| Next changeset 1:f05c3732764a (2023-03-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka commit 4f57302e4d14a2b32bcd9d41d25d987a29317bf3 |
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added:
macros.xml pharokka.xml test-data/SAOMS1.fasta test-data/pharokka.gbk test-data/pharokka.gff test-data/pharokka_db.loc test-data/subset_pharokka_db/5Jan2023_data.tsv test-data/subset_pharokka_db/5Jan2023_genomes.fa.msh test-data/subset_pharokka_db/CARD test-data/subset_pharokka_db/CARD.dbtype test-data/subset_pharokka_db/CARD.index test-data/subset_pharokka_db/CARD.lookup test-data/subset_pharokka_db/CARD.source test-data/subset_pharokka_db/CARD_h test-data/subset_pharokka_db/CARD_h.dbtype test-data/subset_pharokka_db/CARD_h.index test-data/subset_pharokka_db/VFDB_setB_pro.fas test-data/subset_pharokka_db/aro_index.tsv test-data/subset_pharokka_db/phrog_annot_v4.tsv test-data/subset_pharokka_db/phrog_hhm_db test-data/subset_pharokka_db/phrog_hhm_db.index test-data/subset_pharokka_db/phrogs_db test-data/subset_pharokka_db/phrogs_db.dbtype test-data/subset_pharokka_db/phrogs_db.index test-data/subset_pharokka_db/phrogs_profile_db test-data/subset_pharokka_db/phrogs_profile_db.dbtype test-data/subset_pharokka_db/phrogs_profile_db.index test-data/subset_pharokka_db/phrogs_profile_db_consensus test-data/subset_pharokka_db/phrogs_profile_db_consensus.dbtype test-data/subset_pharokka_db/phrogs_profile_db_consensus.index test-data/subset_pharokka_db/phrogs_profile_db_h test-data/subset_pharokka_db/phrogs_profile_db_h.dbtype test-data/subset_pharokka_db/phrogs_profile_db_h.index test-data/subset_pharokka_db/phrogs_profile_db_seq test-data/subset_pharokka_db/phrogs_profile_db_seq.dbtype test-data/subset_pharokka_db/phrogs_profile_db_seq.index test-data/subset_pharokka_db/phrogs_profile_db_seq_h test-data/subset_pharokka_db/phrogs_profile_db_seq_h.index test-data/subset_pharokka_db/protein_fasta_protein_homolog_model.fasta test-data/subset_pharokka_db/vfdb test-data/subset_pharokka_db/vfdb.dbtype test-data/subset_pharokka_db/vfdb.index test-data/subset_pharokka_db/vfdb.lookup test-data/subset_pharokka_db/vfdb.source test-data/subset_pharokka_db/vfdb_h test-data/subset_pharokka_db/vfdb_h.dbtype test-data/subset_pharokka_db/vfdb_h.index tool-data/pharokka_db.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 1d4fcd38d899 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 02 16:21:40 2023 +0000 |
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| @@ -0,0 +1,40 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">1.2.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <xml name="biotools"> + <xrefs> + <xref type="bio.tools"> + pharokka + </xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@"> + pharokka + </requirement> + <requirement type="package" version="3.0"> + zip + </requirement> + </requirements> + </xml> + <xml name="version"> + <version_command> + pharokka.py --version + </version_command> + </xml> + <xml name="citations"> + <citations> + <citation type="doi"> + 10.1093/bioinformatics/btac776 + </citation> + </citations> + </xml> + <xml name="creator"> + <creator> + <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" /> + </creator> + </xml> +</macros> |
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| diff -r 000000000000 -r 1d4fcd38d899 pharokka.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pharokka.xml Thu Mar 02 16:21:40 2023 +0000 |
| [ |
| @@ -0,0 +1,165 @@ +<tool id="pharokka" name="bacteriophage annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description> + rapid standardised annotation tool for bacteriophage genomes and metagenomes + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="biotools" /> + <expand macro="requirements" /> + <expand macro="version" /> + <command detect_errors="exit_code"> + <![CDATA[ + + ##run tool + #if str( $terminase.terminase_selector ) == 'no_terminase': + pharokka.py + -i '$fasta' + -o pharokka_output + -d '$db_cached.fields.path' + -t \${GALAXY_SLOTS:-8} + $gene_predictor + $meta + -e '$evalue' + #else: + pharokka.py + -i '$fasta' + -o pharokka_output + -d '$db_cached.fields.path' + -t \${GALAXY_SLOTS:-8} + $gene_predictor + $meta + -e '$evalue' + --terminase + --terminase_strand '$terminase.terminase_strand' + --terminase_start '$terminase.terminase_start' + #end if + + ## create output + #if $zip_output == 'true': + && zip -r out.zip pharokka_output + #end if + ]]> + </command> + <inputs> + <!-- the genome --> + <param type="data" name="fasta" format="fasta" help="Please upload an genome file of a bacteriophage in fasta format." label="Bacteriophage genome" /> + <param name="db_cached" type="select" label="Using built-in pharokka DB" help="Using built-in pharokka DB"> + <options from_data_table="pharokka_db"> + </options> + <validator type="no_options" message="A built-in pharokka DB is not available. Please ask the galaxy admins to install one on the server." /> + </param> + <param name="gene_predictor" type="select" label="User specified gene predictor"> + <option value="-g phanotate"> + Phanotate + </option> + <option value="-g prodigal"> + Prodigal + </option> + </param> + <param name="meta" type="boolean" checked="false" truevalue="--meta" falsevalue="" label="meta mode for metavirome input samples" /> + <param name="evalue" type="float" value="1E-5" min="1E-20" max="10" label="E-value threshold for mmseqs2 PHROGs database search. Defaults to 1E-05." /> + <!