KPLBOJCC_00245,NCFNLLIC_00245\n+group_145,,hypothetical protein,2,2,1.0,1,239,,,,633,633,633.0,KPLBOJCC_00218,NCFNLLIC_00218\n+kstR2_1,kstR2_1,HTH-type transcriptional repressor KstR2,2,2,1.0,1,238,,,,645,645,645.0,KPLBOJCC_00067,NCFNLLIC_00067\n+ybgJ,ybgJ,putative protein YbgJ,2,2,1.0,1,237,,,,654,654,654.0,KPLBOJCC_00177,NCFNLLIC_00177\n+group_144,,hypothetical protein,2,2,1.0,1,236,,,,657,657,657.0,KPLBOJCC_00224,NCFNLLIC_00224\n+pcm,pcm,Protein-L-isoaspartate O-methyltransferase,2,2,1.0,1,235,,,,657,657,657.0,KPLBOJCC_00097,NCFNLLIC_00097\n+group_143,,hypothetical protein,2,2,1.0,1,234,,,,660,660,660.0,KPLBOJCC_00111,NCFNLLIC_00111\n+group_142,,hypothetical protein,2,2,1.0,1,233,,,,663,663,663.0,KPLBOJCC_00236,NCFNLLIC_00236\n+group_141,,hypothetical protein,2,2,1.0,1,232,,,,663,663,663.0,KPLBOJCC_00229,NCFNLLIC_00229\n+pcp,pcp,Pyrrolidone-carboxylate peptidase,2,2,1.0,1,231,,,,669,669,669.0,KPLBOJCC_00235,NCFNLLIC_00235\n+mshB_1,mshB_1,1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase,2,2,1.0,1,230,,,,672,672,672.0,KPLBOJCC_00239,NCFNLLIC_00239\n+group_140,,hypothetical protein,2,2,1.0,1,229,,,,681,681,681.0,KPLBOJCC_00240,NCFNLLIC_00240\n+group_139,,hypothetical protein,2,2,1.0,1,228,,,,690,690,690.0,KPLBOJCC_00145,NCFNLLIC_00145\n+group_138,,hypothetical protein,2,2,1.0,1,227,,,,690,690,690.0,KPLBOJCC_00112,NCFNLLIC_00112\n+group_137,,hypothetical protein,2,2,1.0,1,226,,,,708,708,708.0,KPLBOJCC_00084,NCFNLLIC_00084\n+group_136,,hypothetical protein,2,2,1.0,1,225,,,,717,717,717.0,KPLBOJCC_00223,NCFNLLIC_00223\n+bluB,bluB,56-dimethylbenzimidazole synthase,2,2,1.0,1,224,,,,726,726,726.0,KPLBOJCC_00221,NCFNLLIC_00221\n+group_135,,hypothetical protein,2,2,1.0,1,223,,,,735,735,735.0,KPLBOJCC_00189,NCFNLLIC_00189\n+group_134,,hypothetical protein,2,2,1.0,1,222,,,,735,735,735.0,KPLBOJCC_00119,NCFNLLIC_00119\n+group_133,,Putative quercetin 23-dioxygenase,2,2,1.0,1,221,,,,735,735,735.0,KPLBOJCC_00090,NCFNLLIC_00090\n+group_132,,hypothetical protein,2,2,1.0,1,220,,,,735,735,735.0,KPLBOJCC_00087,NCFNLLIC_00087\n+ugpQ,ugpQ,Glycerophosphodiester phosphodiesterase cytoplasmic,2,2,1.0,1,219,,,,738,738,738.0,KPLBOJCC_00232,NCFNLLIC_00232\n+group_131,,hypothetical protein,2,2,1.0,1,218,,,,741,741,741.0,KPLBOJCC_00246,NCFNLLIC_00246\n+group_130,,hypothetical protein,2,2,1.0,1,217,,,,744,744,744.0,KPLBOJCC_00172,NCFNLLIC_00172\n+frdB_1,frdB_1,Fumarate reductase iron-sulfur subunit,2,2,1.0,1,216,,,,747,747,747.0,KPLBOJCC_00161,NCFNLLIC_00161\n+group_129,,hypothetical protein,2,2,1.0,1,215,,,,750,750,750.0,KPLBOJCC_00093,NCFNLLIC_00093\n+glpG,g'..b"+eccA3,eccA3,ESX-3 secretion system protein EccA3,2,2,1.0,1,39,,,,1896,1896,1896.0,KPLBOJCC_00198,NCFNLLIC_00198\n+group_21,,hypothetical protein,2,2,1.0,1,38,,,,456,456,456.0,KPLBOJCC_00171,NCFNLLIC_00171\n+sdhA_1,sdhA_1,Succinate dehydrogenase flavoprotein