├── .gitattributes ├── .github └── workflows │ ├── ci.yml │ ├── publish_mkdocs.yml │ ├── publish_to_pypi.yml │ └── push_docker_image.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .streamlit └── config.toml ├── CITATION.cff ├── Dockerfile ├── LICENSE ├── README.md ├── docs ├── api-docs │ ├── genbank.md │ ├── genomeviz.md │ ├── gff.md │ ├── segment.md │ ├── track.md │ └── utils.md ├── cli-docs │ ├── pgv-blast.md │ ├── pgv-mmseqs.md │ ├── pgv-mummer.md │ └── pgv-pmauve.md ├── example_gallery.ipynb ├── getting_started.ipynb ├── gui-docs │ └── pgv-gui.md ├── images │ ├── example │ │ ├── exon_features.png │ │ ├── features.png │ │ ├── genbank_comparison_by_blast.png │ │ ├── genbank_features.png │ │ ├── gff_contigs.png │ │ ├── gff_features.png │ │ ├── styled_features.png │ │ └── tracks_and_links.png │ ├── pgv-blast_example1.png │ ├── pgv-blast_example2.png │ ├── pgv-gui_screen.png │ ├── pgv-mmseqs_example1.png │ ├── pgv-mmseqs_example2.png │ ├── pgv-mmseqs_example3.png │ ├── pgv-mummer_example1.png │ ├── pgv-mummer_example2.png │ ├── pgv-mummer_example3.png │ ├── pgv-pmauve_example1.png │ ├── pgv-pmauve_example2.png │ ├── pgv-viewer-demo.gif │ ├── pgv-viewer_demo1.html │ ├── pgv-viewer_demo2.html │ ├── pycirclize_example.png │ └── pygenomeviz_gallery.png ├── index.md └── plot_tips.ipynb ├── mkdocs.yml ├── notebooks ├── example.ipynb └── fastANI │ ├── B_henselae.fna │ ├── B_quintana.fna │ ├── README.md │ ├── example01.png │ ├── example02.png │ ├── fastani.out │ ├── fastani.out.visual │ └── visualize.py ├── packages.txt ├── pyproject.toml ├── requirements-dev.lock ├── requirements.lock ├── requirements.txt ├── src └── pygenomeviz │ ├── __init__.py │ ├── align │ ├── __init__.py │ ├── coord.py │ └── tool │ │ ├── __init__.py │ │ ├── base.py │ │ ├── blast.py │ │ ├── last.py │ │ ├── mmseqs.py │ │ ├── mummer.py │ │ └── pmauve.py │ ├── const.py │ ├── exception.py │ ├── genomeviz.py │ ├── gui │ ├── __init__.py │ ├── app.py │ ├── assets │ │ └── pgv_demo.gif │ ├── config.py │ ├── plot.py │ └── utils.py │ ├── logger.py │ ├── parser │ ├── __init__.py │ ├── fasta.py │ ├── genbank.py │ └── gff.py │ ├── patches.py │ ├── scripts │ ├── __init__.py │ ├── blast.py │ ├── download.py │ ├── gui.py │ ├── mmseqs.py │ ├── mummer.py │ └── pmauve.py │ ├── segment │ ├── __init__.py │ └── feature.py │ ├── track │ ├── __init__.py │ ├── base.py │ ├── feature.py │ └── link.py │ ├── typing.py │ ├── utils │ ├── __init__.py │ ├── download.py │ ├── helper.py │ └── plot.py │ └── viewer │ ├── __init__.py │ ├── assets │ ├── lib │ │ ├── LICENSE │ │ │ ├── LICENSE.jquery │ │ │ ├── LICENSE.micromodal │ │ │ ├── LICENSE.panzoom │ │ │ ├── LICENSE.popper │ │ │ ├── LICENSE.spectrum │ │ │ ├── LICENSE.tabulator │ │ │ └── LICENSE.tippy │ │ ├── jquery.min.js │ │ ├── micromodal.css │ │ ├── micromodal.min.js │ │ ├── panzoom.min.js │ │ ├── popper.min.js │ │ ├── spectrum.min.css │ │ ├── spectrum.min.js │ │ ├── tabulator.min.css │ │ ├── tabulator.min.js │ │ ├── tippy-bundle.umd.min.js │ │ └── types │ │ │ ├── micromodal.d.ts │ │ │ └── tabulator.d.ts │ └── pgv-viewer.js │ └── pgv-viewer-template.html └── tests ├── __init__.py ├── align ├── __init__.py ├── test_coord.py └── tool │ ├── __init__.py │ ├── test_base.py │ ├── test_blast.py │ ├── test_last.py │ ├── test_mmseqs.py │ ├── test_mummer.py │ └── test_pmauve.py ├── conftest.py ├── gui ├── __init__.py └── test_app.py ├── marker.py ├── parser ├── __init__.py ├── test_fasta.py ├── test_genbank.py └── test_gff.py ├── scripts ├── __init__.py ├── test_blast.py ├── test_download.py ├── test_gui.py ├── test_mmseqs.py ├── test_mummer.py └── test_pmauve.py ├── test_genomeviz.py ├── testdata ├── fasta │ ├── influA │ │ ├── influA_California.fna │ │ ├── influA_Korea.fna │ │ ├── influA_NewYork.fna │ │ └── influA_Shanghai.fna │ ├── test.fna │ ├── test.fna.bz2 │ ├── test.fna.gz │ └── test.zip ├── genbank │ ├── influA │ │ ├── influA_California.gbff │ │ ├── influA_Korea.gbff │ │ ├── influA_NewYork.gbff │ │ └── influA_Shanghai.gbff │ ├── multi_record.gbff │ ├── test.gbff │ ├── test.gbff.bz2 │ ├── test.gbff.gz │ └── test.zip └── gff │ ├── multi_record.gff │ ├── test.gff │ ├── test.gff.bz2 │ ├── test.gff.gz │ └── test.zip ├── track └── test_feature.py └── utils ├── __init__.py ├── test_download.py ├── test_helper.py └── test_plot.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.github/workflows/publish_mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/.github/workflows/publish_mkdocs.yml -------------------------------------------------------------------------------- /.github/workflows/publish_to_pypi.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/.github/workflows/publish_to_pypi.yml -------------------------------------------------------------------------------- /.github/workflows/push_docker_image.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/.github/workflows/push_docker_image.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /.streamlit/config.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/.streamlit/config.toml -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/CITATION.cff -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/README.md -------------------------------------------------------------------------------- /docs/api-docs/genbank.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/api-docs/genbank.md -------------------------------------------------------------------------------- /docs/api-docs/genomeviz.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/api-docs/genomeviz.md -------------------------------------------------------------------------------- /docs/api-docs/gff.md: -------------------------------------------------------------------------------- 1 | # Gff Class 2 | 3 | ::: pygenomeviz.parser.gff.Gff 4 | -------------------------------------------------------------------------------- /docs/api-docs/segment.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/api-docs/segment.md -------------------------------------------------------------------------------- /docs/api-docs/track.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/api-docs/track.md -------------------------------------------------------------------------------- /docs/api-docs/utils.md: -------------------------------------------------------------------------------- 1 | ::: pygenomeviz.utils 2 | -------------------------------------------------------------------------------- /docs/cli-docs/pgv-blast.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/cli-docs/pgv-blast.md -------------------------------------------------------------------------------- /docs/cli-docs/pgv-mmseqs.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/cli-docs/pgv-mmseqs.md -------------------------------------------------------------------------------- /docs/cli-docs/pgv-mummer.