Changes - metacpan.org

0.242020  2024-07-20 12:23:52+02:00 Europe/Rome
    - Additions
      - Filterable: new role to generalize filtering of SeqId objects beyond taxonomy
      - Listable: added method desc_seq_len_list
      - SeqId: added method instance for memoized object construction (to speed up Splits analysis)
      - SeqId::Filter: new class to implement method SeqId::family_filter
      - Tree: added method get_node_that_maximizes (e.g., to look for long branch lengths)
      - Tree: added method newick_str as a robust wrapper around Bio::Phylo to_newick method
      - Tree: finally added full-working method root_tree!
      - Tree::Splits: new class to handle splits and preserve node metadata after rooting
      - binaries: added automated rooting on taxon or family to format-tree.pl
    - Changes
      - Listable: refactored complete_seq_list method to optionally report seq lengths
      - Listable: refactored (and renamed) long_leaf_list method (to long_branch_list)
      - SeqId: now automatically (and silently) removes quotes around ids (especially in trees)
      - Taxonomy: reduced redundancy of Note messages about merged taxa
    - Fixes
      - IdList: fixed SeqId-related bug preventing seqs to be batch-extracted in some cases
      - binaries: improved robustness of classify-ali.pl and inst-abbr-ids.pl

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
      - Taxonomy: splitting of lineages should be more robust

0.181180  2018-04-28 13:43:41+02:00 Europe/Brussels
    - Fixes
      - Taxonomy::ColorScheme: fixed bug #125225 (rt.cpan.org): depends on module not on CPAN

0.181170  2018-04-27 14:19:02+02:00 Europe/Brussels
    - Additions
      - Taxonomy::ColorScheme: improved delegation to internal classifier (and tests)
      - Trees: switch_branch_lengths_and_labels_for_entities method is now compatible with treeplot
      
0.181120  2018-04-23 00:34:53+02:00 Europe/Brussels
    - Additions
      - ColorScheme: revamped its internal classifier (which now requires Taxonomy)
      - ColorScheme: added handling of indexed colors (like those required by gnuplot)
      - Taxonomy: new Taxable role to provide a Taxonomy attribute to any class
      - Taxonomy: new alias methods fetch_lineage and compute_lca
    - Changes
      - binaries: removal of classify-ali.pl (now distributed with Bio::MUST::Tools::Mcl)
      - ColorScheme: moved under Taxonomy namespace
      - Taxonomy: again refined handling of taxonomically ambiguous NCBI names

0.181000  2018-04-11 00:27:02+02:00 Europe/Brussels
    - Additions
      - Taxonomy: new eq_tax method
    - Changes
      - Taxonomy: much improved handling of taxonomically ambiguous NCBI names
    - Fixes
      - Taxonomy: (hopefully) at last fixed setup-taxdir.pl warnings

0.180630  2018-03-04 01:54:45+01:00 Europe/Brussels
    - Additions
      - binaries: new script clust2mapper.pl (to reflect clusters in tree formatting)
      - binaries: added option --keep-strain to fetch-tax.pl
    - Changes
      - IdMapper: improved handling of underscore-containing (valid) ids
      - Taxonomy: get_taxonomy_from_seq_id now also accepts lineages (stringified or as ArrayRefs)
    - Fixes
      - Taxonomy: setup-taxdir.pl should be more robust to out-of-sync NCBI files

0.180230  2018-01-23 23:44:19+01:00 Europe/Brussels
    - Additions
      - Ali: added option to allow more control on FASTA file format
      - Ali::Stash: improved documentation
      - Ali::Temporary: added option to control the lifespan of FASTA file
    - Changes
      - GeneticCode::Factory: hard-coded NCBI gc.prt file for robustness
    - Fixes
      - IdList: fixed regression bug preventing FortyTwo to work
      - Taxonomy: improved robustness of setup-taxdir.pl-related methods
      - Taxonomy: better described dependencies for more robust deployment

0.180190  2018-01-19 10:00:47+01:00 Europe/Brussels
    - Changes
      - Ali: improved consistency of guessing default value (always on)
      - Seq: ungapped seqs ending in '*' are now trimmed and considered non-aligned
    - Fixes
      - Ali::Temporary: fixed regression bug preventing IdList application
      - GeneticCode::Factory: tests should now pass on more platforms
      - PostPred::Composition: tests should now pass on more platforms

0.180140  2018-01-14 22:36:55+01:00 Europe/Brussels
    - Additions
      - Ali::Temporary: new args attribute (to fine-tune FASTA file creation)
      - Ali::Temporary: improved documentation

0.173620  2017-12-29 00:58:54+01:00 Europe/Brussels
    - Additions
      - Ali: new clone method
      - Ali: improved documentation
    - Changes
      - Tree: shorten_ids/restore_ids now ignore missing ids in IdMapper
    - Fixes
      - SeqMask::Rates: tests should now pass on more platforms
      - Taxonomy: GCA-based taxon ids now retain their true taxonomic rank

0.173500  2017-12-17 00:35:51+01:00 Europe/Brussels
    - Additions
      - binaries: new script split-matrix.pl (to extract genes from a supermatrix)
    - Changes
      - Taxonomy: LCA inference algorithm can now follow a majority-rule approach
    - Fixes
      - Taxonomy: tests are now disabled by default

0.173470  2017-12-13 09:14:04+01:00 Europe/Brussels
    - first release
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