pygenomeviz - v1.6.1

Fixed

• Fixed pgv-gui bug that caused an error in case aligner tools are only partially installed

- Python
Published by moshi4 about 1 year ago

pygenomeviz - v1.6.0

Added

• Added get_version() class method to AlignTool
• Added support for gz compressed genbank file upload in web app

Changed

• Changed useless expand figure checkbox to wide mode checkbox in web app
• Changed to set on_click="ignore" option in web app download button to avoid rerun web app
• Changed download button UI and layout in web app

Fixed

• Fixed slow completely overlap align coords removal code
• Fixed logging code style based on logging HOWTO best practice

- Python
Published by moshi4 about 1 year ago

pygenomeviz - v1.5.0

Added

• Added Last alignment class experimentally

Fixed

• Fixed too slow completely overlap align coords removal code

- Python
Published by moshi4 over 1 year ago

pygenomeviz - v1.4.2

Fixed

• Fixed track segment separator position adjustment bug (#68)
• Fixed to remove completely overlap alignment links

- Python
Published by moshi4 over 1 year ago

pygenomeviz - v1.4.1

Change Log

Fixed

• Set encoding="utf-8" explicitly to avoid Windows default encoding issue (#63)
• Fixed incorrect gz compressed file extension check logic (#64)

- Python
Published by moshi4 over 1 year ago

pygenomeviz - v1.4.0

Change Log

Added

• Added extra_tooltip argument to add_feature() method explicitly (#61)
• Added get_seqid2record() method to Fasta parser class

Changed

• Dropped python3.8 support

Fixed

• Fixed to skip mmseqs search for no cds genome (#58)
• Fixed get_seqid2seq() method incorrect return type

- Python
Published by moshi4 over 1 year ago

pygenomeviz - v1.3.0

Change Log

New Functionality

• Added theme option (light[default] or dark)
• Added Fasta parser class
• Added load_example_fasta_dataset() utility function
• Added to_stack_features() helper function to avoid feature overlap

Bug Fix

• Fixed to ignore features that have no location (#54)

- Python
Published by moshi4 almost 2 years ago

pygenomeviz - v1.2.1

Change Log

Bug Fix

• Fixed a bug that the dependent libraries for HTML viewer were not packaged correctly

- Python
Published by moshi4 almost 2 years ago

pygenomeviz - v1.2.0

Change Log

New Functionality

• Added Features Table to HTML viewer experimentally (Demo Page)
• Added unit argument to gv.set_scale_xticks() to enable choose Gb, Mb, Kb, bp unit
• Added target_strand & target_range argument to gff.extract_exon_features()

Improvement

• Improved HTML viewer code & UI design
• Fixed to raise error in gv.savefig_html() for invalid figure
• Switched package manager poetry to rye

- Python
Published by moshi4 almost 2 years ago

pygenomeviz - v1.1.0

Change Log

Improvement

• Added reverse complement option to GUI

Bug Fix

• Fixed unexpected sys.exit when calling aligner tool

- Python
Published by moshi4 about 2 years ago

pygenomeviz - v1.0.0

Major Upgrade v1.0.0

See README and document for details.

- Python
Published by moshi4 about 2 years ago

pygenomeviz - v0.4.4

Change Log

Improvement

• Added track.add_features() method

Bug Fix

• Fixed a bug that caused an error in the GUI when uploaded files contain parentheses ().

- Python
Published by moshi4 over 2 years ago

pygenomeviz - v0.4.3

Change Log

Bug Fix

• Fixed bug due to matplotlib v3.8.0 changes (#22)
• Fixed savefig() to suppress memory leak during multiple plots

- Python
Published by moshi4 over 2 years ago

pygenomeviz - v0.4.2

Change Log

Improvement

• Added resource warning message for streamlit cloud deployment

Bug Fix

• Fixed gui run error when upload filename contains space char
• Fixed mmseqs run error when protein_id contains | char
• Fixed a bug that gff.get_seqid2size() got incorrect multi-contig size

https://github.com/moshi4/pyGenomeViz/compare/v0.4.1...v0.4.2

- Python
Published by moshi4 almost 3 years ago

pygenomeviz - v0.4.1

Change Log

Improvement (GUI)

