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Initial prototype #1

Merged
merged 366 commits into from
Mar 27, 2018
Merged

Initial prototype #1

merged 366 commits into from
Mar 27, 2018

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SJShaw
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@SJShaw SJShaw commented Mar 27, 2018

Converted/rewrote all antiSMASH 4 modules with the exceptions of:

  • terpenes
  • NRPS predictors (SANDPUMA, specifically)
  • active site finder

@SJShaw
html: fix badly merged css
3fca1c4
@SJShaw
html: don't stretch cluster column in overview with rename message
f99ae77
@SJShaw
nrps_pks: initial version
0b7ac36
@SJShaw
smcogs: don't crash when running trees and images already exist in ou…
6e8f64c 
…tput dir
@SJShaw
smcogs: only store relative path for images in result JSON
e39751c
@SJShaw
secmet: properly track CAL_domains
0a4b26b
@SJShaw
clusterblast: relabel 'Homologous gene clusters' to 'Similar gene clu…
acfddd2 
…sters'
@SJShaw
nrps_pks: more complete testing of full integration run results
ed5603a
@SJShaw
clusterblast: change integration tests to be end to end and check reuse
c048aff
@SJShaw
secmet: use more meaningful descriptions for gene functions CORE and …
966595a 
…ADDITIONAL
@SJShaw
outputs: add zip file functionality
517bb4b
@SJShaw
serialiser: don't convert feature dicts to strings before jsonification
a39bd85
@SJShaw
lanthipeptides: stick to 1 digit after a decimal point for masses in …
d761d35 
…output
@SJShaw
html: cleanup output javascript creation
8192b32
@SJShaw
html: mark records with no clusters on a per-record basis
96dd341
@SJShaw
nrps_pks: use piping instead of temp files in minowa
79e1b26
@SJShaw
secmet: allow for multiple gene function annotations
3794ca8
@SJShaw
hmm_detection: rework to use a more readable rule format
87cd7f4
@SJShaw
clusterblast: improving alignment of cluster SVGs by strand
6752572
@SJShaw
html: allow for multiple gene functions in genecluster SVG
d44d768
@SJShaw
main: shift nrps_pks results to before clusterblast
eef0d63
@SJShaw
clusterblast: make templates consistent, especially with no results
89825b1
@SJShaw
html: cleanup smcog reference building and remove now unused get_smco…
8701097 
…g_annotations()
@SJShaw
secmet: allow for sec_met without setting as CORE gene function
45e0657
@SJShaw
hmm_detection: track all CDS domains that triggered cluster detection
672b108
@SJShaw
genefinding: fix run_prodigal's use of biopython
396e879
@SJShaw
subprocessing: don't fork in parallel function if only one CPU available
e595978
@SJShaw
common/record_processing: parallelise sequence sanitisation and genef…
09e1dd9 
…inding
@SJShaw
hmm_detection: don't try and deal with other special conditions insid…
a959680 
…e CDSCondition
@SJShaw
subprocessing: move tests to integration instead of unit
1cea4b3
@SJShaw
hmm_detection: remove commented clusterfinder-specific rules
1d1beb6
@SJShaw
main: add type hints and small cleanup
7f92086
@SJShaw
clusterfinder: initial port
6c9d949
@SJShaw
all: improve type hints
2f06986
@SJShaw
record_processing,secmet: shift id/name sanitisation to CDS instantia…
c970e35 
…tion
@SJShaw
secmet: include the offending CDS name when reporting bad translations
e5f3008
@SJShaw
html: properly handle features with multiple EC_numbers
1da5b49
@SJShaw
secmet: support pseudo-CDS features, along with their translation ext…
8e7f78f 
…ractions
@SJShaw
secmet: discard CDS feature translations that contain gaps
0a130dc
@SJShaw
record_processing: check if a record is a WGS before attempting to us…
1e9e728 
…e its sequence
@SJShaw
fullhmmer: fix faulty add_to_record caching
d3bfdc9
@SJShaw
full_hmmer: split into common sections to prepare for cluster_hmmer
f84c8ae
@SJShaw
cluster_hmmer: add PFAM searches within clusters
8fb4404
@SJShaw
*_hmmer: return strings as failure messages, not exceptions
234c539
@SJShaw
main: in an analysis run, only check prereqs and options for modules …
731ea73 
…that are enabled
@SJShaw
hmm_detection: remove --enable commandline option
6bbe0c4
@SJShaw
args, *_hmmer: allow args with only prefix name along with other args
2753db4
@SJShaw
common.record_processing: don't abort when a WSG/supercontig includes…
0439e08 
… the sequence
@SJShaw
secmet: don't try to keep a unique mapping for CDS protein ids
ee4adbf
@SJShaw
secmet: use current border extent when forming clusters, not largest
bc6862b
@SJShaw
main: fix all records sharing same results object
ae545f5
@SJShaw
main: ensure detection results added when relevant
74d3828
@SJShaw
Makefile: use correct path to nisin
6670c9b
@SJShaw
secmet: fix PFAMDomain conversion from biopython
8c7a11a
@SJShaw SJShaw requested a review from kblin March 27, 2018 10:04
@kblin kblin merged commit ea36f7f into antismash:master Mar 27, 2018
@letunglam1991 letunglam1991 mentioned this pull request Jan 10, 2019
Closed
@li0604 li0604 mentioned this pull request Nov 11, 2020
Open
@panchyni panchyni mentioned this pull request Jun 29, 2022
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@kblin kblin kblin approved these changes

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@SJShaw @kblin