PanTools merge requestshttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests2021-03-08T15:13:25Zhttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/1Pantools v32021-03-08T15:13:25ZSmit, SandraPantools v3Initial commit of PanTools v3 (3.0.0)Initial commit of PanTools v3 (3.0.0)Smit, SandraSmit, Sandrahttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/2Pantools v32021-03-09T14:01:40ZJonkheer, EefPantools v3Jonkheer, EefJonkheer, Eefhttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/4Pantools v3 update2021-03-31T21:42:53ZSmit, SandraPantools v3 updateMerge some bug fixes and additions into v3Merge some bug fixes and additions into v3Smit, SandraSmit, Sandrahttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/5Merge pantrools v32021-11-25T12:23:44ZLankveld, Thijs vanMerge pantrools v3This branch should merge the 3.1 changes into the ongoing changes of pantools_v3 and put those together in the master branch.This branch should merge the 3.1 changes into the ongoing changes of pantools_v3 and put those together in the master branch.Jonkheer, EefJonkheer, Eefhttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/6Application note implementation2021-11-26T10:26:25ZLankveld, Thijs vanApplication note implementationA large collection of implementations required for the application of PanTools against five data sets across the tree of life: 12 _Drosophila _species, 25_ Arabidopsis thaliana_ accessions, 100 _Saccharomyces cerevisiae_ strains, 197 str...A large collection of implementations required for the application of PanTools against five data sets across the tree of life: 12 _Drosophila _species, 25_ Arabidopsis thaliana_ accessions, 100 _Saccharomyces cerevisiae_ strains, 197 strains from the _Pectobacterium_ genus and 10.000 SARS-CoV2 genomes.Jonkheer, EefJonkheer, Eefhttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/7Added option to select different BLOSUM matrix when calculating protein simil...2021-12-02T09:19:32ZJonkheer, EefAdded option to select different BLOSUM matrix when calculating protein similarityhttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/8added compilation information to README.md and update consensus_tree help2021-12-02T10:15:06ZWorkum, Dirk-Jan vanadded compilation information to README.md and update consensus_tree helpadded compilation information to README.md and added citation information to consensus_tree function
I also changed the name of phylogeny_using_groups (old name) to consensus_tree (new name) in the help of PanToolsadded compilation information to README.md and added citation information to consensus_tree function
I also changed the name of phylogeny_using_groups (old name) to consensus_tree (new name) in the help of PanToolshttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/9Fix Ant's bundled jar generation2021-12-06T10:00:51ZMoed, MatthijsFix Ant's bundled jar generationFixes generation of a bundled jar with Ant's `package-for-store` task. Previously broken because of missing dependencies in `dist/lib` and because of hitting a file count limit for the number of included class files in the final jar.Fixes generation of a bundled jar with Ant's `package-for-store` task. Previously broken because of missing dependencies in `dist/lib` and because of hitting a file count limit for the number of included class files in the final jar.Jonkheer, EefJonkheer, Eefhttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/10K-mer classification method improvement2021-12-09T10:10:58ZJonkheer, EefK-mer classification method improvementNew k-mer classification method with improved scaling
The output file names and locations have been changed for some functionalities (Sorry DJ).
**kmer_classification**
- kmer_distance_tree.R -> genome_kmer_distance_tree.R
- distance...New k-mer classification method with improved scaling
The output file names and locations have been changed for some functionalities (Sorry DJ).