• Added genome comparison result download functionality
• Improved text contents & widget layout
• Adjusted range label padding size

Bug Fix

• Fixed feature coloring bug when facecolor tag is set

https://github.com/moshi4/pyGenomeViz/compare/v0.4.0...v0.4.1

- Python
Published by moshi4 almost 3 years ago

pygenomeviz - v0.4.0

Change Log

New Functionality

• Added GUI (Web browser) functionality using streamlit (Demo Page)

Improvement

• Improved html viewer tooltip display content
• Changed linter flake8 to ruff

https://github.com/moshi4/pyGenomeViz/compare/v0.3.2...v0.4.0

- Python
Published by moshi4 almost 3 years ago

pygenomeviz - v0.3.2

Change Log

Minor Change

• Added reverse complement option to CLI
• Added target_strand, pseudogene arguments to gff.extract_features() method
• Drop python3.7 support

https://github.com/moshi4/pyGenomeViz/compare/v0.3.1...v0.3.2

- Python
Published by moshi4 over 3 years ago

pygenomeviz - v0.3.1

Change Log

Minor Change

• Added pseudogene option to add_genbank_features() method
• Added --pseudo, --pseudo_color option to pgv-mummer CLI (#7)

https://github.com/moshi4/pyGenomeViz/compare/v0.3.0...v0.3.1

- Python
Published by moshi4 over 3 years ago

pygenomeviz - v0.3.0

Change Log

New Functionality

• Added GFF parser class (parser/gff.py)
• Added GFF features plot method (add_gff_features())

Minor Change

• Added facecolor_handle_func option to add_genbank_features() method
• Added ymargin option to set_sublabel() method
• Improved HTML viewer tooltip display
• Fixed duplicate colorbar display issue for same colors
• Added colorbar width, height control option to CLI (pgv-mummer, pgv-mmseqs)

- Python
Published by moshi4 over 3 years ago

pygenomeviz - v0.2.3

Change Log

New Functionality

• Added interactive HTML viewer output functionality (Demo Page)
• Added new CLI workflow pgv-simpleplot for simple genome visualization

- Python
Published by moshi4 over 3 years ago

pygenomeviz - v0.2.2

Change Log

Minor Change

• Added set_sublabel() method
• Set appropriate matplotlib rc(runtime configuration) params to adjust figure appearence
• Set appropriate GridSpec left-right-bottom-top params to adjust figure appearence
• Used typing.Literal to restrict allowed argument values

- Python
Published by moshi4 almost 4 years ago

pygenomeviz - v0.2.1

Change Log

Minor Change

• Added start_pos option to add_feature_track() method
• Added position option to add_subtrack() method
• Changed GenomeViz default plot_size_thr parameter 0.0005 to 0
• Changed add_link() method to occur error if start-end value is out of track range
• Removed unnecessary maptype option of pgv-mummer cli
• Fixed deprecated typing module type hints style (Use built-in types)

- Python
Published by moshi4 almost 4 years ago

pygenomeviz - v0.2.0

Change Log

New Functionality

• Added genome alignment & visualization CLI workflow

  • pgv-mummer: MUMmer pairwise genome alignment
  • pgv-mmseqs: MMseqs CDS RBH search in each genome
  • pgv-pmauve: progressiveMauve multiple genome alignment

• Added MMseqs, progressiveMauve alignment class

Minor Change

• Changed to plot link line if link width is 0
• Added track label color change option
• Changed to manage subtracks independently from other tracks

- Python
Published by moshi4 almost 4 years ago

pygenomeviz - v0.1.1

Change Log

Minor Change

• Improved subtrack add method
• Changed that link track ratios can be set individually
• Added feature label margin (=0.1)

Bug Fix

• Fixed GC content & GC skew positions misalignment in calculation method
• Fixed incorrect zero-based & one-based position settings mixture (Unified to zero-based)

- Python
Published by moshi4 almost 4 years ago

pygenomeviz - v0.1.0

First Official Release

pyGenomeViz is a genome visualization python package for comparative genomics implemented based on matplotlib.

• Basic functionality implementation is complete
• Still in the development stage

- Python
Published by moshi4 almost 4 years ago