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/cli-docs/pgv-mummer.md -------------------------------------------------------------------------------- /docs/cli-docs/pgv-pmauve.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/cli-docs/pgv-pmauve.md -------------------------------------------------------------------------------- /docs/example_gallery.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/example_gallery.ipynb -------------------------------------------------------------------------------- /docs/getting_started.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/getting_started.ipynb -------------------------------------------------------------------------------- /docs/gui-docs/pgv-gui.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/gui-docs/pgv-gui.md -------------------------------------------------------------------------------- /docs/images/example/exon_features.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/example/exon_features.png -------------------------------------------------------------------------------- /docs/images/example/features.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/example/features.png -------------------------------------------------------------------------------- /docs/images/example/genbank_comparison_by_blast.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/example/genbank_comparison_by_blast.png -------------------------------------------------------------------------------- /docs/images/example/genbank_features.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/example/genbank_features.png -------------------------------------------------------------------------------- /docs/images/example/gff_contigs.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/example/gff_contigs.png -------------------------------------------------------------------------------- /docs/images/example/gff_features.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/example/gff_features.png -------------------------------------------------------------------------------- /docs/images/example/styled_features.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/example/styled_features.png -------------------------------------------------------------------------------- /docs/images/example/tracks_and_links.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/example/tracks_and_links.png -------------------------------------------------------------------------------- /docs/images/pgv-blast_example1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-blast_example1.png -------------------------------------------------------------------------------- /docs/images/pgv-blast_example2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-blast_example2.png -------------------------------------------------------------------------------- /docs/images/pgv-gui_screen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-gui_screen.png -------------------------------------------------------------------------------- /docs/images/pgv-mmseqs_example1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-mmseqs_example1.png -------------------------------------------------------------------------------- /docs/images/pgv-mmseqs_example2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-mmseqs_example2.png -------------------------------------------------------------------------------- /docs/images/pgv-mmseqs_example3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-mmseqs_example3.png -------------------------------------------------------------------------------- /docs/images/pgv-mummer_example1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-mummer_example1.png -------------------------------------------------------------------------------- /docs/images/pgv-mummer_example2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-mummer_example2.png -------------------------------------------------------------------------------- /docs/images/pgv-mummer_example3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-mummer_example3.png -------------------------------------------------------------------------------- /docs/images/pgv-pmauve_example1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-pmauve_example1.png -------------------------------------------------------------------------------- /docs/images/pgv-pmauve_example2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-pmauve_example2.png -------------------------------------------------------------------------------- /docs/images/pgv-viewer-demo.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-viewer-demo.gif -------------------------------------------------------------------------------- /docs/images/pgv-viewer_demo1.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-viewer_demo1.html -------------------------------------------------------------------------------- /docs/images/pgv-viewer_demo2.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pgv-viewer_demo2.html -------------------------------------------------------------------------------- /docs/images/pycirclize_example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pycirclize_example.png -------------------------------------------------------------------------------- /docs/images/pygenomeviz_gallery.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/images/pygenomeviz_gallery.png -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/plot_tips.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/docs/plot_tips.ipynb -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/mkdocs.yml -------------------------------------------------------------------------------- /notebooks/example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/notebooks/example.ipynb -------------------------------------------------------------------------------- /notebooks/fastANI/B_henselae.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/notebooks/fastANI/B_henselae.fna -------------------------------------------------------------------------------- /notebooks/fastANI/B_quintana.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/notebooks/fastANI/B_quintana.fna -------------------------------------------------------------------------------- /notebooks/fastANI/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/notebooks/fastANI/README.md -------------------------------------------------------------------------------- /notebooks/fastANI/example01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/notebooks/fastANI/example01.png -------------------------------------------------------------------------------- /notebooks/fastANI/example02.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/notebooks/fastANI/example02.png -------------------------------------------------------------------------------- /notebooks/fastANI/fastani.