antiSMASH-DB related features and bug fixes.
Kai Blin
Branch: kblin/antismash:master
Branch: antismash/antismash:master
Merged
Merged pull request
output/html: Use smart forwarder for MIBiG links from details table as well
output/html: Use smart forwarder for MIBiG links from details table as well
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