subunit,2,2,1.0,1,37,,,,1941,1941,1941.0,KPLBOJCC_00162,NCFNLLIC_00162\n+group_20,,putative protein,2,2,1.0,1,36,,,,1923,1923,1923.0,KPLBOJCC_00008,NCFNLLIC_00008\n+group_19,,hypothetical protein,2,2,1.0,1,35,,,,456,456,456.0,KPLBOJCC_00072,NCFNLLIC_00072\n+group_18,,putative enoyl-CoA hydratase 1,2,2,1.0,1,34,,,,456,456,456.0,KPLBOJCC_00037,NCFNLLIC_00037\n+pepO,pepO,Neutral endopeptidase,2,2,1.0,1,33,,,,1992,1992,1992.0,KPLBOJCC_00110,NCFNLLIC_00110\n+group_17,,hypothetical protein,2,2,1.0,1,32,,,,2058,2058,2058.0,KPLBOJCC_00017,NCFNLLIC_00017\n+bglB,bglB,Thermostable beta-glucosidase B,2,2,1.0,1,31,,,,2076,2076,2076.0,KPLBOJCC_00095,NCFNLLIC_00095\n+group_16,,hypothetical protein,2,2,1.0,1,30,,,,480,480,480.0,KPLBOJCC_00165,NCFNLLIC_00165\n+group_15,,Elongation factor G-like protein,2,2,1.0,1,29,,,,2145,2145,2145.0,KPLBOJCC_00027,NCFNLLIC_00027\n+group_14,,hypothetical protein,2,2,1.0,1,28,,,,483,483,483.0,KPLBOJCC_00222,NCFNLLIC_00222\n+group_13,,Acyl-CoA dehydrogenase FadE34,2,2,1.0,1,27,,,,2196,2196,2196.0,KPLBOJCC_00184,NCFNLLIC_00184\n+hsaB_1,hsaB_1,Flavin-dependent monooxygenase reductase subunit HsaB,2,2,1.0,1,26,,,,489,489,489.0,KPLBOJCC_00159,NCFNLLIC_00159\n+napA,napA,Nitrate reductase,2,2,1.0,1,25,,,,2247,2247,2247.0,KPLBOJCC_00109,NCFNLLIC_00109\n+ctpB,ctpB,Cation-transporting P-type ATPase B,2,2,1.0,1,24,,,,2259,2259,2259.0,KPLBOJCC_00009,NCFNLLIC_00009\n+baiE,baiE,Bile acid 7-alpha dehydratase,2,2,1.0,1,23,,,,492,492,492.0,KPLBOJCC_00225,NCFNLLIC_00225\n+group_12,,hypothetical protein,2,2,1.0,1,22,,,,504,504,504.0,KPLBOJCC_00113,NCFNLLIC_00113\n+group_11,,hypothetical protein,2,2,1.0,1,21,,,,504,504,504.0,KPLBOJCC_00045,NCFNLLIC_00045\n+nasD,nasD,Nitrite reductase [NAD(P)H],2,2,1.0,1,20,,,,2511,2511,2511.0,KPLBOJCC_00166,NCFNLLIC_00166\n+group_10,,hypothetical protein,2,2,1.0,1,19,,,,2514,2514,2514.0,KPLBOJCC_00194,NCFNLLIC_00194\n+group_9,,hypothetical protein,2,2,1.0,1,18,,,,510,510,510.0,KPLBOJCC_00094,NCFNLLIC_00094\n+group_8,,hypothetical protein,2,2,1.0,1,17,,,,2700,2700,2700.0,KPLBOJCC_00193,NCFNLLIC_00193\n+cobU,cobU,Bifunctional adenosylcobalamin biosynthesis protein CobU,2,2,1.0,1,16,,,,525,525,525.0,KPLBOJCC_00168,NCFNLLIC_00168\n+group_7,,hypothetical protein,2,2,1.0,1,15,,,,2808,2808,2808.0,KPLBOJCC_00192,NCFNLLIC_00192\n+mmpL3_1,mmpL3_1,Trehalose monomycolate exporter MmpL3,2,2,1.0,1,14,,,,2835,2835,2835.0,KPLBOJCC_00118,NCFNLLIC_00118\n+group_6,,Heme uptake protein MmpL11,2,2,1.0,1,13,,,,2898,2898,2898.0,KPLBOJCC_00114,NCFNLLIC_00114\n+aac,aac,Aminoglycoside 2'-N-acetyltransferase,2,2,1.0,1,12,,,,546,546,546.0,KPLBOJCC_00175,NCFNLLIC_00175\n+group_5,,Multidrug efflux ATP-binding/permease protein,2,2,1.0,1,11,,,,3585,3585,3585.0,KPLBOJCC_00106,NCFNLLIC_00106\n+group_4,,hypothetical protein,2,2,1.0,1,10,,,,3630,3630,3630.0,KPLBOJCC_00179,NCFNLLIC_00179\n+group_3,,hypothetical