-- optional arguments --> + <conditional name="terminase"> + <param name="terminase_selector" type="select" label="Runs - terminase large subunit - re-orientation mode. Single genome input only and requires --terminase_strand and --terminase_start to be specified."> + <option value="no_terminase"> + Do not run 'terminase large subunit' re-orientation mode. + </option> + <option value="run_terminase"> + Runs 'terminase large subunit' re-orientation mode. + </option> + </param> + <when value="no_terminase"> + </when> + <when value="run_terminase"> + <param name="terminase_strand" type="select" label="Strand of terminase large subunit."> + <option value="pos"> + Positive + </option> + <option value="neg"> + Negative + </option> + </param> + <param name="terminase_start" type="integer" value="1" label="Start coordinate of the terminase large subunit." /> + </when> + </conditional> + <!-- optional outputs --> + <param name="zip_output" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Create a Zip archive of the complete output for further investigation." /> + </inputs> + <outputs> + <data name="pharokka_gbk" format="genbank" from_work_dir="pharokka_output/pharokka.gbk" label="${tool.name} on ${on_string}: Genbank" /> + <data name="pharokka_gff" format="gff" from_work_dir="pharokka_output/pharokka.gff" label="${tool.name} on ${on_string}: GFF" /> + <data name="archive_output" format="zip" from_work_dir="out.zip" label="${tool.name} on ${on_string}: zip of the complete output" > + <filter>zip_output</filter> + </data> + + </outputs> + <tests> + <!-- test input from DB - no zip --> + <test expect_num_outputs="2"> + <param name="db_cached" value="pharokka_db" /> + <param name="fasta" value="SAOMS1.fasta" /> + <param name="zip_output" value="false" /> + <!-- check file size and text since output is non-deterministic --> + <output name="pharokka_gbk"> + <assert_contents> + <has_size value="353875" delta="10" /> + <has_text text="VERSION MW460250_1" /> + </assert_contents> + </output> + <output name="pharokka_gff"> + <assert_contents> + <has_size value="191497" delta="10" /> + <has_text text="##sequence-region MW460250_1 1 140135" /> + </assert_contents> + </output> + </test> + <!-- test input from DB --> + <test expect_num_outputs="3"> + <param name="db_cached" value="pharokka_db" /> + <param name="fasta" value="SAOMS1.fasta" /> + <param name="zip_output" value="true" /> + <!-- check file size and text since output is non-deterministic --> + <output name="pharokka_gbk"> + <assert_contents> + <has_size value="353875" delta="10" /> + <has_text text="VERSION MW460250_1" /> + </assert_contents> + </output> + <output name="pharokka_gff"> + <assert_contents> + <has_size value="191497" delta="10" /> + <has_text text="##sequence-region MW460250_1 1 140135" /> + </assert_contents> + </output> + <!-- check created zip --> + <output name="archive_output"> + <assert_contents> + <has_archive_member path=".*\/pharokka\.gff" /> + <has_archive_member path=".*\/pharokka\.gbk" /> + <has_archive_member path=".*\/pharokka.*\.log" /> + </assert_contents> + </output> + </test> + </tests> + <help> + <![CDATA[ + Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. + Pharokka identifies predicted coding sequences (CDS), transfer RNAs (tRNAs), + transfer-messenger RNAs (tmRNAs) and clustered regularly interspaced short + palindromic repeats (CRISPRs), providing functional annotation for CDS using the PHROGs database. + + Pharokka requires assembled DNA sequences in FASTA format. + For phage isolates, this usually consists of one complete contig, + but Pharokka can also annotate incomplete assemblies or metavirome samples with multiple + contigs in the multiFASTA format. + Furthermore, metagenomically assembled phage genomes and genomic contigs, + derived using programs such as Virstorter2, Hecatomb and Cenote-taker 2, + are also suitable to be annotated using Pharokka using meta mode. + + If you are looking for rapid standardised annotation of bacterial genomes, please use bakta. + ]]> + </help> + <expand macro="citations" /> + <expand macro="creator" /> +</tool> |
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| diff -r 000000000000 -r 1d4fcd38d899 test-data/SAOMS1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAOMS1.fasta Thu Mar 02 16:21:40 2023 +0000 |
