Bio-MUST-Core
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0.240390 2024-02-08 21:59:31+01:00 Europe/Brussels
- Additions
- Ali: temp_fasta can now be passed an existing IdMapper
- Listable: std_mapper can now accept an offset for numbering seqs
- SeqId: added warning for unparsable ids due to trailing spaces
- Changes
- Listable: changed interface of std_mapper
- Fixes
- binaries: improved robustness of import-itol.pl
0.212670 2021-09-24 16:25:23+02:00 Europe/Brussels
- Changes
- Ali: refactored store_phylip method for speed (visible in ali2phylip.pl)
- Seq: rolled back changes to gapify method (to preserve generality)
0.212650 2021-09-22 22:37:09+02:00 Europe/Brussels
- Changes
- Seq: refactored gapify method for speed (visible in ali2phylip.pl)
0.212530 2021-09-10 23:55:21+02:00 Europe/Brussels
- Changes
- binaries: moved 'inst' executables to 'bin' dir (for default install)
- Fixes
- binaries: improved command-line robustness towards enum-like option values
0.211470 2021-05-27 22:53:20+02:00 Europe/Brussels
- Additions
- binaries: split-rates-ali.pl can now analyse pairs of profiles
- SeqMask::Pmsf: new class to support IQ-TREE sitefreq files
- Taxonomy: added support for GTDB Taxonomy
- Changes
- binaries: prune-tree.pl now preserves bootstrap values
0.210610 2021-03-02 23:22:29+01:00 Europe/Brussels
- Additions
- binaries: new script inst-split-seqs.pl
- Seq: added methods purity and wrapped_str
- SeqId: added method abbr_with_regex
- Changes
- binaries: refactored 'inst' executables (still no default install)
- Ali: cascaded additions and changes in Seq methods
- IdMapper: refactored regex_mapper to use abbr_with_regex
- Seq: changed some method names for API consistency (raw_seq, recode_seq, uc_seq)
- Tree: iTOL output now labels all internal nodes (instead of only collapsed nodes)
0.210380 2021-02-07 12:29:46+01:00 Europe/Brussels
- Additions
- binaries: new script tax-mask-ali.pl
- SeqMask::Rates: added support for IQ-TREE rate files
- Taxonomy::Classifier: added method tax_masks
- Types: reintroduced unused type coercions for IdList
- Changes
- Tree: modified store_itol_datasets to allow coloring leaf labels
- Fixes
- binaries: fixed incorrect outfile names for iTOL output in format-tree.pl
0.210230 2021-01-23 14:01:23+01:00 Europe/Brussels
- Additions
- binaries: new script export-itol.pl
- Changes
- binaries: renamed upload2itol.pl into import-itol.pl and added support for tree id output
- binaries: reinstated extract-ali.pl executable
- binaries: removed clust2mapper.pl executable
- distribution: removed dependency on Bio::FastParsers
- distribution: improved MANIFEST.SKIP
- Fixes
- SeqMask and Tree: tests should now pass on Solaris too (again)
0.210120 2021-01-12 16:53:42+01:00 Europe/Brussels
- Changes
- binaries: reinstated classify-ali.pl and jack-ali-dir.pl executables
- Fixes
- SeqId: expanded max tag length to 6 (lowercase) chars (e.g., nuppct#)
- SeqMask: tests should now pass on Solaris too
- Taxonomy::Criterion: fixed bug for positively avoided taxa (i.e., max_org_count: 0)
0.203490 2020-12-14 13:36:11+01:00 Europe/Brussels
- Additions
- binaries: added new collapsing modes to format-tree.pl
- Changes
- binaries: moved 'inst' executables to 'instant' dir (no default install)
- binaries: moved specialized and obsolete executables to 'private' dir (no default install)
- Constants: expanded suffix list for Ali files
- Taxonomy::ColorScheme and Tree: refactored iTOL coloring and collapsing for robustness
0.202310 2020-08-18 12:59:49+02:00 Europe/Brussels
- Fixes
- binaries: fixed spurious comment line bug in fetch-tax.pl output files
- Taxonomy and Tree: fixed underscore-like bug in iTOL coloring and collapsing
0.202070 2020-07-26 00:24:07+02:00 Europe/Rome
- Additions
- binaries: added support for iTOL coloring and collapsing to format-tree.pl
- binaries: new script upload2itol.pl
- binaries: new scripts inst-abbr-ids.pl, inst-qual-filter.pl and inst-tax-filter.pl
- Taxonomy::ColorScheme: added method store_itol_colors
- Tree: added method store_itol_collapse
- Fixes
- Taxonomy: fixed bug when trying to recover unknown lineages (visible in fetch-tax.pl)
- Taxonomy: updated NCBI Taxonomy ranks
0.201060 2020-04-15 12:27:22+02:00 Europe/Brussels
- Additions
- binaries: added two options (--column and --separator) and --item-type 'lineage' to fetch-tax.pl
- Ali: added method instant_count
- Taxonomy: added method get_taxid_from_taxonomy to parse NCBI (or SILVA) lineages
- Changes
- IdList: improved method load to use any column (from a flat table) as ids
- Taxonomy: revamped handling of ambiguous NCBI names (none is overlooked anymore)
0.200510 2020-02-21 00:18:30+01:00 Europe/Brussels
- Changes
- Taxonomy: improved method eq_tax to optionally return both got and exp labels
- Fixes
- Taxonomy: fixed missing species ranks in GCA-based lineages
- Taxonomy: fixed warnings due to merged/deleted nodes when using setup-taxdir.pl
0.191300 2019-05-10 08:44:29+02:00 Europe/Brussels
- Additions
- Ali: added method all_but_new_seqs
- Seq: added method clear_new_tag (also in Ali as clear_new_tags)
- Changes
- Listable: improved regex to capture multiple chunks (as in abbr-id-fas.pl)
- Fixes
- Taxonomy::ColorScheme: fixed loophole in dependency resolution for Graphics::ColorNames::WWW
- Tree: temporarily disabled tests relying on phyml
0.190900 2019-03-31 22:19:09+02:00 Europe/Brussels
- Changes
- all: improved warning and error messages (now prefixed by [BMC])
- Seq: ungapped seqs ending in '*' are now again considered as aligned (restored Seq-checking behavior to pre-v0.180190)
0.190690 2019-03-10 01:18:33+01:00 Europe/Brussels
- Additions
- Ali: added method all_new_seqs
- Fixes
- IdList: fixed private hash not being updated after adding new ids
0.190500 2019-02-19 15:41:48+01:00 Europe/Brussels
- Additions
- binaries: added --item-type 'strain' to fetch-tax.pl
- Fixes
- Taxonomy::ColorScheme: fixed incompatibility with recent Graphics::ColorNames
0.182420 2018-08-30 15:45:19+02:00 Europe/Brussels
- Additions
- Ali: added class method instant_store
- Fixes
- binaries: fixed --legacy-nom bug in fetch-tax.pl
0.181310 2018-05-11 23:52:11+02:00 Europe/Brussels
- Additions
- GeneticCode::Factory: codes now accept ambiguous codons in translation
- Changes
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