protein,2,2,1.0,1,9,,,,549,549,549.0,KPLBOJCC_00131,NCFNLLIC_00131\n+msrA,msrA,Peptide methionine sulfoxide reductase MsrA,2,2,1.0,1,8,,,,549,549,549.0,KPLBOJCC_00044,NCFNLLIC_00044\n+eccC3,eccC3,ESX-3 secretion system protein EccC3,2,2,1.0,1,7,,,,3993,3993,3993.0,KPLBOJCC_00200,NCFNLLIC_00200\n+aftD,aftD,Alpha-(1->3)-arabinofuranosyltransferase,2,2,1.0,1,6,,,,4203,4203,4203.0,KPLBOJCC_00149,NCFNLLIC_00149\n+group_2,,putative protein,2,2,1.0,1,5,,,,552,552,552.0,KPLBOJCC_00004,NCFNLLIC_00004\n+group_1,,hypothetical protein,2,2,1.0,1,4,,,,555,555,555.0,KPLBOJCC_00086,NCFNLLIC_00086\n+ctpI_1,ctpI_1,putative cation-transporting ATPase I,2,2,1.0,1,3,,,,4878,4878,4878.0,KPLBOJCC_00013,NCFNLLIC_00013\n+dltA,dltA,D-alanine--poly(phosphoribitol) ligase subunit 1,2,2,1.0,1,2,,,,7539,7539,7539.0,KPLBOJCC_00007,NCFNLLIC_00007\n+group_0,,hypothetical protein,2,2,1.0,1,1,,,,9561,9561,9561.0,KPLBOJCC_00220,NCFNLLIC_00220\n" |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/pan_genome_reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pan_genome_reference.fa Tue Aug 27 05:51:12 2024 +0000 |
| b |
| b'@@ -0,0 +1,5055 @@\n+>group_50\n+TTGTGTCACTTCAGTTTCACGGTTATCAGCGGGGCGCTCTTTGTCAGTGCCCGACGTTAT\n+GATTCGAACATGTTAGCGAATAGCCGGGAGGAGCTTGTCGAGGTCTTCGACGCGCTGGAT\n+GCCGACCTGGACCGCTTGGACGAGGTGTCCTTTGAGGTGCTGAGCACCCCGGAACGGCTG\n+CGGTCTCTGGAACGTCTGGAATGCTTGGCGCGCCGGCTACCGGCGGCCCAGCACACGTTG\n+ATCAACCAACTCGACACCCAAGCCAGCGAGGAAGAACTGGGCGGCACGCTGTGCTGCGCG\n+CTGGCCAACCGGCTGCGCATCACCAAGCCCGAAGCCGGCCGACGCAGCGCCGAAGCCAAG\n+CCTTAG\n+>group_61\n+ATGGCTATACCACCGGAGGTGCACTCGGGCCTGTTGAGCGCCGGGTGCGGTCCGGGATCA\n+TTGCTTGTTGCCGCGCAGCAGTGGCAAGAACTTAGTGATCAGTACGCACTCGCATGCGCC\n+GAGTTGGGCCAATTGTTGGGCGAGGTTCAGGCCAGCAGCTGGCAGGGAACCGCCGCCACC\n+CAGTACGTGGCTGCCCATGGCCCCTATCTGGCCTGGCTTGAGCAAACCGCGATCAACAGC\n+GCCGTCACCGCCGCACAGCACGTAGCGGCTGCCGCTGCCTACTGCAGCGCCCTGGCCGCG\n+ATGCCCACCCCAGCAGAGCTGGCCGCCAACCACGCCATTCATGGCGTTCTGATCGCCACC\n+AACTTCTTCGGGATCAACACCGTTCCGATCGCGCTCAACGAAGCCGATTATGTCCGCATG\n+TGGCTGCAAGCCGCCGACACCATGGCCGCCTACCAGGCCGTCGCCGATGCGGCCACGGTG\n+GCCGTACCGTCCACCCAACCGGCGCCACCGATCCGCGCGCCCGGCGGCGATGCCGCAGAT\n+ACCCGGCTAGACGTATTGAGTTCAATTGGTCAGCTCATCCGGGATATCTTGGATTTCATT\n+GCCAACCCGTACAAGTATTTTCTGGAGTTTTTCGAGCAATTCGGCTTCAGCCCGGCCGTA\n+ACGGTCGTCCTTGCCCTTGTTGCCCTGCAGCTGTACGACTTTCTTTGGTATCCCTATTAC\n+GCCTCGTACGGCCTGCTCCTGCTTCCGTTCTTCACTCCCACCTTGAGCGCGTTGACCGCC\n+CTAAGCGCGCTGATCCATTTGCTGAACCTGCCCCCGGCTGGACTGCTTCCTATCGCCGCA\n+GCGCTCGGTCCCGGCGACCAATGGGGCGCAAACTTGGCTGTGGCTGTCACGCCGGCCACG\n+GCGGCCGTGCCCGGCGGAAGCCCGCCCACCAGCAACCCCGCGCCCGCCGCTCCCAGCTCG\n+AACTCGGTTGGCAGCGCTTCGGCTGCACCCGGCATCAGCTATGCCGTGCCCGGCCTGGCG\n+CCACCCGGGGTTAGCTCTGGCCCTAAAGCCGGCACCAAATCACCTGACACCGCCGCCGAC\n+ACCCTTGCAACCGCGGGCGCAGCACGACCGGGCCTCGCCCGAGCCCACCGAAGAAAGCGC\n+AGCGAAAGCGGCGTCGGGATACGCGGTTACCGCGACGAATTTTTGGACGCGACCGCCACG\n+GTGGACGCCGCTACGGATGTGCCCGCTCCCGCCAACGCGGCTGGCAGTCAAGGTGCCGGC\n+ACTCTCGGCTTTGCCGGTACCGCACCGACAACCAGCGGCGCCGCGGCCGGAATGGTTCAA\n+CTGTCGTCGCACAGCACAAGCACTACAGTCCCGTTGCTGCCCACTACCTGGACAACCGAC\n+GCCGAACAATGA\n+>group_113\n+ATGACGCTTAAGGTCAAAGGCGAGGGACTCGGTGCGCAGGTCACAGGGGTCGATCCCAAG\n+AATCTGGACGATATAACCACCGACGAGATCCGGGATATCGTTTACACGAACAAGCTCGTT\n+GTGCTAAAAGACGTCCATCCGTCTCCGCGGGAGTTCATCAAACTCGGCAGGATAATTGGA\n+CAAATCGTTCCGTATTACGAACCCATGTACCATCACGAAGACCACCCGGAGATCTTTGTC\n+TCCTCCACTGAGGAAGGTCAGGGGGTCCCAAAAACCGGCGCGTTCTGGCATATCGACTAT\n+ATGTTTATGCCGGAACCTTTCGCGTTTTCCATGGTGCTGCCGCTGGCGGTGCCTGGACAC\n+GACCGCGGGACCTATTTCATCGATCTCGCCAGGGTCTGGCAGTCGCTGCCCGCCGCCAAG\n+CGAGACCCGGCCCGCGGAACCGTCAGCACCCACGACCCTCGACGCCACATCAAGATCCGA\n+CCCAGCGACGTCTACCGGCCCATCGGAGAGGTATGGGACGAGATCAACCGGACCACGCCC\n+CCAATAAAGTGGCCTACGGTCATCCGGCACCCAAAGACCGGCCAAGAGATCCTCTACATC\n+TGCGCGACGGGCACCACCAAGATCGAGGACAAGGACGGCAATCCGGTTGATCCGGAGGTG\n+CTGCAAGAACTCATGGCCGCGACCGGACAGCTCGATCCTGAGTACCAGTCGCCGTTCATA\n+CATACTCAGCACTACCAGGTTGGCGACATCATCTTGTGGGACAACCGGGTTCTCATGCAC\n+CGAGCGAAGCACGGCAGCGCCGCGGGCACTCTGACGACCTACCGCCTGACCATGCTTGAT\n+GGCCTCAAGACGCCGGGATACGCGGCATGA\n+>group_2\n+ATGAGCCACACCGACTTGACGCCCTGCACACGGGTGCTGGCATCCAGCGGCACGGTTCCG\n+ATCGCAGAGGAACTGCTGGCCAGAGTGCTCGAGCCCTACTCCTGCAAAGGATGTCGCTAC\n+CTCATCGACGCACAGTACAGCGCCACCGAGGATTCGGTTCTTGCCTATGGCAACTTCACG\n+ATCGGTGAGTCCGCCTATATTCGAAGCACGGGGCACTTCAACGCGGTCGAACTGATTCTG\n+TGTTTCAATCAGCTCGCCTACAGCGCCTTCGCTCCGGCCGTCCTCAACGAGGAAATCCGG\n+GTGCTTCGCGGCTGGTCGATCGACGACTACTGCCAACACCAGCTCTCTAGCATGCTGATC\n+AGGAAGGCATCATCGCGGTTCAGAAAACCGCTGAACCCGCAAAAGTTCTCTGCCCGCCTC\n+CTGTGTCGAGATCTGCAGGTCATCGAACGAACCTGGCGCTATCTCAAGGTCCCGTGCGTC\n+ATCGAGTTCTGGGACGAGAACGGCGGGGCGGCGTCCGGTGAGATCGAACTAGCGGCCCTC\n+AACATTCCGTAA\n+>group_40\n+ATGCCTCAGTTGCCATCTACCGTGCTGGACCGGGTCTTCGAGCAGGCACGGCAGCAGCCG\n+GAAGCAATCGCCTTGCGTCGCTGCGACGGCACTAGCGCACTGCGGTACCGTGAACTCGTC\n+GCCGAAGTTGGTGGCCTTGCCGCGGATTTGCGTGCCCAGTCGGTTAGCCGGGGTTCTAGG\n+GTGCTGGTCATTTCCGACAATGGACCCGAGACGTACCTGTCGGTGCTGGCGTGTGCAAAG\n+CTCGGGGCGATCGCCGTCATGGCCGACGGCAATCTTCCGATCGCAGCCATCGAACGATTC\n+TGTCAGATCACCGACCCCGCAGCGGCTCTCGTCGCACCAGGGAGCAAGATGGCATCTTCC\n+GCCGTTCCCGAGGCGCTGCACTCGATACCAGTGATCGCGGTCGACATAGCCGCTGTTACA\n+CGGGAATCCGAGCATTCCTTGGATGCAGCCAGCCTCGCCGGGAACGCGGACCAGGGGAGC\n+GAGGATCCGCTGGCGATGATCTTCACCAGCGGTACCACGGGCGAGCCCAAGGCTGTGCTA\n+CTGGCCAACCGCACCTTCTTCGCCGTCCCGGACATCTTGCAAAAAGAGGGTTTGAACTGG\n+GTCACTTGGGTC'..b'TGTGGAAACGCCGGTGTGGACCTTCCTCGGACCGCGCCCG\n+GCGGGCTGGTGGGTTCGGCGGCGGCTACACGAGGTCGCAGTGCACCGCGCCGACGTGGCG\n+ATCACCGTCGGGGGCGAATTCACACTGGAACCGAACGTGGCAGCCGACGGGATCAGCGAA\n+TTCCTGGAGCGCATAGCGGTCCAGGCCGGCAGCGGCGGCACGCCATTACCGCTCGAAGAC\n+GACGACACCTTACATCTGCACGCCACCGATCCGGGGCTTCTTGAAGCCGGCGAATGGACG\n+GTTCGTCGCGACGAGCGCGGCGTCACCTGGTCGCATCGGCACGGAAAGGGTGCCGTGGCA\n+CTGCGTGGCGGCGCCACCGAGCTGCTGCTGGCGATGGTGCGCCGACTCTCGGTTGCCGAC\n+ACCGGCATCGAGCTGTTGGGGGATGCCGGGGTATGGCAAAAATGGCTGGATCGCACGCCG