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/notebooks/fastANI/fastani.out -------------------------------------------------------------------------------- /notebooks/fastANI/fastani.out.visual: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/notebooks/fastANI/fastani.out.visual -------------------------------------------------------------------------------- /notebooks/fastANI/visualize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/notebooks/fastANI/visualize.py -------------------------------------------------------------------------------- /packages.txt: -------------------------------------------------------------------------------- 1 | ncbi-blast+ 2 | mummer 3 | mmseqs2 4 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/pyproject.toml -------------------------------------------------------------------------------- /requirements-dev.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/requirements-dev.lock -------------------------------------------------------------------------------- /requirements.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/requirements.lock -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | requirements.lock -------------------------------------------------------------------------------- /src/pygenomeviz/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/__init__.py -------------------------------------------------------------------------------- /src/pygenomeviz/align/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/align/__init__.py -------------------------------------------------------------------------------- /src/pygenomeviz/align/coord.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/align/coord.py -------------------------------------------------------------------------------- /src/pygenomeviz/align/tool/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/align/tool/__init__.py -------------------------------------------------------------------------------- /src/pygenomeviz/align/tool/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/align/tool/base.py -------------------------------------------------------------------------------- /src/pygenomeviz/align/tool/blast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/align/tool/blast.py -------------------------------------------------------------------------------- /src/pygenomeviz/align/tool/last.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/align/tool/last.py -------------------------------------------------------------------------------- /src/pygenomeviz/align/tool/mmseqs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/align/tool/mmseqs.py -------------------------------------------------------------------------------- /src/pygenomeviz/align/tool/mummer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/align/tool/mummer.py -------------------------------------------------------------------------------- /src/pygenomeviz/align/tool/pmauve.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/align/tool/pmauve.py -------------------------------------------------------------------------------- /src/pygenomeviz/const.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/const.py -------------------------------------------------------------------------------- /src/pygenomeviz/exception.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/exception.py -------------------------------------------------------------------------------- /src/pygenomeviz/genomeviz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/genomeviz.py -------------------------------------------------------------------------------- /src/pygenomeviz/gui/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/pygenomeviz/gui/app.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/gui/app.py -------------------------------------------------------------------------------- /src/pygenomeviz/gui/assets/pgv_demo.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/gui/assets/pgv_demo.gif -------------------------------------------------------------------------------- /src/pygenomeviz/gui/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/gui/config.py -------------------------------------------------------------------------------- /src/pygenomeviz/gui/plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/gui/plot.py -------------------------------------------------------------------------------- /src/pygenomeviz/gui/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/gui/utils.py -------------------------------------------------------------------------------- /src/pygenomeviz/logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/logger.py -------------------------------------------------------------------------------- /src/pygenomeviz/parser/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/parser/__init__.py -------------------------------------------------------------------------------- /src/pygenomeviz/parser/fasta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/parser/fasta.py -------------------------------------------------------------------------------- /src/pygenomeviz/parser/genbank.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/parser/genbank.py -------------------------------------------------------------------------------- /src/pygenomeviz/parser/gff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/parser/gff.py -------------------------------------------------------------------------------- /src/pygenomeviz/patches.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/patches.py -------------------------------------------------------------------------------- /src/pygenomeviz/scripts/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/scripts/__init__.py -------------------------------------------------------------------------------- /src/pygenomeviz/scripts/blast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/scripts/blast.py -------------------------------------------------------------------------------- /src/pygenomeviz/scripts/download.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/scripts/download.py -------------------------------------------------------------------------------- /src/pygenomeviz/scripts/gui.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/scripts/gui.py -------------------------------------------------------------------------------- /src/pygenomeviz/scripts/mmseqs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/scripts/mmseqs.py -------------------------------------------------------------------------------- /src/pygenomeviz/scripts/mummer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/scripts/mummer.py -------------------------------------------------------------------------------- /src/pygenomeviz/scripts/pmauve.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/scripts/pmauve.py -------------------------------------------------------------------------------- /src/pygenomeviz/segment/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/segment/__init__.py -------------------------------------------------------------------------------- /src/pygenomeviz/segment/feature.