| Previous changeset 19:cc91d730cc4f (2023-01-16) Next changeset 21:6ba37b7dea42 (2023-05-26) |
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Commit message:
Regenerate Galaxy test files with Pyrodigal `v2.1.0` |
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modified:
gecco.xml test-data/BGC0001866.1_cluster_1.gbk |
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added:
test-data/BGC0001866.sideload.json |
| b |
| diff -r cc91d730cc4f -r 64b724dd8d04 gecco.xml --- a/gecco.xml Mon Jan 16 18:35:56 2023 +0000 +++ b/gecco.xml Mon Mar 27 13:32:49 2023 +0000 |
| b |
| @@ -28,6 +28,7 @@ --genome input_tempfile.$file_extension --postproc $postproc --force-tsv + --jobs "\${GALAXY_SLOTS:-4}" #if $edge_distance --edge-distance $edge_distance #end if |
| b |
| diff -r cc91d730cc4f -r 64b724dd8d04 test-data/BGC0001866.1_cluster_1.gbk --- a/test-data/BGC0001866.1_cluster_1.gbk Mon Jan 16 18:35:56 2023 +0000 +++ b/test-data/BGC0001866.1_cluster_1.gbk Mon Mar 27 13:32:49 2023 +0000 |
| b |
| b'@@ -1,4 +1,4 @@\n-LOCUS BGC0001866.1_cluster_1 32633 bp DNA linear UNK 16-JAN-2023\n+LOCUS BGC0001866.1_cluster_1 32633 bp DNA linear UNK 27-MAR-2023\n DEFINITION BGC0001866.1 Byssochlamys spectabilis strain CBS 101075 chromosome\n Unknown C8Q69scaffold_14, whole genome shotgun sequence.\n ACCESSION BGC0001866.1_cluster_1\n@@ -16,7 +16,7 @@\n REMARK doi:10.1101/2021.05.03.442509\n COMMENT ##GECCO-Data-START##\n version :: GECCO v0.9.6\n- creation_date :: 2023-01-16T17:20:45.175113\n+ creation_date :: 2023-03-27T15:09:19.052491\n cluster_type :: Polyketide\n alkaloid_probability :: 0.010\n nrp_probability :: 0.140\n@@ -27,7 +27,7 @@\n ##GECCO-Data-END##\n FEATURES Location/Qualifiers\n CDS complement(1..1143)\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_1"\n /translation="MWIYEVDGHYIEPRRADTFLIWAGERYSAMIRLDKKPMDYSIRVP\n@@ -61,7 +61,7 @@\n /function="Multicopper oxidase, C-terminal"\n /standard_name="PF07731"\n CDS 1179..1670\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_2"\n /translation="MSSLRSSSHSPSGLPGQPRLPLLDRSREHSLPGDRAGWRTRSRLR\n@@ -73,7 +73,7 @@\n /ApEinfo_fwdcolor="#808080"\n /ApEinfo_revcolor="#808080"\n CDS complement(2167..2376)\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_3"\n /translation="MPAYLLLLACNVLLVLGAHVQRELVLTWEEGAPNGQSRQMIKTNG\n@@ -83,7 +83,7 @@\n /ApEinfo_fwdcolor="#808080"\n /ApEinfo_revcolor="#808080"\n CDS 2559..3032\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_4"\n /translation="MLFNSEVGVEEHVVLWSFQETTSITMAEEIKLTPLETFAQAISAS\n@@ -94,7 +94,7 @@\n /ApEinfo_fwdcolor="#808080"\n /ApEinfo_revcolor="#808080"\n CDS 3007..3576\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_5"\n /translation="MQGTRTYYELATEAKVPLHQLQSIARMAITGSFLREPEPNIVAHS\n@@ -106,7 +106,7 @@\n /ApEinfo_fwdcolor="#808080"\n /ApEinfo_revcolor="#808080"\n CDS 3600..4043\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_6"\n /translation="MVTSTSKDNREKTPLPETVASRISFESHDFFKPQPVQNADVYLLR\n@@ -126,7 +126,7 @@\n /function="O-methyltransferase domain"\n /standard_name="PF00891"\n CDS 4337..4792\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_7"\n '..b'ansl_table=11\n /locus_tag="BGC0001866.1_15"\n /translation="MTFEEMLSRPSPPPFAGPSHNSNRPTNMASTNQDQYYHDKGKHGE\n@@ -317,7 +317,7 @@\n /function="Aflatoxin regulatory protein"\n /standard_name="PF08493"\n CDS 16827..18797\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_16"\n /translation="MAICGIAVRLPGGISNDAQLWDFLLAKRDARSQVPGSRYNISGYH\n@@ -369,7 +369,7 @@\n /function="Acyl transferase"\n /standard_name="PF00698"\n CDS 18806..22078\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_17"\n /translation="MVVACENSPSSVTISGDIDQVQYVMQEISLAHPEILCRQIKSDTA\n@@ -451,7 +451,7 @@\n /function="Methyltransferase type 11"\n /standard_name="PF08241"\n CDS 22416..22889\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_18"\n /translation="MQTVLINSASDGVGLAAIQISKMIGATIYATVIGEDKVEYLTASH\n@@ -470,7 +470,7 @@\n /function="Alcohol dehydrogenase-like, C-terminal"\n /standard_name="PF00107"\n CDS 22922..24277\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_19"\n /translation="MELYKQGHIQPITPVKTFTATDIRQCFDYMQSGQHIGQLRLSLKS\n@@ -510,7 +510,7 @@\n /function="Phosphopantetheine binding ACP domain"\n /standard_name="PF00550"\n CDS 25423..25710\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_20"\n /translation="MAQKLRFYLFGDQTYDYDEQLRALLTSHDPVVRSFLERAYYTLRA\n@@ -528,7 +528,7 @@\n /function="Starter unit:ACP transacylase"\n /standard_name="PF16073"\n CDS 26198..29653\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_21"\n /translation="MSRPYISAYASGGVTISGPPSVLAELRNTPGLSKLRAKDIPIHAP\n@@ -596,7 +596,7 @@\n /function="Acyl transferase"\n /standard_name="PF00698"\n CDS 29804..30544\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_22"\n /translation="MVIEKALMPLNAGPQLLRVTASLIWSEKEASVRFYSVDVRRPSSK\n@@ -617,7 +617,7 @@\n /function="Polyketide synthase, dehydratase domain"\n /standard_name="PF14765"\n CDS 30591..32633\n- /inference="ab initio prediction:Pyrodigal:2.0.4"\n+ /inference="ab initio prediction:Pyrodigal:2.1.0"\n /transl_table=11\n /locus_tag="BGC0001866.1_23"\n /translation="MLTTFQIQGVPRRVLRYILQSSAKTTQTATSSVPAPSQAPVMVPQ\n' |
| b |
| diff -r cc91d730cc4f -r 64b724dd8d04 test-data/BGC0001866.sideload.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BGC0001866.sideload.json Mon Mar 27 13:32:49 2023 +0000 |
| [ |
| @@ -0,0 +1,39 @@ +{ + "records": [ + { + "name": "BGC0001866.1", + "subregions": [ + { + "details": { + "alkaloid_probability": "0.010", + "average_p": "0.996", + "max_p": "1.000", + "nrp_probability": "0.140", + "polyketide_probability": "0.960", + "ripp_probability": "0.000", + "saccharide_probability": "0.000", + "terpene_probability": "0.010" + }, + "end": 32979, + "label": "Polyketide", + "start": 347 + } + ] + } + ], + "tool": { + "configuration": { + "cds": "3", + "e-filter": "None", + "edge-distance": "0", + "mask": "False", + "no-pad": "False", + "p-filter": "1e-09", + "postproc": "'gecco'", + "threshold": "0.8" + }, + "description": "Biosynthetic Gene Cluster prediction with Conditional Random Fields.", + "name": "GECCO", + "version": "0.9.6" + } +} \ No newline at end of file |