antiSMASH-DB related features and bug fixes.

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#148 · Created  · Last updated

Merged pull request

output/html: Use smart forwarder for MIBiG links from details table as well

57e4d2c·Author: ·Closed by: ·2018-07-31

Description

  • Bump version to 4.3.0dev

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • hmm_detection: Furans might miss MmyO but have AvrD

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • output/html: refactor generate_searchgtr_htmls

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • output/html: Use HTTPS links for MIBiG

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • output/svg: Use HTTPS links for antismash-db and mibig

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • output/svg: Use smart redirect URLs instead of deep links for antismash-db and MIBiG

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • scmogs: Add option to run smCoG calculation without building trees

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • tta: Add a TTA-auto mode that will run only when GC content > 0.65

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • clusterblast: Remove '_biosynthetic_gene_cluster' from KCB result lines

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • clusterblast: Rename non-counter var i in read_clusterblastfile

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • clusterblast: further clean up hit line annotations

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • output/html: Use smart redirect links for MIBiG from html output

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • output/html: Downgrade 'no knowncluster' log level from warning to debug

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • output/html: Add some padding to details text, fix kcb div left padding

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • output/html: Add a note about detailed predictions for --minimal runs

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • output/html: Add a warning on the cluster page if the cluster is at a contig edge

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • run_antismash: Add antiSMASH version and run date as a structured comment

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • nrpspks: Add mafft dependency check

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • run_antismash: Actually create an UnknownSeq with a lenght for the fake record in protein input mode

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • run_antismash: Don't length-filter protein input sequences

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • clusterblast: use gene_ids instead of gene_accs for organising outputs

    In RefSeq, protein IDs are no longer guaranteed to be unique. get_gene_acc prefers IDs, so use get_gene_id instead.

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • output/genbank: Fix changed biopython string representations in tests

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • clusterfinder: Ensure all cluster features have a contig_edge qualifier

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

  • output/html: Also colour cf_putative clusters

    Signed-off-by: Kai Blin kblin@biosustain.dtu.dk

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