\n+CTGTAG\n+>group_33\n+ATGGCAAAAATGGCTGGATCGCACGCCGCTGTAGCCGCCGCACACGGTAACTTTCAGACC\n+ATGACCACATCGGAGATCGCTACCGTGCTGGCCTGGCACGACGCCCTCAATGCCGCCGAC\n+ATTGAGACCCTCGTGGCGTTGTCTACTGACGACATCGACATCGGTGACGCGCACGGGGCT\n+GTACAGGGCCACGATGCGCTGCGCGGGTGGGCCAGCTCGCTCACCACAACCGCAGAACTT\n+GGCCGCATGTACGTGCACCACGGAGTCGTGGTCGTCGAACAAAAGATCACCAGCGGCGAA\n+GATCCGGGCATCGCCAGGACCGGCGCCGCGGCGTTCCGTGTGGTCCAAGACCACGTCGCA\n+TCGGTTTTCCGGCACGAAGACTTGGCGTCGGCGCTGGCGGCCACCGAACTCACCGAGGAC\n+GATTTGGTCGATTGA\n+>rmlA\n+ATGCGCGGGATCATCTTGGCCGGCGGTTCGGGCACCCGGCTGTACCCGATCACCATGGGG\n+ATCAGCAAGCAGCTGCTGCCGGTCTACGACAAACCGATGATCTACTACCCGCTCACCACG\n+CTGATGATGGCTGGGATCCGAGACATTCAGTTGATCACCACCCCGCATGACGCGCCCGGC\n+TTTCATCGACTCCTGGGCGACGGCGCGCACTTGGGAGTGAACATCAGCTACGCCACCCAG\n+GATCAGCCTGACGGTCTGGCGCAGGCGTTCGTCATTGGCGCCAACCACATCGGCGCCGAT\n+TCGGTGGCATTGGTGTTGGGGGACAACATCTTCTACGGCCCAGGTCTGGGGACCAGCCTG\n+AAGCGCTTCCAATCCATCAGTGGTGGAGCAATTTTCGCCTATTGGGTAGCCAACCCGTCG\n+GCCTATGGTGTCGTTGAGTTCGGCGCCGAGGGCATGGCGCTGTCTCTGGAGGAGAAGCCG\n+GTGACCCCGAAGTCGAATTACGCGGTGCCGGGCCTGTATTTCTATGACAACGATGTGATC\n+GAAATCGCCAGGGGTTTAAAGAAATCAGCGCGCGGGGAGTACGAGATCACCGAGGTCAAC\n+CAGGTCTACCTCAATCAGGGTAGGTTGGCGGTCGAGGTGCTGGCCCGCGGGACAGCGTGG\n+CTGGACACCGGGACATTCGACTCGCTGCTGGACGCCGCCGATTTCGTCCGGACCCTGGAG\n+CGTCGGCAGGGCCTGAAGGTCAGCATCCCCGAAGAAGTGGCGTGGCGCATGGGCTGGATC\n+GACGACGAGCAGCTGGTGCAGCGAGCCCGTGCTCTGGTCAAGTCCGGATATGGTAACTAC\n+CTGCTGGAGTTGTTGGAGCGCAACTGA\n+>group_149\n+ATGGTAACTACCTGCTGGAGTTGTTGGAGCGCAACTGATTTCGGCGGGTTATTGTCGGTG\n+ATTATGGAACCCCCTGGTAGCCCGTCCTGGATGAGCAGCCCACCGGACCAGCCATTGCCG\n+AACAGCCCGCCGTTGGCGCCGTTGGCGATCAGCGGGCCCCAACAGCGCCTGGGTCGGCGC\n+ATCGGCGGTGGTCTCGGCGCTGGCACACGAGCCCGCACCCACGTTCAGGTTCTGTGCAAA\n+CTGGCCATGGAACGCCGCCGCCTGATTGTTGAGGGAGTGATGCCGCCGACCGTGTGCGGA\n+AATCAGTGCCGCGACGGCCGCCGACACCTCGTCTTCGGCCGCCGCCAGCACGCGGGTCTT\n+GTGGCGCTTCGGCGGGAAGTTGCTGATCCGAGATGCTGGCGGCTGGTTTCCTTGTGGTGG\n+CCTGGGCCGGGTGGTGGCGCACAGTGGGCCCGGTGGGGTCGCGGCCGGCCGGGCAAGAAC\n+GCTGCGCCCTGGCCGGGCCATGAGCGGAGCCGGCAAGCTCGACGGCGCCCGGCATGCGCG\n+GTGCAAGAACCCCATGGACCGCACCGAGTGCCGTGCTCGCCCTCGGCGGCTACCGAGCCG\n+GTGTCTCCCTAG\n+>group_55\n+GTGTCGGCGGCGTTCATCGATCGGATCTGCTCGGCGACTCGGGCCGAAAACCGGGCCGCT\n+GCGGCGCAGTTGGTGGCGTTGGGGGAGTTGTTCGCCTATCGGTGGTCGCGTTGCGGGGGC\n+CGCGAGGAGTGGGTGATGGACACCATGGCGGCGGTGGCCGCCGAGGTGGCGGCGGCGTTG\n+CGGATCAGTCAGGGTCTGGCGGCCAGCCGGTTGCGGTATGCGCGGGCGATGCGTGAGCGG\n+CTGCCTAAGACGGCTGAGGTGTTTAGCGCCGGCGACATCGGCTATCTGATGTTTGCCACG\n+ATTGTGTATCGCACCGACTTGATCGTTGACCCTGATGTTTTGGCGGCGGTGGATGCGCAG\n+TTGGCCGCCAATGTGGCGCGTTGGCCCTCGATGACCAAGGCCCGCCTGGCTGGGCAGGTC\n+GATAAGATCGTGGCGCGTGCCGATGCCGATGCGGTGCGGCGGCGCAAGGAGTATCAGGCC\n+CAGCGCCAGTTCTGGGTCGGGGAAAGCCAAGACGGTGTGTGCCAGATCGGTGGCAGCCTG\n+TTGGCCGTCGACGCACACGCCCTCGATGCGCGGTTGAGCGCGTTGGCGGGCACCGTGTGT\n+GAGCACGATCCGCGCAGCCGTGAGCAGCGCCGCGCGGACGCGTTGGGGGCGTTGGCGGGC\n+GGGGCCGATCGGCTGGGCTGTGGCTGTGGGCGCGCTGATTGTGCGGCCGGGAAGCGGCCT\n+GCGGCCCCGCCGGTGGTGATTCACCTGATCGCCGAGGCGGCCACGATCAATGGCACGGGC\n+TCGGCGCCGGCATCGCAGATGAACGCCGACGGGCTGATCACCGCCGAACTGGTGGCCGAG\n+CTGGCCAAGACGGCCACGCTGGTGCCGCTGGTTCATCCCGGCGATGCGCCGCCCGAGCCG\n+GGGTATGCGCCGTCGAAAGCGCTCGCCGATTTCGTTCGCTGCCGGGATCTGACGTGTCGC\n+TGGCCCGGCTGTGATGAGCCCGCCACCAATTGCGACCTGGATCATACGATCCCGTATGCC\n+GCTGGTGGGCCCACCCATGCGTCGAACCTGAAATGTTACTGCCGTACCCATCACCTGGTG\n+AAAACGTTTTGGGGATGGCGTGATCAACAGCTACCCGACGGCACCCTGATTTTGACCTCC\n+CCGTCCGGGCATACCTATGTCAGCACCCCGGGCAGTGCGCTGCTGTTCCCCAGCTTGTGC\n+CACTTCAGCGGCGGCATCCCGGCACCGGAAGCCGACCCACCCTACGACCATTGCGACCAG\n+CGCACAGCGATGATGCCCAAACGCCGGCGCACCCGCGCCCAAGACCGGGCCTATCGCATC\n+GCCACCGAACGTCGACAAAACCACGCCGCCCGCCAGCGCGCCCAGGTGCTCACCCAGACC\n+GCCGCGGCCACCGACACCCACGGCCCACCACCGGATCCCAACGACGACCCACCGCCGTTT\n+TGA\n' |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/pre_filt_graph.gml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pre_filt_graph.gml Tue Aug 27 05:51:12 2024 +0000 |
| [ |
| b'@@ -0,0 +1,24099 @@\n+graph [\n+ node [\n+ id 0\n+ label "625"\n+ size 2\n+ centroid "_networkx_list_start"\n+ centroid "\'0_0_0\'"\n+ maxLenId 0\n+ members "[0,1]"\n+ seqIDs "[\'0_0_0\',\'1_0_0\']"\n+ hasEnd 1\n+ protein "_networkx_list_start"\n+ protein "\'MCHFSFTVISGALFVSARRYDSNMLANSREELVEVFDALDADLDRLDEVSFEVLSTPERLRSLERLECLARRLPAAQHTLINQLDTQASEEELGGTLCCALANRLRITKPEAGRRSAEAKP\'"\n+ dna "_networkx_list_start"\n+ dna "\'TTGTGTCACTTCAGTTTCACGGTTATCAGCGGGGCGCTCTTTGTCAGTGCCCGACGTTATGATTCGAACATGTTAGCGAATAGCCGGGAGGAGCTTGTCGAGGTCTTCGACGCGCTGGATGCCGACCTGGACCGCTTGGACGAGGTGTCCTTTGAGGTGCTGAGCACCCCGGAACGGCTGCGGTCTCTGGAACGTCTGGAATGCTTGGCGCGCCGGCTACCGGCGGCCCAGCACACGTTGATCAACCAACTCGACACCCAAGCCAGCGAGGAAGAACTGGGCGGCACGCTGTGCTGCGCGCTGGCCAACCGGCTGCGCATCACCAAGCCCGAAGCCGGCCGACGCAGCGCCGAAGCCAAGCCTTAG\'"\n+ annotation "\'\'"\n+ description "\'putative protein\'"\n+ lengths 366\n+ lengths 366\n+ longCentroidID 366\n+ longCentroidID "\'0_0_0\'"\n+ paralog 0\n+ mergedDNA 0\n+ genomeIDs "\'0;1\'"\n+ geneIDs "\'0_0_0;1_0_0\'"\n+ degrees 1\n+ ]\n+ node [\n+ id 1\n+ label "145"\n+ size 2\n+ centroid "_networkx_list_start"\n+ centroid "\'0_0_1\'"\n+ maxLenId 0\n+ members "[0,1]"\n+ seqIDs "[\'0_0_1\',\'1_0_1\']"\n+ hasEnd 0\n+ protein "_networkx_list_start"\n+ protein "\'MAIPPEVHSGLLSAGCGPGSLLVAAQQWQELSDQYALACAELGQLLGEVQASSWQGTAATQYVAAHGPYLAWLEQTAINSAVTAAQHVAAAAAYCSALAAMPTPAELAANHAIHGVLIATNFFGINTVPIALNEADYVRMWLQAADTMAAYQAVADAATVAVPSTQPAPPIRAPGGDAADTRLDVLSSIGQLIRDILDFIANPYKYFLEFFEQFGFSPAVTVVLALVALQLYDFLWYPYYASYGLLLLPFFTPTLSALTALSALIHLLNLPPAGLLPIAAALGPGDQWGANLAVAVTPATAAVPGGSPPTSNPAPAAPSSNSVGSASAAPGISYAVPGLAPPGVSSGPKAGTKSPDTAADTLATAGAARPGLARAHRRKRSESGVGIRGYRDEFLDATATVDAATDVPAPANAAGSQGAGTLGFAGTAPTTSGAAAGMVQLSSHSTSTTVPLLPTTWTTDAEQ\'"\n+ dna "_networkx_list_start"\n+ dna "\'ATGGCTATACCACCGGAGGTGCACTCGGGCCTGTTGAGCGCCGGGTGCGGTCCGGGATCATTGCTTGTTGCCGCGCAGCAGTGGCAAGAACTTAGTGATCAGTACGCACTCGCATGCGCCGAGTTGGGCCAATTGTTGGGCGAGGTTCAGGCCAGCAGCTGGCAGGGAACCGCCGCCACCCAGTACGTGGCTGCCCATGGCCCCTATCTGGCCTGGCTTGAGCAAACCGCGATCAACAGCGCCGTCACCGCCGCACAGCACGTAGCGGCTGCCGCTGCCTACTGCAGCGCCCTGGCCGCGATGCCCACCCCAGCAGAGCTGGCCGCCAACCACGCCATTCATGGCGTTCTGATCGCCACCAACTTCTTCGGGATCAACACCGTTCCGATCGCGCTCAACGAAGCCGATTATGTCCGCATGTGGCTGCAAGCCGCCGACACCATGGCCGCCTACCAGGCCGTCGCCGATGCGGCCACGGTGGCCGTACCGTCCACCCAACCGGCGCCACCGATCCGCGCGCCCGGCGGCGATGCCGCAGATACCCGGCTAGACGTATTGAGTTCAATTGGTCAGCTCATCCGGGATATCTTGGATTTCATTGCCAACCCGTACAAGTATTTTCTGGAGTTTTTCGAGCAATTCGGCTTCAGCCCGGCCGTAACGGTCGTCCTTGCCCTTGTTGCCCTGCAGCTGTACGACTTTCTTTGGTATCCCTATTACGCCTCGTACGGCCTGCTCCTGCTTCCGTTCTTCACTCCCACCTTGAGCGCGTTGACCGCCCTAAGCGCGCTGATCCATTTGCTGAACCTGCCCCCGGCTGGACTGCTTCCTATCGCCGCAGCGCTCGGTCCCGGCGACCAATGGGGCGCAAACTTGGCTGTGGCTGTCACGCCGGCCACGGCGGCCGTGCCCGGCGGAAGCCCGCCCACCAGCAACCCCGCGCCCGCCGCTCCCAGCTCGAACTCGGTTGGCAGCGCTTCGGCTGCACCCGGCATCAGCTATGCCGTGCCCGGCCTGGCGCCACCCGGGGTTAGCTCTGGCCCTAAAGCCGGCACCAAATCACCTGACACCGCCGCCGACACCCTTGCAACCGCGGGCGCAGCACGACCGGGCCTCGCCCGAGCCCACCGAAGAAAGCGCAGCGAAAGCGGCGTCGGGATACGCGGTTACCGCGACGAATTTTTGGACGCGACCGCCACGGTGGACGCCGCTACGGATGTGCCCGCTCCCGCCAACGCGGCTGGCAGTCAAGGTGCCGGCACTCTCGGCTTTGCCGGTACCGCACCGACAACCAGCGGCGCCGCGGCCGGAATGGTTCAACTGTCGTCGCACAGCACAAGCACTACAGTCCCGTTGCTGCCCACTACCTGGACAACCGACGCCGAACAATGA\'"\n+ annotation "\'\'"\n+ description "\'hypothetical protein\'"\n+ lengths 1392\n+ lengths 1392\n+ longCentroidID 1392\n+ longCentroidID "\'0_0_1\'"\n+ paralog 0\n+ mergedDNA 0\n+ genomeIDs "\'0;1\'"\n+ geneIDs "\'0_0_1;1_0_1\'"\n+ degrees 2\n+ ]\n+ node [\n+ id 2\n+ label "325"\n+ size 2\n+ centroid "_networkx_list_start"\n+ centroid "\'0_0_2\'"\n+ maxLenId 0\n+ members "[0,1]"\n+ seqIDs "[\'0_0_2\',\'1_0_2\']"\n+ hasEnd 0\n+ protein "_networkx_list_start"\n+ protein "\'MTLKVKGEGLGAQVTGVDPKNLDDITTDEIRDIVYTNKLVVLKDVHPSPREFIKLGRIIGQIVPYYEPMYHHEDHPEIFVSSTEEGQGVPKTGAFWHIDYMFMPEPFAFSMVLPLAVPGHDRGTYFIDLARVWQSLPAAKRDPARGTVSTHDPRRHIKIRPSDVYRPIGEVWDEINRTTPPIKWPTVIRHPKTGQEILYICATGTTKIEDKDGNPVDPEVLQELMAATGQLDPEYQSPFIHTQHYQVGDIILWDNRVLMHRAKHGSAAGTLTTYRLTMLDGLKTPGYAA'..b'ers "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 689\n+ target 690\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 690\n+ target 691\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 691\n+ target 692\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 692\n+ target 693\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 693\n+ target 694\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 694\n+ target 695\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 695\n+ target 696\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 696\n+ target 697\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 697\n+ target 698\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 698\n+ target 699\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 699\n+ target 