clinker - clinker v0.0.31

Full Changelog: https://github.com/gamcil/clinker/compare/v0.0.30...v0.0.31

• Fix bug in logger statement when shifting origin
• Check for undefined sequence when parsing input files (requires BioPython >=1.80)

- Python
Published by gamcil over 1 year ago

clinker - clinker v0.0.30

What's Changed

• ✨ feat: enhancement #113 by @Aurorabili in https://github.com/gamcil/clinker/pull/114

New Contributors

• @Aurorabili made their first contribution in https://github.com/gamcil/clinker/pull/114

Full Changelog: https://github.com/gamcil/clinker/compare/v0.0.29...v0.0.30

- Python
Published by gamcil over 1 year ago

clinker - clinker v0.0.29

Full Changelog: https://github.com/gamcil/clinker/compare/v0.0.28...v0.0.29

• Add uppercase ID to list of gene identifiers (fixes #110)

- Python
Published by gamcil almost 2 years ago

clinker - clinker v0.0.28

• Added colour map argument when specifying groups

- Python
Published by gamcil almost 3 years ago

clinker - clinker v0.0.27

• Explicitly check for BioPython version when splitting Alignment/PairwiseAlignment objects instead of try/except

- Python
Published by gamcil over 3 years ago

clinker - clinker v0.0.26

• Fixed an issue with parsing pairwise alignments after changes to default printed format in BioPython v1.80 (https://github.com/biopython/biopython/issues/4183). Should now work fine pre/post v1.80. (https://github.com/gamcil/clinker/issues/91)

- Python
Published by gamcil over 3 years ago

clinker - clinker v0.0.25

• Fix crash when no CDS features are found parsing GFF records (#10)

- Python
Published by gamcil over 3 years ago

clinker - clinker v0.0.24

• Don't open web browser after creating static HTML when file name is provided (#88)

- Python
Published by gamcil almost 4 years ago

clinker - clinker v0.0.23

• Added -gf/--gene_functions argument for grouping genes by shared function/category, instead of just sequence similarity.

Given a 2-column CSV resembling:

GENE_001,Cytochrome P450 GENE_002,Cytochrome P450 GENE_003,Methyltransferase GENE_004,Methyltransferase

Two groups are generated, Cytochrome P450 (GENE001 and 002), and Methyltransferase (GENE003, GENE_004).

• Updated clustermap.js. Gene groups now have tooltips when the corresponding label in the legend is right-clicked, and can now be easily merged to combine groups that share some function/category that did not group together by similarity alone

- Python
Published by gamcil over 4 years ago

clinker - clinker v0.0.22

• Bumped BioPython minimum version to >=1.78 for select method in substitution matrices (https://github.com/biopython/biopython/issues/3205)
• Added -mo, --matrix_out argument for saving cluster alignment distance matrix to a file

- Python
Published by gamcil over 4 years ago

clinker - clinker v0.0.21

• Fix matrix not being extended

- Python
Published by gamcil about 5 years ago

clinker - clinker v0.0.20

• Allow parsing of sequence ranges with -r/--ranges (https://github.com/gamcil/clinker/issues/36)
• Extend substitution matrices to include extra IUPAC codes to avoid translation crashes (https://github.com/gamcil/clinker/pull/55)

- Python
Published by gamcil about 5 years ago

clinker - clinker v0.0.19

• Make sure new SVG node is selected when saving to prevent stale nodes (https://github.com/gamcil/clinker/commit/18a3825f4bd43a0dd684572c8ed976e9dea22822)

- Python
Published by gamcil about 5 years ago

clinker - clinker v0.0.18

• Fix bug when calculating bounding box during SVG save (https://github.com/gamcil/clinker/pull/54)

- Python
Published by gamcil about 5 years ago

clinker - clinker v0.0.17

• Gene stroke colour/width adjustment
• Gene label positions
• Save/load clustermap data object
• Remove hidden elements when saving SVG
• Allow runs with no files to open empty web app
• Change individual gene colours
• Restore gene groups when loading JSON (https://github.com/gamcil/clinker/pull/52)
• Use disjoint-set structure to form gene groups (https://github.com/gamcil/clinker/pull/50)

- Python
Published by gamcil about 5 years ago

clinker - clinker v0.0.16

• Change gene grouping algorithm to iterative version since recursive hits maximum recursion depth with larger input size (#48)

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.15

• Gene grouping is now performed in Python instead of JavaScript
• Added Group class for gene groups, mostly for compatibility with the cblaster implementation (i.e. can now mock groups in Python and pass them to the visualisation)

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.14

• Fixed incorrect gene coordinates being read from GFF files (#39)
• Fixed xlmns value in
• Added default values and some usage examples to help (#41)

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.13

• Fix locus bounds being reset after drag resizing

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.12

• Fix translations for reverse strand CDS features in GFF files
• Fix crash related to saving empty gene features

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.11

Hotfix for locus resizing bug in Chromium based browsers

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.10

• Added ability to draw genes unscaled without intergenic gaps (#17)
• Added toggle for drawing links as lines instead of boxes
• Added toggle for straight/curved links
• Added toggle for colouring links by similarity group colour, not identity
• Added multiprocessing for cluster alignments using -j/--jobs flag (#22)
• Added GFF3/FASTA parser (#10)
• clinker now looks for file extensions: GenBank = .gb, .gbk, .genbank, .gbf or .gbff, GFF = .gtf, .gff, .gff3, FASTA = .fa, .faa, .fna, .fsa, .fasta
• Fixed some invalid SVG tags

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.9

Minor update to fix gene colours not changing when choosing colours from legend entries

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.8

• Reworked simlarity grouping (https://github.com/gamcil/clustermap.js/commit/d44f094734042deeb6e9c30f396eb130fe3954cd)
• Groups now shown in gene tooltips
• More gene qualifiers are saved and shown in gene tooltips
• Added ability to change gene labels in bulk from sidebar (https://github.com/gamcil/clinker/issues/6)
• Added ability to show similarity scores on gene links

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.7

• Added session serialisation using -s/--session flag. Sessions can be loaded alongside new file paths to add them to the session without redoing all alignments
• Extended list of valid gene name qualifiers (fixes #4)
• Use uuid4 to generate object identifiers, not incrementing integers
• Added right-click menu to gene polygons for changing labels manually (#6)
• Fixed bug in cluster dragging where clusters would go below scale bar
• Added --usefileorder argument so cluster order can be determined by input rather than hierarchical clustering (#15)
• Added bioRxiv citation to web app

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.6

• Fixed clinker reading in and translating pseudo CDS features, which caused errors when aligning
• Added -na/--no_align flag to allow clinker to visualise clusters without performing alignments

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.4

• Visualisation is no longer generated automatically by default; use the -p/--plot argument to generate it (optional: pass a file name to generate a static HTML document)

- Python
Published by gamcil over 5 years ago

clinker - clinker v0.0.2

Initial release of clinker

- Python
Published by gamcil over 5 years ago