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Update pharokka DM #6680

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36f7dbf
update DM, add new test DB
paulzierep Jan 16, 2025
4c0776c
remove hidden files
paulzierep Feb 11, 2025
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2 changes: 1 addition & 1 deletion ...ers/data_manager_pharokka_database_fetcher/data_manager/data_manager_fetch_pharokka_db.py
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Expand Up @@ -46,7 +46,7 @@ def main():
sys.exit(return_code)

# copy the test DB
test_db_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "subset_pharokka_db")
test_db_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "pharokka_test_db_1.7.4")
command_args = ["cp", "-r", test_db_path, db_path]
else:
command_args = ["install_databases.py", "-o", db_path]
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2 changes: 1 addition & 1 deletion data_managers/data_manager_pharokka_database_fetcher/data_manager/macros.xml
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@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">1.3.2</token>
<token name="@TOOL_VERSION@">1.7.4</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">22.05</token>
<xml name="biotools">
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9 changes: 4 additions & 5 deletions data_managers/data_manager_pharokka_database_fetcher/data_manager/pharokka_db_fetcher.xml
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Expand Up @@ -18,30 +18,29 @@
<param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Copy minimal test DB and create mock data table entry." />

<!-- <param name="test_data_manager" type="text" value=""/> -->
<param argument="--version" type="text" value="1.2.0" help="Check https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102 for current version. The default value is recommended."/>
<param argument="--version" type="text" value="1.7.4" help="Downloads: https://zenodo.org/records/8276347"/>
</inputs>
<outputs>
<data format="data_manager_json" name="out_file" />
</outputs>
<tests>
<test expect_num_outputs="1">
<param name="test_data_manager" value="--test"/>
<param name="version" value="v1.2.0"/>
<param name="version" value="1.7.4"/>
<output name="out_file">
<assert_contents>
<has_text text="Pharokka DB version"/>
<has_text text="db_from_"/>
<has_text text="pharokka_db"/>
<has_text text="v1.2.0"/>
<has_text text="1.7.4"/>
</assert_contents>
</output>
</test>
</tests>
<help>
<![CDATA[
Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
This data manager fetches the DB using the build-in tool download script.
The version must be checked here: https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102
This data manager fetches the DB using the build-in tool download script (https://zenodo.org/records/8276347).
]]>
</help>
<expand macro="citations" />
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0 ...ager/subset_pharokka_db/5Jan2023_data.tsv → .../pharokka_test_db_1.7.4/1Aug2023_data.tsv
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0 ...ubset_pharokka_db/5Jan2023_genomes.fa.msh → ...kka_test_db_1.7.4/1Aug2023_genomes.fa.msh
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0 ...cher/data_manager/subset_pharokka_db/CARD → .../data_manager/pharokka_test_db_1.7.4/CARD
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0 ...ta_manager/subset_pharokka_db/CARD.source → ...anager/pharokka_test_db_1.7.4/CARD.source
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0 ...er/data_manager/subset_pharokka_db/CARD_h → ...ata_manager/pharokka_test_db_1.7.4/CARD_h
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0 ..._manager/subset_pharokka_db/CARD_h.dbtype → ...ager/pharokka_test_db_1.7.4/CARD_h.dbtype
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0 ...a_manager/subset_pharokka_db/CARD_h.index → ...nager/pharokka_test_db_1.7.4/CARD_h.index
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10 changes: 10 additions & 0 deletions ..._pharokka_database_fetcher/data_manager/pharokka_test_db_1.7.4/VFDBclusterRes_cluster.tsv