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| b'@@ -0,0 +1,2003 @@\n+>MW460250_1\n+CCCCACCCCGCCATCCCCGATTCATGAGCTATGTTCTAAGTCGATACCATTTAATAAGATAGGGTCATCT\n+TCTTTACCTACCATATAATCAGATAGTAAGTCTGCTTCAGCTTTTTGCCCTGGTCGTGATAGTTTAGATT\n+TCTTAGTTTCAATACGCATAATGTGACCATTGTATTAAATAATTAGAATACTATTTTAAAAGATTCTATT\n+CTGTTTGGATTAATATATACTTGAGGTGAAGTTATAGCACTTTCAGTATATACTTTTATAGAGGTTTCAT\n+CCATTCCTCTTAACATATAATCTATATCTTGCCTATTGTAACTCTTTTCATCAGTAGATACTAAAAAGTA\n+TTTAGCTCCACTTGACATTGTTATTTCAATATGTTTTGACATCTACAATCTCTCCTATGCAAATTTGTTA\n+AAGACAAAGGATAATATAGCTCCTAGAACAAGTAAAAGAACCTTCTCAGTTGTATCCTTTTTCTCAGTAT\n+CCTTAGTTTTTGTACTTTCAGCAAGTTCTGAAATCTTTTCATCAAGTCTTTCTAATTGGACGTAAATTGC\n+TGATTGTTTTTCACTATTGACAGCTACATCTTTATCTATACTAACTATCATTTTTCTTAGTTCAGCTACC\n+TCAACTTCTAAATCTTTGAAAGTTCCTCTATCTATATAATTACCTTCTTGTATCTTAGACTTAATAGTTT\n+CTACTTGAGAAACAAGGTTGTTTATCTCCTTATCCAACTAGAATCACCTCTAAGGTCTAACCGTTTCAGA\n+TTCAGAATGGATATCATAATTTTCTAAGAAATCATTGATAATCTCCATATAATTATCCGTAACGACTTTT\n+CCGTAAGATGTTTTTGTATCAATTTCAAACCTAAGCTTACCAAAACTTTGGAGGTCTAATTCTTTTATTA\n+CAATATTAGGGTCATCAGAAGGAAGGTAATAATAGTCGAAGTATATAATTGAGCCATTTATTAATACTCT\n+GTCTATTCTATAGACGTGGAAATAGCGTCTGTCTCTTTTAAAATGGGCTAGTGCATCTTTAAACTCTAAC\n+TTAAGGATATCCTTATATTTAATCAAAGTGGTAACCTCCTTACTATTAATTTTTAAATTTACTTATTTTG\n+TGGTATAATAGTTATGATAAAGGCAGTTATTATAATTATATTAAGAATAATGATAATAATTATTTTTTCT\n+GAGAAAATAAGCCAAATACTAAAAACAGATAAAGCATAGATAGCTGATAGATATACTATATTAAGAGTTA\n+CCTTACTTTTATCTTTTCTATAGATAGAATAACCTAAAGACGTTGTAACACCACTAAGTATAAAATAATA\n+GAAACAAAAAAGAGGTATAGACAGAAAAAAAGATACGATAATCATTGTTAAACACCTATTTCTTTTTGAC\n+CTATTATTTCTAGAACTTTTAGATTACACCACTAATATAACATTAAAAGCCAGTCATAAAAGTCAATTGT\n+TAGATTAATAATATAATAAAAAAAGACAATAGGAGGTTAAAGTGGTTGAATAATAACATAGCTATATTCA\n+TATTCAAAACACTGGTTATCATTATATTCTTACTACTAATTTTGTCTGTTATTAATTCCTTGTCCCTTAT\n+TTACTCAATAAGACCGAGTGTAGTTATGACATACTTTATCTTTGGTGGTATTGTTTCTAATGTCGCACTT\n+ACTGTAACAGATAAGTTCTTACTGAAGAAAGAAGACCCCCTACCTGAATATGTTCTTAAAAAAGTAGAGA\n+TAAATGATAAAGAAATAAGAATAATCAAGAAAATAATAGAAAGTAATTATGGTATAACAGCAGAAGAGAT\n+AAAAGTTAGGGCTAAAGCACAAAGAAGAGTAGAGGAAGATAGTAAAAAGGAAGATTACAATGAAAACAAA\n+GAAAGAAATTAAAGAACAAAGGAAAGAACTTAAGGATGGTGCTACATCTGTTTCTTTAGTAAAAAAGGGA\n+GATAAGAGAATAGCTAGCCCTAGTAGAATCTGTAGTCTATGTGGTCAGCAGTTATCAGGTATGAATTACA\n+CTAAAGGAAAAGCATTATCAAAAGTTAATCATTTTCATTTACAGTATTCTAAGTATATTTATTTTGATAT\n+TTGCGCAGATATCAACAATTGTTATAAAAATTTAAGAAAACGAGGTGAAATGGATTGAGTGCAGAAAATA\n+TTAGAGATATAATTAACAAGAAAAAGTTAGAAGAAGAGGATACAAGAAAATATATAGCTGATGGGTTTAT\n+GAATGGTATCGGTAAATTAATGTACGAATTCAATAAGAAAGTAGATAACAAAGAAATAGAAGTTAAAGAC\n+CCGAATGATTTATACAAATTATTTGTGATATTCTCTCAAATGCAAAATATGGTCAATGAAACTTCTGAAG\n+GAGGAGCAATACCTCAACTATCTAGACCTCAACAGGAATTATTTGATGAGATTACAACAGAAGATAGTAA\n+TGGAGAATCTACAGTTGATTTACAGAAGATATCAGAAATGTCAGCGGAAGATATTACAGCAATGATTTCT\n+GAAAAGGAAAAAGTAATGAATGAGGAAAATTCAGAAACATTCTAAGGAGAAAGATATAAATGGATGGAAA\n+AGAACTAATTAAGATAGCACAAGAAACATTTCAAACTGAAAAAATAACAAGAGAACAGATAGACCATATA\n+ATCAATATGCTAAATCCTTCTACCTATATGCTTAAGTATCATACACTGAGAGGGCATCCTATAACTTTTA\n+GTATTCCTAATAGAGATAGAAGTAAAGCACAGGCTCATAGACCGTAAATTTTGTTGCGGTCTCTAAACTC\n+TGTTAAACGGGCATAGTAAAATAATGTATAGAAAAATAATATACTGGTAAGAAACCCTAAATCTGACTAT\n+ACACAGACAGTGGGAACCAACCGTGCTAAATCTGTAATTTAATTATTGACAAAATAACAATATATGATAT\n+AATTATATTATAGTAAAAGCCTAACGACTAAATTTCTAGTTATCTATATAAATGGATATAGTGAGAACTA\n+GATAAGAAAATTAACTATACTTAAAAAAACTAAAATATTTTAAAAGAGAGGTGAAAACAGTTGACATTAG\n+AAAAGAGAAAACAAGAATATCTTAAGAAGTTAAAGCAAATTAAAAATGATGAGTTTGAATTGCTAGGAGG\n+ATTTACTAAAACAAGAGAGAAAGCTTTATTTAAACATAAAGTTTGTGGTTATGAATGGTATACTACTCCT\n+TATAATTTATTGAAGTCTAAAGGGACAGGATGTCCTAAATGTCAATACAGAGATAAATCATATACTACTG\n+ATGAATTTAAAAAGAAACTTAAAGATAAATTTGGTTATGAATATGAGTTAATAGAAGGACAAGAGTATAA\n+AAATAGTAGAGAAAAATTATTGTTTATTCATAATAAGTGCGGTACTGAATTTAAAATTACAAGTGATAGT\n+TTATTTCGAAGTAAAGTACCTTGTCATAAATGTTCTAAAGAAAATAGAAAAACTAAAAAGAAAACAACAG\n+AACAGTTTAAAAATGAATTGTATAATAAACATAAAGATGAATATATACTTGTTGAAGGGTCAGAATATAA\n+GACAGCTCTTGAAAAGGTTAGAATAATTCATACGAAATGTGGATATACATGGGATGTTAGAGCCTCACAT\n+ATTTTGCATACTAGTAAATGTCCTAATTGTAATGAGTCTAAAGGTGAGAGTTTAATTAAAGACATTCTTG\n+AAGATAATAATTTTTCTTATATAAGAGAGTATACTTTTGAAGATTTAAAGAATGTTAAAAAATTACCTTT\n+TGATTTTGCACTATTCATTGATAATGAATTAGTAGGTTTAATTGAATATGATGGTTCTCAACACTTTATT\n+CCTTTT'..b'TAAATTTCCTACACTATTATCATTTTTACCATTTAAATGGTTA\n+ACTTGTTCTTTATTATCAGGATTAGGTATAAAAGCCATAGCAACTAAACGATGTATTTTAGGTGAATGGT\n+ATCGTAACCTTACAAACAAGTAACCCTTGTTATTTTTTTGAAGTTTTAACTTTTTAGGCTCTTTACCTTT\n+ATAAGATATTACTTCTCCTTTATCAGTAATAGTGTAATTTTCATATATTTCTAATCCAGGTATTTCATTT\n+AATTTCTTTTCCATAATAACATCTCCTTTACTTAAGTATATAGGAAAGTTATTATGTTGTCAAGTAGTTT\n+TTTAAAACAATATTCTTGGATGCTGATTAGCATAGCTTGATAGCCTTAGCCTCCCAGTCAATTAAAAGAA\n+CTTTCATTATACATTACTGTATAACAGGGCAATTTATTTACCCGTGTGCCAAGCAATTTGATTCTTAGCA\n+TCTATTGCTTCCCATACATAACCTTCAGAGCCGTAGTAATGAGCAATACCATTAGCGTATCTAGCATAAC\n+CTGCATTAGCTAATGAATTCTCGTATTGTTGTCCTGAAGAACGACCTGCATCGTTGTGTATTACCATTCC\n+TTCAGGTTTTTTACCACGTTTATCCATTGTATAGTTAATGTGATTCTTAGAAACTTTTAGTGTTGCTTTC\n+TTTTTAGGTGCAGGCGTTTTACTTGCGCTTTTCTTAGCTGTTTCTTTTTTAACAGTAGTTCCTGCTTTTA\n+CAGGTATTTCAATGAAGTGAGTTAATCCGTAATAATTATCTACACGTTTTGTAGGTTTTTTATTAGCATA\n+ACCATTCCAGTTTTGCTCTAAAATAGTAAATGTAGAAGTATTACCTCCATCATATACAATACCTATGTGA\n+CCCCACTGTTCATAACTACCGGATGTAAATACCGCAATCCAACCTTTTTTAGGTACAGTAGAAGGTTTAT\n+TTTCATGTATTTTAAATCCAGTACCATAACTCTGTTTAATTTGGTCTTTAGCATTACCCCAAGTTCTAAC\n+TTTATTATCTGTTAACCATAAAACATAGTCTGTAATAAGGTCTTGACACTGAGCGTGATAGTAACCATCT\n+GCATCAATGGCTCCTGCTTCCATTACACCAAATGATGGGTCATAACTTGTAGCTTTTTTAACTCTGTAAG\n+GGCTATCTACTGTTCCTTTTGCATAAGCATCTAAACGTTTATTTATTTCTGCTTGAGTCTTAGCCATTAC\n+TTAACTTCCTCCTCTGCAAATACTTTACCATGTTCCTCGGTATCTTCTTCATCTTGAGAAGGTGCTGAAC\n+CACCATCAATTTCATCTTCAATAGCAGGTACTTCATCACTATCATCTGTGTCAGGTTCTGCATTGTTTTC\n+GTAGCTGTCTATCTCAAAAGTACTAGTGTTATTTGCATTTGCTTGCCATTGAACGAATTCATTAGGGTCT\n+TTACTATCACGAGGTTTAAGATAGTCTGTTTGAACAATATCACTATCTTTAAGACCTTTAGTATTATTAT\n+CAACAATAATACCTAAACCTGCTAATAGTGTTAGTATAGAACCTACAATATTTACACCTTGCTCAATTTG\n+AGCTGAGTAGTCTAAACCGAAAGCACCTATAATTTGGTTAGCAAATAATGCTACTGCTGATATAATTGCT\n+ACCCAAAATGTTTTGCTCTTAGTTCTTGTGCTAAGGTTTATTCCTCCAACAACTTTAGGTTGTTTAGTTT\n+CATTAGCCATTAAAAAACCGACCTTTCTATTATATTTATTTCTAACAATAATATAACAGTAGGTCGGTCA\n+TGTTTATCTATATTAATTTAACACTTACTCATTAATTTGGTTTAGTTTTTTGATAACTTCAGACATTTGT\n+TTGTTATCTAAATCTTCTAATTTAGTTTCAGGAAGTAGCTCTAACTTATCCCAAACTTCTTCTTTATTAG\n+ATACTTTATTATTAATAATTGCCTTACCAACTAAACTTTCCGTATAATATAATTGTTTTGCTGATGCCAT\n+TTGTATCTCTCCTTTTAAATATGTAAAGTATATAGCTAGTATCGTATCCTAGGAACAAACACTTGCGCTA\n+TATACTCAATGAAATCCTACCCTCATTCGAGGACACAGCAAACCGGTTCGTCAACCGCACATATGAATTC\n+TCAGATTTCATTTATGTAAAACACACCCTCTTTGATTTGCACAAAGACTAAGGGTTTTGGAGACCCTTGT\n+ACTACTAATTATACTAAGGGTGTTTATTATGGTTTCTATTGGATTTGAACCAATGACACCTAGAGCTTCA\n+ATCTAGTGCTCTACCATCTGAGCTAAGAAACCTTAAAACGACCCATACGAGACTCGAACTCGTACTCTCT\n+GCCGTGACAGGGCAGTGTGTTAACCAGTTACACCAATGAGCCAAAATTATAATGCTATACCCTAACCTTA\n+CCTTAATGTATAGCAGGTTTTTATATAAGCTCGAAGCAACGATTATTACCACTCATAACAACTATATATT\n+AAGTGAAAGGAGGTGAAATGAACAAAACGTGGTAATTGGTACTTATATAGGAAATATGTATAATCTACAA\n+GGAGTAAGTTATTGGTTCATAAAGGAGTGTGAACAATAAATACATGAAAGAGTGAAAGTTTACTCCCTGT\n+AGATTCTTTTTTTAATTATCAATCAAAGGAGGAAACTGATAATTGTTAATAATAAACTATAAAGAGGAAA\n+ATATTTATAGTCACATTCTGATATAATGCAACTAAATATCCAAGCATAACCCGTCTCACGAGGAACCTAC\n+CTATAAGACCTGTTATTAAGTGAATCACTACGATTGACTCTATTAAGGAGCTACCTTAAGTCCATCTCAC\n+GCAATTTAAAAGGGACTTACAAACCGTAAAACGGTAATAAGTTTATTAAATAATGTGATATTAACATATT\n+AGTTAATAACTTTCACATGGTCGAAGAAAAGTAAATTTATTTGATTACCAAATTATTTTTATCAAATATA\n+GCTCTTTTGAACCTGTAGATTTATGCTACTTATACTGATAACCTCTATTATCTAACACATTTCTGTGCTC\n+CAACTACAGTTAGTCGTTACAGCGTATCTTTCTAGGATTCCGCTAAGACCCTAAAAAGAAATTAAACCCT\n+AGCCGTTATCATACTCTACAGACCTTATAAGTAAGTACCAAGTATACCAATCGTATTTAACAATACTAAT\n+GACGACCCATCCTACCGATATATCTCCGATAGGTTTTGATTCGTTTGATTATCTTGTACCTTATGACTAC\n+CAAATCATTATTCAGTCACTATGCTCAGATATTTAGTTGTATTATTTATATATTAATTATAACATAATTT\n+TTATTACTTGTCAAGTTAATTTCAAAAAAATTATAGAAGTAGGGACGTTTACCTACTTCTATTTAATTTA\n+CACAAGGATGATAACATTGTTATTGTTTTATACTGGAAAACAATGTAATAAAAACAGTGATGTGTAAGGT\n+ATTTGTTTTATTGTTAATTATATTATAGCATATACTGATACCTTTGTCAAGTTAATTTAATACTTTTTTT\n+AAAACATTAGTTATCTTTTGTTAGTTCCTCCTGAATAGCATCCCATCTTCTTTCTGCTTCACTACGATTA\n+TCTTCTATATGTTTTGTAGTTTTACAACATTTGATACAATATATATCTTTGATATGACCTTCTTCTCTTT\n+TATTTGCTCTTTTTCTTGGTACTTTGAATACATTTCCACATTCTTTACATATTAAACTTGAGTAAAACAT\n+TTTTTGTCTTTTCATAATTAATCAATTCCTTTTCTCTTTTATTTGATAATTTAACTATATACTATATTGA\n+TAAATAAGTCAACAGTTTTCTAAAAATAATTTAAATTATTTTGAAGAATACTTTAATATCAAGGG\n' |
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| diff -r 000000000000 -r 1d4fcd38d899 test-data/pharokka.gbk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pharokka.gbk Thu Mar 02 16:21:40 2023 +0000 |
| b |
| b'@@ -0,0 +1,5739 @@\n+LOCUS MW460250_1 140135 bp DNA linear VRL 14-FEB-2023\n+DEFINITION MW460250_1.\n+ACCESSION MW460250_1\n+VERSION MW460250_1\n+KEYWORDS .\n+SOURCE .\n+ ORGANISM .\n+ .\n+FEATURES Location/Qualifiers\n+ CDS complement(22..159)\n+ /ID="SLQLISVF_CDS_0001"\n+ /phrog="No_PHROG"\n+ /top_hit="No_PHROG"\n+ /locus_tag="SLQLISVF_CDS_0001"\n+ /function="unknown function"\n+ /product="hypothetical protein"\n+ /source="PHANOTATE"\n+ /score="-15.399247982708186"\n+ /phase="0"\n+ /translation="MRIETKKSKLSRPGQKAEADLLSDYMVGKEDDPILLNGIDLEHSS\n+ "\n+ CDS complement(183..392)\n+ /ID="SLQLISVF_CDS_0002"\n+ /phrog="No_PHROG"\n+ /top_hit="No_PHROG"\n+ /locus_tag="SLQLISVF_CDS_0002"\n+ /function="unknown function"\n+ /product="hypothetical protein"\n+ /source="PHANOTATE"\n+ /score="-39.52422521577095"\n+ /phase="0"\n+ /translation="MSKHIEITMSSGAKYFLVSTDEKSYNRQDIDYMLRGMDETSIKVY\n+ TESAITSPQVYINPNRIESFKIVF"\n+ CDS complement(405..737)\n+ /ID="SLQLISVF_CDS_0003"\n+ /phrog="No_PHROG"\n+ /top_hit="No_PHROG"\n+ /locus_tag="SLQLISVF_CDS_0003"\n+ /function="unknown function"\n+ /product="hypothetical protein"\n+ /source="PHANOTATE"\n+ /score="-307.9875183481112"\n+ /phase="0"\n+ /translation="LDKEINNLVSQVETIKSKIQEGNYIDRGTFKDLEVEVAELRKMIV\n+ SIDKDVAVNSEKQSAIYVQLERLDEKISELAESTKTKDTEKKDTTEKVLLLVLGAILSF\n+ VFNKFA"\n+ CDS complement(750..1076)\n+ /ID="SLQLISVF_CDS_0004"\n+ /phrog="No_PHROG"\n+ /top_hit="No_PHROG"\n+ /locus_tag="SLQLISVF_CDS_0004"\n+ /function="unknown function"\n+ /product="hypothetical protein"\n+ /source="PHANOTATE"\n+ /score="-8.448608623432387"\n+ /phase="0"\n+ /translation="LIKYKDILKLEFKDALAHFKRDRRYFHVYRIDRVLINGSIIYFDY\n+ YYLPSDDPNIVIKELDLQSFGKLRFEIDTKTSYGKVVTDNYMEIINDFLENYDIHSESE\n+ TVRP"\n+ CDS complement(1109..1375)\n+ /ID="SLQLISVF_CDS_0005"\n+ /phrog="No_PHROG"\n+ /top_hit="No_PHROG"\n+ /locus_tag="SLQLISVF_CDS_0005"\n+ /function="unknown function"\n+ /product="hypothetical protein"\n+ /source="PHANOTATE"\n+ /score="-7.658463659485386"\n+ /phase="0"\n+ /translation="MIIVSFFLSIPLFCFYYFILSGVTTSLGYSIYRKDKSKVTLNIVY\n+ LSAIYALSVFSIWLIFSEKIIIIIILNIIIITAFIITIIPQNK"\n+ CDS complement(1470..1562)\n+ /ID="SLQLISVF_CDS_0006"\n+ /phrog="No_PHROG"\n+ /top_hit="No_PHROG"\n+ /locus_tag="SLQLISVF_CDS_0006"\n+ /function="unknown function"\n+ /product="hypothetical protein"\n+ /source="PHANOTATE"\n+ /score="-0.9164331843686035"\n+ /phase="0"\n+ /translation="MITSVLNMNIAMLLFNHFNLLLSFFIILLI"\n+ CDS 1636..1902\n+ /ID="SLQLISVF_CDS_0007"\n+ /phrog="No_PHROG"\n+ /top_hit="No_P'..b'attatc tacacgtttt\n+ 137041 gtaggttttt tattagcata accattccag ttttgctcta aaatagtaaa tgtagaagta\n+ 137101 ttacctccat catatacaat acctatgtga ccccactgtt cataactacc ggatgtaaat\n+ 137161 accgcaatcc aacctttttt aggtacagta gaaggtttat tttcatgtat tttaaatcca\n+ 137221 gtaccataac tctgtttaat ttggtcttta gcattacccc aagttctaac