PPanGGOLiN 2.0.5

Bug Fixes

• Resolved dead links in documentation (reported in issue #189, fixed in PR #190).
• Addressed missing metadata separation when utilizing metadata in 'proksee' output (PR #188).
• Added missing documentation for the ppanggolin fasta command (reported in issue #191, fixed in PR #192).
• Fixed error occurring in ppanggolin msa command when using all genes (PR #196, reported in #198).

Full Changelog: 2.0.4...2.0.5

PPanGGOLiN 2.0.4

Bug Fixes

• Fixed division by zero issue when no module is predicted. (Pull Request #183)
• Improved error messages during input file parsing for enhanced clarity, helping users in troubleshooting (see issue #185). Additionally, this update adds more flexibility when scanning the first line of input files to identify the GFF file format. Details can be found in (Pull Request #186)

Full Changelog: 2.0.3...2.0.4

PPanGGOLiN 2.0.3

This release addresses several minor bugs identified in the previous version (v2.0.2) of PPanGGOLiN.

Bug fixes

• Fixes Pyrodigal meta mode and improves training: Resolved an issue related to Pyrodigal meta mode and introduced enhancements in the training process. #177

• Fix ppanggolin fasta Command: Addressed multiple issues associated with the ppanggolin fasta command (refer to Issue #179). #180

• Handling cases where two Genes share the same stop: Implemented a solution to manage scenarios where two genes share a common stop position, preventing errors in the gene addition process. #181

• Unique tmpdir name in clustering step: The tmpdir name generated during the clustering step is now truly unique, preventing any potential conflicts. #178

• Fix for HTML spot plot radio buttons: Resolved an issue with radio buttons in the HTML spot plot that had become non-functional since bokeh v3. #176

Full Changelog: 2.0.2...2.0.3

PPanGGOLiN 2.0.2

Bug fixes

• Fix use of non-unique gene IDs when writing sequences in PR #173.
  This PR fixes a bug where the 'all' command fails due to non-unique gene IDs in the input genome annotation files. In this case, PPanGGOLiN now uses custom gene IDs to ensure their uniqueness. This PR should fix issue #172.

• Minor documentation update in #170

• Fix workflow that checks the bioconda recipe in #171

Full changelog: 2.0.1...2.0.2

PPanGGOLiN 2.0.1

Bug Fixes

Made minor patches to ensure the compilation of bioconda recipe on macOS. Version 2.0.0 faced issues on macOS when compiling C code with Clang. This has been resolved by adding a flag in setup.py (#169).

Full Changelog: 2.0.0 to 2.0.1

PPanGGOLiN 2.0.0

New commands

• projection: to annotate external genomes using an existing pre-computed reference pangenome (#119, see doc).

• rgp_cluster: to cluster RGP based on their gene family content (#117, see doc).

• metadata: add metadata linked to various pangenome elements using simple TSV files (#111, see doc).

• the write command is split in two commands (#140):

  • write_pangenome: write outputs at the pangenome level (see doc)
  • write_genomes: write genome outputs with pangenome annotation. Three formats are available for outputs: table, GFF and JSON Proksee (#139, see doc).

• utils: a small side command to generate a default configuration file for any commands (#112, see doc).

New features

• A new, improved documentation hosted by readthedoc replacing the github wiki.
• GFF export of genomes with pangenome annotation (#139, see doc).
• JSON Map for Proksee to visualize interactively each genome and their pangenome annotation (#139, see doc).
• Configuration file can now be used to set all or some parameters of PPanGGOLiN commands (#112, see doc).

Major change

BREAKING: New structure of the pangenome file to make it much lighter and faster to read (#110). ⚠️ Break the compatibility with PPanGGOLiN v1 pangenome HDF-5 files.

Minor change

• Replacing Prodigal by pyrodigal for the annotation command (#138).
• The context command has a window parameter to define the number of neighboring genes that are considered on each side of a gene of interest when searching for contexts (#137, see doc).
• Replace all option keyword by synteny option keyword for draw –spots to draw spots with different RGP syntenies. Now all will draw all pangenome spots (#129)

Bug Fixes

• Writing out only the RGP and spot of the gene with --projection (#130). Please note that, in version 2, the --projection parameter in the write command has been renamed to --table and now belongs to the write_genomes command (check the documentation of the write_genomes command for more details).
• Make deterministic clustering (#116)

PPanGGOLiN 1.2.105

A lot of the code was rewritten, but that should be relatively transparent for users

Bugfixes

• Shell subpartitions are properly saved in the HDF5 file and used in the different figures
• --meta option for annotate to annotate genomes using the metagenome mode of prodigal
• --single_copy for msa to compute MSA using 'mostly single copy' persistent genes only
• Cope with drawing more than 2000 identical spots in the same figure

PPanGGOLiN 1.2.74

New commands

• metrics to compute a list of metrics about the pangenome.

New features

• The projection option from write subcommand, can give now, information about RGPs, Spots and modules
• With the new command metrics is now possible to compute the genomic
  fluidity of the pangenome.
• With the new command metrics is now possible to get some more information
  about the module. This information will be computed and shown as statistics on families and partitions of modules
• All the metrics are saved in pangenome file and could be print with info
  subcommand.

Bug fixes

• fix crazy cluster assignment in clustering step
• fix align when using a pangenome constructed from user-provided
  annotations with prokka-like identifiers
• fix check information on few subcommand option to help user

PPanGGOLiN 1.2.63

• identifiers used in provided annotation files (gff or gbff, through --anno) will be used by default, unless they are not unique within the pangenome
• additional column in context output indicating family partition
• Always save the gene sequences when building a pangenome (which gives more flexibility when doing additional analysis with ppanggolin)

Bugfixes

• fix a bug preventing you from doing a new clustering if partitions were not computed
• fix genome sizes drawn with draw --spots

PPanGGOLiN 1.2.46

New commands

• module to predict conserved modules in variable parts of a pangenome
• context to find which gene families are conserved in the same genomic context than sequences of interest
• all to run all possible analysis with PPanGGOLiN.
• panmodule to run the panModule workflow

Bug fixes

• improved pseudogene reading and gff/gbff parsing
• fixed gff parser to cope with bakta gff files (reported in #66)
• fixed gexf formatting in the rare case of having '&' in the 'product' field of gene annotations (reported in #61)
• fixed rare crash happening when a partition has only 1 gene family ( see #64 )
• fixed compilation issue with gcc 10.* and above (reported in #69 )

Other:

• Allow to compute K=2 if forced by the user in partition or rarefaction(by default, K is still picked between 3 and 20). (see #65 )
• removed R, rpy2 and genoPlot-R dependencies (#47 shall never be a problem anymore)
• added a new bokeh dependency
• remove spot --draw_hotspots and related options. To realize the same thing, use draw --spots once the spots have been computed.
• added a --spots option to draw to have interactive figures for spots of interest, replacing the former figures drawn with R.
• align can compare a set of sequences of interest to a pangenome, and draw related elements, but cannot compare a genome to a pangenome anymore