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/segment/feature.py -------------------------------------------------------------------------------- /src/pygenomeviz/track/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/track/__init__.py -------------------------------------------------------------------------------- /src/pygenomeviz/track/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/track/base.py -------------------------------------------------------------------------------- /src/pygenomeviz/track/feature.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/track/feature.py -------------------------------------------------------------------------------- /src/pygenomeviz/track/link.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/track/link.py -------------------------------------------------------------------------------- /src/pygenomeviz/typing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/typing.py -------------------------------------------------------------------------------- /src/pygenomeviz/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/utils/__init__.py -------------------------------------------------------------------------------- /src/pygenomeviz/utils/download.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/utils/download.py -------------------------------------------------------------------------------- /src/pygenomeviz/utils/helper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/utils/helper.py -------------------------------------------------------------------------------- /src/pygenomeviz/utils/plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/utils/plot.py -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/__init__.py -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.jquery: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.jquery -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.micromodal: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.micromodal -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.panzoom: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.panzoom -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.popper: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.popper -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.spectrum: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.spectrum -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.tabulator: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.tabulator -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.tippy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/LICENSE/LICENSE.tippy -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/jquery.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/jquery.min.js -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/micromodal.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/micromodal.css -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/micromodal.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/micromodal.min.js -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/panzoom.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/panzoom.min.js -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/popper.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/popper.min.js -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/spectrum.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/spectrum.min.css -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/spectrum.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/spectrum.min.js -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/tabulator.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/tabulator.min.css -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/tabulator.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/tabulator.min.js -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/tippy-bundle.umd.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/tippy-bundle.umd.min.js -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/types/micromodal.d.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/types/micromodal.d.ts -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/lib/types/tabulator.d.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/lib/types/tabulator.d.ts -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/assets/pgv-viewer.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/assets/pgv-viewer.js -------------------------------------------------------------------------------- /src/pygenomeviz/viewer/pgv-viewer-template.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/src/pygenomeviz/viewer/pgv-viewer-template.html -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/align/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/align/test_coord.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/align/test_coord.py -------------------------------------------------------------------------------- /tests/align/tool/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/align/tool/test_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/align/tool/test_base.py -------------------------------------------------------------------------------- /tests/align/tool/test_blast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/align/tool/test_blast.py -------------------------------------------------------------------------------- /tests/align/tool/test_last.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/align/tool/test_last.py -------------------------------------------------------------------------------- /tests/align/tool/test_mmseqs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/align/tool/test_mmseqs.py -------------------------------------------------------------------------------- /tests/align/tool/test_mummer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/align/tool/test_mummer.py -------------------------------------------------------------------------------- /tests/align/tool/test_pmauve.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/align/tool/test_pmauve.py -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/gui/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/gui/test_app.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/gui/test_app.py -------------------------------------------------------------------------------- /tests/marker.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/marker.py -------------------------------------------------------------------------------- /tests/parser/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/parser/test_fasta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/parser/test_fasta.py -------------------------------------------------------------------------------- /tests/parser/test_genbank.