tttattatct\n+ 137281 gttaaccata aaacatagtc tgtaataagg tcttgacact gagcgtgata gtaaccatct\n+ 137341 gcatcaatgg ctcctgcttc cattacacca aatgatgggt cataacttgt agctttttta\n+ 137401 actctgtaag ggctatctac tgttcctttt gcataagcat ctaaacgttt atttatttct\n+ 137461 gcttgagtct tagccattac ttaacttcct cctctgcaaa tactttacca tgttcctcgg\n+ 137521 tatcttcttc atcttgagaa ggtgctgaac caccatcaat ttcatcttca atagcaggta\n+ 137581 cttcatcact atcatctgtg tcaggttctg cattgttttc gtagctgtct atctcaaaag\n+ 137641 tactagtgtt atttgcattt gcttgccatt gaacgaattc attagggtct ttactatcac\n+ 137701 gaggtttaag atagtctgtt tgaacaatat cactatcttt aagaccttta gtattattat\n+ 137761 caacaataat acctaaacct gctaatagtg ttagtataga acctacaata tttacacctt\n+ 137821 gctcaatttg agctgagtag tctaaaccga aagcacctat aatttggtta gcaaataatg\n+ 137881 ctactgctga tataattgct acccaaaatg ttttgctctt agttcttgtg ctaaggttta\n+ 137941 ttcctccaac aactttaggt tgtttagttt cattagccat taaaaaaccg acctttctat\n+ 138001 tatatttatt tctaacaata atataacagt aggtcggtca tgtttatcta tattaattta\n+ 138061 acacttactc attaatttgg tttagttttt tgataacttc agacatttgt ttgttatcta\n+ 138121 aatcttctaa tttagtttca ggaagtagct ctaacttatc ccaaacttct tctttattag\n+ 138181 atactttatt attaataatt gccttaccaa ctaaactttc cgtataatat aattgttttg\n+ 138241 ctgatgccat ttgtatctct ccttttaaat atgtaaagta tatagctagt atcgtatcct\n+ 138301 aggaacaaac acttgcgcta tatactcaat gaaatcctac cctcattcga ggacacagca\n+ 138361 aaccggttcg tcaaccgcac atatgaattc tcagatttca tttatgtaaa acacaccctc\n+ 138421 tttgatttgc acaaagacta agggttttgg agacccttgt actactaatt atactaaggg\n+ 138481 tgtttattat ggtttctatt ggatttgaac caatgacacc tagagcttca atctagtgct\n+ 138541 ctaccatctg agctaagaaa ccttaaaacg acccatacga gactcgaact cgtactctct\n+ 138601 gccgtgacag ggcagtgtgt taaccagtta caccaatgag ccaaaattat aatgctatac\n+ 138661 cctaacctta ccttaatgta tagcaggttt ttatataagc tcgaagcaac gattattacc\n+ 138721 actcataaca actatatatt aagtgaaagg aggtgaaatg aacaaaacgt ggtaattggt\n+ 138781 acttatatag gaaatatgta taatctacaa ggagtaagtt attggttcat aaaggagtgt\n+ 138841 gaacaataaa tacatgaaag agtgaaagtt tactccctgt agattctttt tttaattatc\n+ 138901 aatcaaagga ggaaactgat aattgttaat aataaactat aaagaggaaa atatttatag\n+ 138961 tcacattctg atataatgca actaaatatc caagcataac ccgtctcacg aggaacctac\n+ 139021 ctataagacc tgttattaag tgaatcacta cgattgactc tattaaggag ctaccttaag\n+ 139081 tccatctcac gcaatttaaa agggacttac aaaccgtaaa acggtaataa gtttattaaa\n+ 139141 taatgtgata ttaacatatt agttaataac tttcacatgg tcgaagaaaa gtaaatttat\n+ 139201 ttgattacca aattattttt atcaaatata gctcttttga acctgtagat ttatgctact\n+ 139261 tatactgata acctctatta tctaacacat ttctgtgctc caactacagt tagtcgttac\n+ 139321 agcgtatctt tctaggattc cgctaagacc ctaaaaagaa attaaaccct agccgttatc\n+ 139381 atactctaca gaccttataa gtaagtacca agtataccaa tcgtatttaa caatactaat\n+ 139441 gacgacccat cctaccgata tatctccgat aggttttgat tcgtttgatt atcttgtacc\n+ 139501 ttatgactac caaatcatta ttcagtcact atgctcagat atttagttgt attatttata\n+ 139561 tattaattat aacataattt ttattacttg tcaagttaat ttcaaaaaaa ttatagaagt\n+ 139621 agggacgttt acctacttct atttaattta cacaaggatg ataacattgt tattgtttta\n+ 139681 tactggaaaa caatgtaata aaaacagtga tgtgtaaggt atttgtttta ttgttaatta\n+ 139741 tattatagca tatactgata cctttgtcaa gttaatttaa tacttttttt aaaacattag\n+ 139801 ttatcttttg ttagttcctc ctgaatagca tcccatcttc tttctgcttc actacgatta\n+ 139861 tcttctatat gttttgtagt tttacaacat ttgatacaat atatatcttt gatatgacct\n+ 139921 tcttctcttt tatttgctct ttttcttggt actttgaata catttccaca ttctttacat\n+ 139981 attaaacttg agtaaaacat tttttgtctt ttcataatta atcaattcct tttctctttt\n+ 140041 atttgataat ttaactatat actatattga taaataagtc aacagttttc taaaaataat\n+ 140101 ttaaattatt ttgaagaata ctttaatatc aaggg\n+//\n' |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/pharokka.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pharokka.gff Thu Mar 02 16:21:40 2023 +0000 |
| b |
| b'@@ -0,0 +1,2589 @@\n+##gff-version 3\n+##sequence-region MW460250_1 1 140135\n+MW460250_1\tPHANOTATE\tCDS\t22\t159\t-15.399247982708186\t-\t0\tID=SLQLISVF_CDS_0001;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0001;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t183\t392\t-39.52422521577095\t-\t0\tID=SLQLISVF_CDS_0002;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0002;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t405\t737\t-307.9875183481112\t-\t0\tID=SLQLISVF_CDS_0003;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0003;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t750\t1076\t-8.448608623432387\t-\t0\tID=SLQLISVF_CDS_0004;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0004;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t1109\t1375\t-7.658463659485386\t-\t0\tID=SLQLISVF_CDS_0005;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0005;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t1470\t1562\t-0.9164331843686035\t-\t0\tID=SLQLISVF_CDS_0006;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0006;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t1636\t1902\t-288.8081246860113\t+\t0\tID=SLQLISVF_CDS_0007;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0007;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t1880\t2158\t-76.27345803195993\t+\t0\tID=SLQLISVF_CDS_0008;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0008;