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VFG037177(gb|WP_000632986) VFG037177(gb|WP_000632986)
VFG037177(gb|WP_000632986) VFG037173(gb|WP_000633004)
VFG037177(gb|WP_000632986) VFG037179(gb|YP_001085084)
VFG037177(gb|WP_000632986) VFG037185(gb|WP_020753227)
VFG037177(gb|WP_000632986) VFG037189(gb|WP_000632992)
VFG037177(gb|WP_000632986) VFG037195(gb|WP_000633005)
VFG037177(gb|WP_000632986) VFG037170(gb|WP_001081754)
VFG037177(gb|WP_000632986) VFG037172(gb|WP_001081748)
VFG037177(gb|WP_000632986) VFG037176(gb|WP_001081735)
VFG037177(gb|WP_000632986) VFG037178(gb|YP_001083140)
10 changes: 10 additions & 0 deletions ...harokka_database_fetcher/data_manager/pharokka_test_db_1.7.4/VFDBclusterRes_rep_seq.fasta
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>VFG037177(gb|WP_000632986) (plc2) phospholipase C [Phospholipase C (VF0470) - Exotoxin (VFC0235)] [Acinetobacter baumannii ACICU]
MITRRKFLNYSLNMGFGAAALAAFPSSIQKALAIPANNKTGTIQDVEHVIILMQENRSFDHYFGTLKGVRGFADRFTIPLPNGRRVWEQLRSNGQVLTPFHLDGTANNAQRADGTPHTWDDSQLAWDNGRMANWPTHKTDISMGYFKEKEIPYQFALANAFTICDAYHCSMHTGTDANRSFHLTGTNGATPTKRSFVNNEWDWIDGNPATADRGYTWKTYAERLEEAGISWICYQNMPDEWGDNMLGAFRSFRKANIASGYPVSSGGEPNKPYADTGQKLPYKAYDAATDNAKNPLYKGIANTLPGNKPEEYLDAFKRDIREGKLPQVSWINAPSIYCEHPDPSSPVQGAWFIQEIIDALTAVPEVWSKTALLINFDENDGYFDHMPSPSAPSRLKNGQYAGKSTLSNADMQDEYFDHAAPEGSHSQPTPDGRVYGPGPRVPLYVISPWSRGGWVNSQVFDHTSVLMFLEKRFGVKEPNISPYRRAVCGDLTSAFNFKTPNADVLPQLSGKQTRLQADALRENQEALPAVPVPTDIKLPIQQSGIRLSRALPYELHTSARCKADGKVQLIFSNTGKQAAVFHVYDKLNLDRIPKRYIVEPNKTLDDEWDALNDNLGRYDLWVLGPNGYHRHFKGDAQRIIDSGVKPEIRVCYDIANGDVYVELMNEGTKDTILTVKPCAYRQDAPLQLTVKAGQVVKQHWSLADVGHWYDFEVTSESDPYYYRRFAGRVETGEDSFSDPAMI
>VFG037203(gb|WP_000079188) (plcD) phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Phospholipase D (VF0469) - Exotoxin (VFC0235)] [Acinetobacter baumannii ACICU]
MAQSFHSKQLQTHQLANGFLIKASIVVCSSFAVALTGCSTLPKHSPEPIQYARDIDTSQTSLSKIITPLREKNPNLTGYHLLNDPLEALAARLRLIDKAEKTLDLQYYIWDNDKVGALALHAIIRAADRGVKVRLLIDDNNAKKMEGVLLALSQHKNIEVKLFNPYRFRKYRAMDMILDLKRINRRMHNKSFIADNQVALIGGRNMTNQYYNVSDSYQFSDVDVMLVGAAVDDIVNSFDDYWNHEYAYSVQSIVSAQQHRLRYESLKQQLDAHYQQATVQNFLDLTSRSHAFDKWLDRNIKFDWVKAEVVKDSPDKIRSKAKKEEHLNFQLINHLEKPESNVDLISAYFIPEKQGAKILSTLAKEGVEVRVLTNSFKANDVAVVHAFYGKYRKELLKNGVQLYEFLPTPDKRDLNKNTDELATKAKVNMKGLSRSSLHTKLMALDEQVFIGSFNFDPRSAYLNTEIGVILDSPSLAKTIHHTMDENLNKYAYKLKLDPNNHIYWQQETPKGPVIYKKEPEMKWWQKAGMKLLSWLPLEGFM
>VFG037218(gb|WP_000983821) (basJ) acinetobactin biosynthesis protein BasJ [Acinetobactin (VF0467) - Nutritional/Metabolic factor (VFC0272)] [Acinetobacter baumannii ACICU]
MMQTQISVEQNLDHIGQKKFSCFSTKNYYLEVNEFVKTLNTPAANTALLNEEIAKCFEEIKKQGHQNPVLIGAIPFDITKKSSLNFYADHKKITQSSSTINSLKNRNNIEIINKSLLIQRQKFEGTVQLALDAFEKKKVEKVVLSQAVEYEFNRHQEPENLLAALLKQNPNAYNFVIPVEHNNYILGASPELLLSKQGRIVTSNPLAGSRPKSQISEKNFVSQQELNHSEKDQHEHRIVVENIIRNLATHCVELKVSEFPDILETSTMLHLSSEFQGVLKQQAPDALNLALELHPTPAVCGSPTHVAKQFILDHEGYDRHYYTGLVGWMDAEGNGEWVVTIRCGLLSENKMRLYAGAGIVEGSDAEAEWLETEAKMQTMLNILNTKVAV
>VFG037232(gb|WP_001093095) (basI) phosphopantetheinyl transferase component of acinetobactin biosynthesis protein BasI [Acinetobactin (VF0467) - Nutritional/Metabolic factor (VFC0272)] [Acinetobacter baumannii ACICU]
MNTKKQLSRGANSCLDEINIQYEKLTAFGIDIHKVQLSEIKEIPQLDHIYQELNIFLPPNIKSSRFIRQLEFLTGRLAAKYALQRFNLQDSIVHQGKQGEPLWPEGVMGGISHVGSKKSCHAIAYVRNNTLKEKIFGIDIESQKHHIFFQKKDEFYDVFLNKNEQAEIEKLLKDQAYLYLVIFSAKESIIKAFYLKYKQIIDFKNIKFKALDGAFLYFYLRQESLIEITLEVKVYFFHTNNEIITISCIEN
>VFG037243(gb|WP_001032913) (basH) non-ribosomal peptide biosynthesis thioesterase BasH [Acinetobactin (VF0467) - Nutritional/Metabolic factor (VFC0272)] [Acinetobacter baumannii 1656-2]
MNKHQYNMFCLPPAGSSVSIYHPWKKQISDNIRIIPIEYSGHGIKINEPLIDDPDLLAMQIANEIQAYSDTPFILFGHSVGGGLIWKVLNYLNEKPIIDQLRLIVISSRPEHHYIQHMRYKHELTDEKIIDELKRYNNFPDEILNNQEALTFFLKIIRNDFYLSDQLLSEKIHKTEVPIVAFYGKQDPDIPNKRMMDAWQQHTENWLGSIEFEGDHFYFLNPETRVKMLENIAAIVETLTVNIE
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14 changes: 0 additions & 14 deletions .../data_manager_pharokka_database_fetcher/data_manager/subset_pharokka_db/VFDB_setB_pro.fas
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