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/parser/test_genbank.py -------------------------------------------------------------------------------- /tests/parser/test_gff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/parser/test_gff.py -------------------------------------------------------------------------------- /tests/scripts/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/scripts/test_blast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/scripts/test_blast.py -------------------------------------------------------------------------------- /tests/scripts/test_download.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/scripts/test_download.py -------------------------------------------------------------------------------- /tests/scripts/test_gui.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/scripts/test_gui.py -------------------------------------------------------------------------------- /tests/scripts/test_mmseqs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/scripts/test_mmseqs.py -------------------------------------------------------------------------------- /tests/scripts/test_mummer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/scripts/test_mummer.py -------------------------------------------------------------------------------- /tests/scripts/test_pmauve.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/scripts/test_pmauve.py -------------------------------------------------------------------------------- /tests/test_genomeviz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/test_genomeviz.py -------------------------------------------------------------------------------- /tests/testdata/fasta/influA/influA_California.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/fasta/influA/influA_California.fna -------------------------------------------------------------------------------- /tests/testdata/fasta/influA/influA_Korea.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/fasta/influA/influA_Korea.fna -------------------------------------------------------------------------------- /tests/testdata/fasta/influA/influA_NewYork.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/fasta/influA/influA_NewYork.fna -------------------------------------------------------------------------------- /tests/testdata/fasta/influA/influA_Shanghai.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/fasta/influA/influA_Shanghai.fna -------------------------------------------------------------------------------- /tests/testdata/fasta/test.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/fasta/test.fna -------------------------------------------------------------------------------- /tests/testdata/fasta/test.fna.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/fasta/test.fna.bz2 -------------------------------------------------------------------------------- /tests/testdata/fasta/test.fna.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/fasta/test.fna.gz -------------------------------------------------------------------------------- /tests/testdata/fasta/test.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/fasta/test.zip -------------------------------------------------------------------------------- /tests/testdata/genbank/influA/influA_California.gbff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/genbank/influA/influA_California.gbff -------------------------------------------------------------------------------- /tests/testdata/genbank/influA/influA_Korea.gbff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/genbank/influA/influA_Korea.gbff -------------------------------------------------------------------------------- /tests/testdata/genbank/influA/influA_NewYork.gbff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/genbank/influA/influA_NewYork.gbff -------------------------------------------------------------------------------- /tests/testdata/genbank/influA/influA_Shanghai.gbff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/genbank/influA/influA_Shanghai.gbff -------------------------------------------------------------------------------- /tests/testdata/genbank/multi_record.gbff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/genbank/multi_record.gbff -------------------------------------------------------------------------------- /tests/testdata/genbank/test.gbff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/genbank/test.gbff -------------------------------------------------------------------------------- /tests/testdata/genbank/test.gbff.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/genbank/test.gbff.bz2 -------------------------------------------------------------------------------- /tests/testdata/genbank/test.gbff.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/genbank/test.gbff.gz -------------------------------------------------------------------------------- /tests/testdata/genbank/test.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/genbank/test.zip -------------------------------------------------------------------------------- /tests/testdata/gff/multi_record.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/gff/multi_record.gff -------------------------------------------------------------------------------- /tests/testdata/gff/test.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/gff/test.gff -------------------------------------------------------------------------------- /tests/testdata/gff/test.gff.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/gff/test.gff.bz2 -------------------------------------------------------------------------------- /tests/testdata/gff/test.gff.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/gff/test.gff.gz -------------------------------------------------------------------------------- /tests/testdata/gff/test.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/testdata/gff/test.zip -------------------------------------------------------------------------------- /tests/track/test_feature.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/track/test_feature.py -------------------------------------------------------------------------------- /tests/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/utils/test_download.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/utils/test_download.py -------------------------------------------------------------------------------- /tests/utils/test_helper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/utils/test_helper.py -------------------------------------------------------------------------------- /tests/utils/test_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/pyGenomeViz/HEAD/tests/utils/test_plot.py --------------------------------------------------------------------------------