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t2239\t2565\t-866.1511100970354\t+\t0\tID=SLQLISVF_CDS_0009;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0009;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t2580\t2777\t-82.44911427554912\t+\t0\tID=SLQLISVF_CDS_0010;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0010;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t3071\t4042\t-2179259576.416292\t+\t0\tID=SLQLISVF_CDS_0011;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0011;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t4183\t5730\t-664781254181330.5\t+\t0\tID=SLQLISVF_CDS_0012;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0012;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t5723\t6544\t-111100907389.75069\t+\t0\tID=SLQLISVF_CDS_0013;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0013;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t6615\t6704\t-6.909502262400356\t+\t0\tID=SLQLISVF_CDS_0014;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0014;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t6701\t7180\t-3232611.9712114143\t+\t0\tID=SLQLISVF_CDS_0015;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0015;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t7273\t8415\t-175147462430.0088\t+\t0\tID=SLQLISVF_CDS_0016;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0016;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t8558\t8842\t-706.13273617966\t+\t0\tID=SLQLISVF_CDS_0017;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0017;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t8920\t9231\t-751.5376752780932\t+\t0\tID=SLQLISVF_CDS_0018;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0018;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t9235\t10926\t-1.1007237496073629e+17\t+\t0\tID=SLQLISVF_CDS_0019;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0019;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCDS\t11153\t11893\t-27852504.233262\t+\t0\tID=SLQLISVF_CDS_0020;phrog=No_PHROG;top_hit=No_PHROG;locus_tag=SLQLISVF_CDS_0020;function=unknown function;product=hypothetical protein\n+MW460250_1\tPHANOTATE\tCD'..b'ATCATTTTTACCATTTAAATGGTTAACTTGTTCTTTATTATCAGGATTAGGTATA\n+AAAGCCATAGCAACTAAACGATGTATTTTAGGTGAATGGTATCGTAACCTTACAAACAAG\n+TAACCCTTGTTATTTTTTTGAAGTTTTAACTTTTTAGGCTCTTTACCTTTATAAGATATT\n+ACTTCTCCTTTATCAGTAATAGTGTAATTTTCATATATTTCTAATCCAGGTATTTCATTT\n+AATTTCTTTTCCATAATAACATCTCCTTTACTTAAGTATATAGGAAAGTTATTATGTTGT\n+CAAGTAGTTTTTTAAAACAATATTCTTGGATGCTGATTAGCATAGCTTGATAGCCTTAGC\n+CTCCCAGTCAATTAAAAGAACTTTCATTATACATTACTGTATAACAGGGCAATTTATTTA\n+CCCGTGTGCCAAGCAATTTGATTCTTAGCATCTATTGCTTCCCATACATAACCTTCAGAG\n+CCGTAGTAATGAGCAATACCATTAGCGTATCTAGCATAACCTGCATTAGCTAATGAATTC\n+TCGTATTGTTGTCCTGAAGAACGACCTGCATCGTTGTGTATTACCATTCCTTCAGGTTTT\n+TTACCACGTTTATCCATTGTATAGTTAATGTGATTCTTAGAAACTTTTAGTGTTGCTTTC\n+TTTTTAGGTGCAGGCGTTTTACTTGCGCTTTTCTTAGCTGTTTCTTTTTTAACAGTAGTT\n+CCTGCTTTTACAGGTATTTCAATGAAGTGAGTTAATCCGTAATAATTATCTACACGTTTT\n+GTAGGTTTTTTATTAGCATAACCATTCCAGTTTTGCTCTAAAATAGTAAATGTAGAAGTA\n+TTACCTCCATCATATACAATACCTATGTGACCCCACTGTTCATAACTACCGGATGTAAAT\n+ACCGCAATCCAACCTTTTTTAGGTACAGTAGAAGGTTTATTTTCATGTATTTTAAATCCA\n+GTACCATAACTCTGTTTAATTTGGTCTTTAGCATTACCCCAAGTTCTAACTTTATTATCT\n+GTTAACCATAAAACATAGTCTGTAATAAGGTCTTGACACTGAGCGTGATAGTAACCATCT\n+GCATCAATGGCTCCTGCTTCCATTACACCAAATGATGGGTCATAACTTGTAGCTTTTTTA\n+ACTCTGTAAGGGCTATCTACTGTTCCTTTTGCATAAGCATCTAAACGTTTATTTATTTCT\n+GCTTGAGTCTTAGCCATTACTTAACTTCCTCCTCTGCAAATACTTTACCATGTTCCTCGG\n+TATCTTCTTCATCTTGAGAAGGTGCTGAACCACCATCAATTTCATCTTCAATAGCAGGTA\n+CTTCATCACTATCATCTGTGTCAGGTTCTGCATTGTTTTCGTAGCTGTCTATCTCAAAAG\n+TACTAGTGTTATTTGCATTTGCTTGCCATTGAACGAATTCATTAGGGTCTTTACTATCAC\n+GAGGTTTAAGATAGTCTGTTTGAACAATATCACTATCTTTAAGACCTTTAGTATTATTAT\n+CAACAATAATACCTAAACCTGCTAATAGTGTTAGTATAGAACCTACAATATTTACACCTT\n+GCTCAATTTGAGCTGAGTAGTCTAAACCGAAAGCACCTATAATTTGGTTAGCAAATAATG\n+CTACTGCTGATATAATTGCTACCCAAAATGTTTTGCTCTTAGTTCTTGTGCTAAGGTTTA\n+TTCCTCCAACAACTTTAGGTTGTTTAGTTTCATTAGCCATTAAAAAACCGACCTTTCTAT\n+TATATTTATTTCTAACAATAATATAACAGTAGGTCGGTCATGTTTATCTATATTAATTTA\n+ACACTTACTCATTAATTTGGTTTAGTTTTTTGATAACTTCAGACATTTGTTTGTTATCTA\n+AATCTTCTAATTTAGTTTCAGGAAGTAGCTCTAACTTATCCCAAACTTCTTCTTTATTAG\n+ATACTTTATTATTAATAATTGCCTTACCAACTAAACTTTCCGTATAATATAATTGTTTTG\n+CTGATGCCATTTGTATCTCTCCTTTTAAATATGTAAAGTATATAGCTAGTATCGTATCCT\n+AGGAACAAACACTTGCGCTATATACTCAATGAAATCCTACCCTCATTCGAGGACACAGCA\n+AACCGGTTCGTCAACCGCACATATGAATTCTCAGATTTCATTTATGTAAAACACACCCTC\n+TTTGATTTGCACAAAGACTAAGGGTTTTGGAGACCCTTGTACTACTAATTATACTAAGGG\n+TGTTTATTATGGTTTCTATTGGATTTGAACCAATGACACCTAGAGCTTCAATCTAGTGCT\n+CTACCATCTGAGCTAAGAAACCTTAAAACGACCCATACGAGACTCGAACTCGTACTCTCT\n+GCCGTGACAGGGCAGTGTGTTAACCAGTTACACCAATGAGCCAAAATTATAATGCTATAC\n+CCTAACCTTACCTTAATGTATAGCAGGTTTTTATATAAGCTCGAAGCAACGATTATTACC\n+ACTCATAACAACTATATATTAAGTGAAAGGAGGTGAAATGAACAAAACGTGGTAATTGGT\n+ACTTATATAGGAAATATGTATAATCTACAAGGAGTAAGTTATTGGTTCATAAAGGAGTGT\n+GAACAATAAATACATGAAAGAGTGAAAGTTTACTCCCTGTAGATTCTTTTTTTAATTATC\n+AATCAAAGGAGGAAACTGATAATTGTTAATAATAAACTATAAAGAGGAAAATATTTATAG\n+TCACATTCTGATATAATGCAACTAAATATCCAAGCATAACCCGTCTCACGAGGAACCTAC\n+CTATAAGACCTGTTATTAAGTGAATCACTACGATTGACTCTATTAAGGAGCTACCTTAAG\n+TCCATCTCACGCAATTTAAAAGGGACTTACAAACCGTAAAACGGTAATAAGTTTATTAAA\n+TAATGTGATATTAACATATTAGTTAATAACTTTCACATGGTCGAAGAAAAGTAAATTTAT\n+TTGATTACCAAATTATTTTTATCAAATATAGCTCTTTTGAACCTGTAGATTTATGCTACT\n+TATACTGATAACCTCTATTATCTAACACATTTCTGTGCTCCAACTACAGTTAGTCGTTAC\n+AGCGTATCTTTCTAGGATTCCGCTAAGACCCTAAAAAGAAATTAAACCCTAGCCGTTATC\n+ATACTCTACAGACCTTATAAGTAAGTACCAAGTATACCAATCGTATTTAACAATACTAAT\n+GACGACCCATCCTACCGATATATCTCCGATAGGTTTTGATTCGTTTGATTATCTTGTACC\n+TTATGACTACCAAATCATTATTCAGTCACTATGCTCAGATATTTAGTTGTATTATTTATA\n+TATTAATTATAACATAATTTTTATTACTTGTCAAGTTAATTTCAAAAAAATTATAGAAGT\n+AGGGACGTTTACCTACTTCTATTTAATTTACACAAGGATGATAACATTGTTATTGTTTTA\n+TACTGGAAAACAATGTAATAAAAACAGTGATGTGTAAGGTATTTGTTTTATTGTTAATTA\n+TATTATAGCATATACTGATACCTTTGTCAAGTTAATTTAATACTTTTTTTAAAACATTAG\n+TTATCTTTTGTTAGTTCCTCCTGAATAGCATCCCATCTTCTTTCTGCTTCACTACGATTA\n+TCTTCTATATGTTTTGTAGTTTTACAACATTTGATACAATATATATCTTTGATATGACCT\n+TCTTCTCTTTTATTTGCTCTTTTTCTTGGTACTTTGAATACATTTCCACATTCTTTACAT\n+ATTAAACTTGAGTAAAACATTTTTTGTCTTTTCATAATTAATCAATTCCTTTTCTCTTTT\n+ATTTGATAATTTAACTATATACTATATTGATAAATAAGTCAACAGTTTTCTAAAAATAAT\n+TTAAATTATTTTGAAGAATACTTTAATATCAAGGG\n' |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/pharokka_db.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pharokka_db.loc Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +pharokka_db pharokka_db Minimal DB for testing ${__HERE__}/subset_pharokka_db |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/5Jan2023_data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/5Jan2023_data.tsv Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Accession Description Classification Genome Length (bp) Jumbophage molGC (%) Molecule Modification Date Number CDS Positive Strand (%) Negative Strand (%) Coding Capacity (%) Low Coding Capacity Warning tRNAs Host Lowest Taxa Genus Sub-family Family Order Class Phylum Kingdom Realm Baltimore Group Genbank Division Isolation Host (beware inconsistent and nonsense values) +MF417929 Uncultured Caudovirales phage clone 2F_1 Uncultured Caudovirales phage clone 2F_1 Bracchivirus U2F1 Bracchivirus Peduoviridae Caudoviricetes Uroviricota Heunggongvirae Duplodnaviria Viruses 32618 FALSE 39.218 DNA 1-Nov-22 42 16.66666667 83.33333333 89.41688638 NA 0 Unspecified Bracchivirus Bracchivirus Unclassified Peduoviridae Caudovirales Caudoviricetes Uroviricota Heunggongvirae Duplodnaviria Group I ENV Unspecified \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/5Jan2023_genomes.fa.msh |
| b |
| Binary file test-data/subset_pharokka_db/5Jan2023_genomes.fa.msh has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/CARD |
| b |
| Binary file test-data/subset_pharokka_db/CARD has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/CARD.dbtype |
| b |
| Binary file test-data/subset_pharokka_db/CARD.dbtype has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/CARD.index --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/CARD.index Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +0 0 298 +1 298 288 |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/CARD.lookup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/CARD.lookup Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +0 ACT97415.1 0 +1 AEJ08681.1 0 |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/CARD.source --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/CARD.source Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +0 protein_fasta_protein_homolog_model.fasta |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/CARD_h |
| b |
| Binary file test-data/subset_pharokka_db/CARD_h has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/CARD_h.dbtype |
| b |
| Binary file test-data/subset_pharokka_db/CARD_h.dbtype has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/CARD_h.index --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/CARD_h.index Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +0 0 75 +1 75 59 |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/VFDB_setB_pro.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/VFDB_setB_pro.fas Thu Mar 02 16:21:40 2023 +0000 |
| [ |
| @@ -0,0 +1,14 @@ +>VFG037170(gb|WP_001081754) (plc1) phospholipase C [Phospholipase C (VF0470) - Exotoxin (VFC0235)] [Acinetobacter baumannii 1656-2] +MNRREFLLNSTKTMFGTAALASFPLSIQKALAIDAKVESGTIQDVKHIVILTQENRSFDN +YFGTLKGVRGFGDRFTIPMTEGRKVWEQYDANKKKVLPYHLDSRLGNAQRVTGTNHSWSD +GQGAWDNGRMSDWVAHKQPQSMGYYKKQEVEYQFALANAFTICDAYHCAMHAGTNPNRKF +IWTGTNGPTGAGVASVVNEFDGIGPSTEGYEWTTYPERLQQAGVTWKVYQNMPDNFTDNP +LAGFKQYRRANEQSGQPVSNDTLICLAYDEKIDATQPLYKGIANTMPDGGFLGAFKADIA +QGKLPQVSWLVAPATYSEHPGPSSPVQGAWYIQEVLNALTENTQVWSQTVLLVNFDENDG +FFDHVPSPSAPSKDINGVVYGKTTLTDQQVSYEYFNHPAVATSKSQPETDGRVYGPGVRV +PMYVISPWSRGGWVNSQVFDHTSILQFLEKRFGVQEPNISPYRRAVCGDLTTAFNFKTPN +LLPVAELDGKKTKAEADAIRVAQELLPQVSVPSQQQFPQQEIGIRPSRALPYILHTSAKV +DVTQKTVKLMFSNTGKQAAVFHVYNRLDLTAIPRRYMVEAGKQLDDAWNTINGQYDLWVL +GPNGFHRAFKGNLSQANQTQALPEIRVCVEECDANLYLKVRHDGNKSVKLNVKANAYLPN +KTWMIETNSSEKELVWDMSEFGGWYDFTVTLADDATFSRRFAGRIETQEDSISDPYMGYL +ES \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/aro_index.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/aro_index.tsv Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ +ARO Accession CVTERM ID Model Sequence ID Model ID Model Name ARO Name Protein Accession DNA Accession AMR Gene Family Drug Class Resistance Mechanism CARD Short Name +ARO:3001109 37489 1393 4 SHV-52 SHV-52 AEJ08681.1 HQ845196.1 SHV beta-lactamase carbapenem;cephalosporin;penam antibiotic inactivation SHV-52 +ARO:3002999 39433 1188 2 CblA-1 CblA-1 ACT97415.1 GQ343019.1 CblA beta-lactamase cephalosporin antibiotic inactivation CblA-1 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/phrog_annot_v4.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/phrog_annot_v4.tsv Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +phrog color annot category +1 #fea328 integrase integration and excision \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/phrog_hhm_db |