**kmer_classification**
- kmer_distance_tree.R -> genome_kmer_distance_tree.R
- distance_inf_distinct_kmers.csv -> removed
- mash_distance.csv -> distances_for_tree/genome_mash_distance.csv
- distance_distinct_kmers.csv -> distances_for_tree/genome_distance_distinct_kmers.csv
- distance_all_kmers.csv -> distances_for_tree/genome_distance_all_kmers.csv
- core_kmers.csv -> kmer_identifiers/core_kmers.csv
- accessory_kmers.csv -> kmer_identifiers/accessory_kmers.csv
- unique_kmers.csv -> kmer_identifiers/unique_kmers.csv
- phenotype_shared_kmers.csv -> kmer_identifiers/phenotype_shared_kmers.csv
- phenotype_specific_kmers.csv -> kmer_identifiers/phenotype_specific_kmers.csv
- phenotype_exclusive_kmers.csv -> kmer_identifiers/phenotype_exclusive_kmers.csv
**function_overview**
- function_overview_per_group.csv -> removed
- go_overview.txt -> go_overview.csv
- pfam_overview.txt -> pfam_overview.csv
- tigrfam_overview.txt -> tigrfam_overview.csv
- interpro_overview.txt -> interpro_overview.csv
- bgc_overview.txt -> bgc_overview.csv
- phobius_overview.txt -> phobius_signalp_overview.txt
- cog_overview.txt -> cog_overview.csv
**rename_phylogeny**
- tree.newick_RENAMED -> tree_RENAMED.newick
**msa_of_group**
- informative/variable_sites.csv -> informative/variable_site_counts.csv
**calculate_ANI**
- ani.tree -> ANI.newickhttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/11Update to PanTools manual2021-12-10T09:16:08ZJonkheer, EefUpdate to PanTools manualUpdate to PanTools manual & interpro.xml bugfixUpdate to PanTools manual & interpro.xml bugfixhttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/12Update help section2021-12-14T09:37:35ZJonkheer, EefUpdate help sectionExtensive update to the built-in manualExtensive update to the built-in manualhttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/13Reverse completement regions in a --regions-file file now require a minus symbol2021-12-17T15:30:54ZJonkheer, EefReverse completement regions in a --regions-file file now require a minus symbolInclude a minus symbol behind the region file given by `--region-file` to retrieve the reverse complement. Previously, the user had to include 'rv'.
Was tested on using `msa_of_regions` on the lettuce_plastid_pangenome with the followi...Include a minus symbol behind the region file given by `--region-file` to retrieve the reverse complement. Previously, the user had to include 'rv'.
Was tested on using `msa_of_regions` on the lettuce_plastid_pangenome with the following file.
```
3 1 29210 30325 -
7 1 29119 30233 -
5 1 29008 30121 -
11 1 29206 30331 -
8 1 29197 30311 -
9 1 28960 30080 -
2 1 29038 30152 -
1 1 5188 6302 -
13 1 29049 30177 -
12 1 30149 31263 -
6 1 29264 30378 -
4 1 29201 30315 -
10 1 30322 31448 -
```https://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/14Update to GO and Pfam functional databases2021-12-20T20:13:54ZJonkheer, EefUpdate to GO and Pfam functional databasesUpdated three files in addons to update the GO and Pfam databasesUpdated three files in addons to update the GO and Pfam databaseshttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/15Improved error handling MLSA method2021-12-23T08:55:41ZJonkheer, EefImproved error handling MLSA methodhttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/16Migrate to Maven2021-12-23T10:28:31ZMoed, MatthijsMigrate to MavenNotes:
- Test code is taken from directory `test/`
- Directory `test_code/` removed as its contents were identical to those
in `test/`
- All (test) code namespace to `nl.wur.bif.pantools`
- Added Maven and IntelliJ entries to .gitignor...Notes:
- Test code is taken from directory `test/`
- Directory `test_code/` removed as its contents were identical to those
in `test/`
- All (test) code namespace to `nl.wur.bif.pantools`
- Added Maven and IntelliJ entries to .gitignore
- Tests are still broken
- Upgrade to Neo4j 3.5.40https://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/17Fix nucleotide checks for gzip-compressed input files2021-12-23T12:10:54ZMoed, MatthijsFix nucleotide checks for gzip-compressed input filesSee #5.See #5.Jonkheer, EefJonkheer, Eefhttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/18Bugfix core snp nj tree2022-01-05T15:08:23ZJonkheer, EefBugfix core snp nj treehttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/19Update to the retrieve functionalities2022-01-07T15:44:21ZJonkheer, EefUpdate to the retrieve functionalitiesThe functionalities of **retrieve_genomes** and **retrieve_regions** were somewhat redundant. Therefore, I integrated the option to retrieve complete genomes into **retrieve_regions**.
For **retrieve_features** it is now possible to sel...The functionalities of **retrieve_genomes** and **retrieve_regions** were somewhat redundant. Therefore, I integrated the option to retrieve complete genomes into **retrieve_regions**.
For **retrieve_features** it is now possible to select genomes with `--skip` or `--reference` in addition to using a file with`--genome-numbers`.
Proper error handling was added to all both functions.https://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/20Resolved an issue in kmer_classification when skipping certain sequences2022-01-18T14:32:58ZJonkheer, EefResolved an issue in kmer_classification when skipping certain sequencesSee titleSee titlehttps://git.wageningenur.nl/bioinformatics/pantools/-/merge_requests/21added conda environment yaml file2022-01-24T13:20:37ZWorkum, Dirk-Jan vanadded conda environment yaml filethe added yaml file works for the current master branch; it would be good to keep this yaml file updated with novel additionsthe added yaml file works for the current master branch; it would be good to keep this yaml file updated with novel additions