700\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 700\n+ target 701\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 701\n+ target 702\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 702\n+ target 703\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 703\n+ target 704\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 704\n+ target 705\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 705\n+ target 706\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 706\n+ target 707\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 707\n+ target 708\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 708\n+ target 709\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 709\n+ target 710\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 710\n+ target 711\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 711\n+ target 712\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 712\n+ target 713\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 713\n+ target 714\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 714\n+ target 715\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 715\n+ target 716\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 716\n+ target 717\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 717\n+ target 718\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 718\n+ target 719\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 719\n+ target 720\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 720\n+ target 721\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 721\n+ target 722\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 722\n+ target 723\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 723\n+ target 724\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 724\n+ target 725\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 725\n+ target 726\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 726\n+ target 727\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 727\n+ target 728\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+ edge [\n+ source 728\n+ target 729\n+ size 1\n+ members "[1]"\n+ genomeIDs "\'1\'"\n+ ]\n+]\n' |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/struct_presence_absence.Rtab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/struct_presence_absence.Rtab Tue Aug 27 05:51:12 2024 +0000 |
| b |
| @@ -0,0 +1,1 @@ +Gene 10_small 11_small |
| b |
| diff -r 000000000000 -r 01864c78c5a5 test-data/summary_statistics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_statistics.txt Tue Aug 27 05:51:12 2024 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Core genes (99% <= strains <= 100%) 251 +Soft core genes (95% <= strains < 99%) 0 +Shell genes (15% <= strains < 95%) 0 +Cloud genes (0% <= strains < 15%) 0 +Total genes (0% <= strains <= 100%) 251 \ No newline at end of file |