| b |
| Binary file test-data/subset_pharokka_db/phrog_hhm_db has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/phrog_hhm_db.index --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/phrog_hhm_db.index Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +phrog_1.hhm 0 95355 |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/phrogs_profile_db |
| b |
| Binary file test-data/subset_pharokka_db/phrogs_profile_db has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/phrogs_profile_db.dbtype |
| b |
| Binary file test-data/subset_pharokka_db/phrogs_profile_db.dbtype has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/phrogs_profile_db.index --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/phrogs_profile_db.index Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +0 0 15802 |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/phrogs_profile_db_h |
| b |
| Binary file test-data/subset_pharokka_db/phrogs_profile_db_h has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/phrogs_profile_db_h.dbtype |
| b |
| Binary file test-data/subset_pharokka_db/phrogs_profile_db_h.dbtype has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/phrogs_profile_db_h.index --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/phrogs_profile_db_h.index Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +0 0 18 |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/protein_fasta_protein_homolog_model.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/protein_fasta_protein_homolog_model.fasta Thu Mar 02 16:21:40 2023 +0000 |
| [ |
| @@ -0,0 +1,4 @@ +>gb|ACT97415.1|ARO:3002999|CblA-1 [mixed culture bacterium AX_gF3SD01_15] +MKAYFIAILTLFTCIATVVRAQQMSELENRIDSLLNGKKATVGIAVWTDKGDMLRYNDHVHFPLLSVFKFHVALAVLDKMDKQSISLDSIVSIKASQMPPNTYSPLRKKFPDQDFTITLRELMQYSISQSDNNACDILIEYAGGIKHINDYIHRLSIDSFNLSETEDGMHSSFEAVYRNWSTPSAMVRLLRTADEKELFSNKELKDFLWQTMIDTETGANKLKGMLPAKTVVGHKTGSSDRNADGMKTADNDAGLVILPDGRKYYIAAFVMDSYETDEDNANIIARISRMVYDAMR +>gb|AEJ08681.1|ARO:3001109|SHV-52 [Klebsiella pneumoniae] +MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLAIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/vfdb |
| b |
| Binary file test-data/subset_pharokka_db/vfdb has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/vfdb.dbtype |
| b |
| Binary file test-data/subset_pharokka_db/vfdb.dbtype has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/vfdb.index --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/vfdb.index Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +0 0 724 |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/vfdb.lookup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/vfdb.lookup Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +0 VFG037170(gb|WP_001081754) 0 |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/vfdb.source --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/vfdb.source Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +0 VFDB_setB_pro.fas |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/vfdb_h |
| b |
| Binary file test-data/subset_pharokka_db/vfdb_h has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/vfdb_h.dbtype |
| b |
| Binary file test-data/subset_pharokka_db/vfdb_h.dbtype has changed |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 test-data/subset_pharokka_db/vfdb_h.index --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_pharokka_db/vfdb_h.index Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +0 0 132 |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 tool-data/pharokka_db.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pharokka_db.loc.sample Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,12 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a pharokka DB folder. The pharokka_db.loc +#file needs this format (longer white space is the TAB character): + +#<unique_build_id> <dbkey> <display_name> <DB_folder_path> + +# for example: + +# pharokka_db pharokka_db Pharokka Database v1.2.0 /data/pharokka_db + +# To retrieve the complete DB look at https://github.com/gbouras13/pharokka or +# use `wget "https://zenodo.org/record/7563578/files/pharokka_v1.2.0_database.tar.gz"` (14.02.2023) \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Location of pharokka DB file --> + <table name="pharokka_db" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/pharokka_db.loc" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1d4fcd38d899 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Mar 02 16:21:40 2023 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Location of pharokka DB file --> + <table name="pharokka_db" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/pharokka_db.loc" /> + </table> +</tables> \ No newline at end of file |