snipgenie

• snipgenie package
  • Submodules
  • snipgenie.gui module
    • App
      • App.about()
      • App.add_dock()
      • App.add_file()
      • App.add_gc_mean()
      • App.add_mapping_stats()
      • App.add_mask()
      • App.add_mean_depth()
      • App.add_plugin_dock()
      • App.add_read_lengths()
      • App.add_recent_file()
      • App.align_files()
      • App.alignment_completed()
      • App.calling_completed()
      • App.check_contamination()
      • App.check_fastq_table()
      • App.check_files()
      • App.check_heterozygosity()
      • App.check_missing_files()
      • App.check_output_folder()
      • App.clean_up()
      • App.clear_plugins()
      • App.clear_tabs()
      • App.closeEvent()
      • App.close_right_tab()
      • App.close_tab()
      • App.create_menu()
      • App.create_tool_bar()
      • App.csq_viewer()
      • App.discover_plugins()
      • App.fastq_quality_report()
      • App.get_fasta_reads()
      • App.get_right_tabs()
      • App.get_selected()
      • App.get_tab_indices()
      • App.get_tab_names()
      • App.get_tabs()
      • App.import_results_folder()
      • App.load_fastq_files_dialog()
      • App.load_fastq_folder_dialog()
      • App.load_fastq_table()
      • App.load_plugin()
      • App.load_preset_genome()
      • App.load_presets_menu()
      • App.load_project()
      • App.load_project_dialog()
      • App.load_settings()
      • App.load_test()
      • App.make_phylo_tree()
      • App.mapping_stats()
      • App.merge_meta_data()
      • App.missing_sites()
      • App.new_project()
      • App.online_documentation()
      • App.phylogeny_completed()
      • App.plot_dist_matrix()
      • App.preferences()
      • App.processing_completed()
      • App.progress_fn()
      • App.quality_summary()
      • App.quit()
      • App.rd_analysis()
      • App.rd_analysis_completed()
      • App.read_distributon()
      • App.redirect_stdout()
      • App.run()
      • App.run_threaded_process()
      • App.run_trimming()
      • App.sample_details()
      • App.save_plugin_data()
      • App.save_project()
      • App.save_project_dialog()
      • App.save_settings()
      • App.set_annotation()
      • App.set_mask()
      • App.set_output_folder()
      • App.set_reference()
      • App.set_style()
      • App.setup_gui()
      • App.setup_paths()
      • App.show_bam_viewer()
      • App.show_blast_url()
      • App.show_browser_tab()
      • App.show_error_log()
      • App.show_info()
      • App.show_map()
      • App.show_nucldb_url()
      • App.show_phylogeny()
      • App.show_plugin()
      • App.show_recent_files()
      • App.show_ref_annotation()
      • App.show_snpdist()
      • App.show_variants()
      • App.snp_alignment()
      • App.snp_typing()
      • App.snp_viewer()
      • App.start_logging()
      • App.staticMetaObject
      • App.tree_viewer()
      • App.update_labels()
      • App.update_mask()
      • App.update_plugin_menu()
      • App.update_ref_genome()
      • App.update_table()
      • App.variant_calling()
      • App.vcf_viewer()
      • App.zoom_in()
      • App.zoom_out()
    • AppOptions
    • Communicate
      • Communicate.newproj
      • Communicate.staticMetaObject
    • StdoutRedirect
      • StdoutRedirect.printOccur
      • StdoutRedirect.start()
      • StdoutRedirect.staticMetaObject
      • StdoutRedirect.stop()
      • StdoutRedirect.write()
    • Worker
      • Worker.run()
    • WorkerSignals
      • WorkerSignals.error
      • WorkerSignals.finished
      • WorkerSignals.progress
      • WorkerSignals.result
      • WorkerSignals.staticMetaObject
    • main()
  • snipgenie.widgets module
    • BaseOptions
      • BaseOptions.apply()
      • BaseOptions.applyOptions()
      • BaseOptions.increment()
      • BaseOptions.setWidgetValue()
      • BaseOptions.showDialog()
      • BaseOptions.updateWidgets()
    • BasicDialog
      • BasicDialog.apply()
      • BasicDialog.close()
      • BasicDialog.copy_to_clipboard()
      • BasicDialog.createButtons()
      • BasicDialog.createWidgets()
      • BasicDialog.staticMetaObject
      • BasicDialog.update()
    • BrowserViewer
      • BrowserViewer.add_widgets()
      • BrowserViewer.load_page()
      • BrowserViewer.navigate_to_url()
      • BrowserViewer.staticMetaObject
      • BrowserViewer.update_urlbar()
      • BrowserViewer.zoom()
    • ColorButton
      • ColorButton.color()
      • ColorButton.colorChanged
      • ColorButton.mousePressEvent()
      • ColorButton.onColorPicker()
      • ColorButton.setColor()
      • ColorButton.staticMetaObject
    • DynamicDialog
      • DynamicDialog.get_values()
      • DynamicDialog.staticMetaObject
    • Editor
      • Editor.contextMenuEvent()
      • Editor.insert()
      • Editor.staticMetaObject
      • Editor.zoom()
    • FileViewer
      • FileViewer.show_records()
      • FileViewer.staticMetaObject
    • GraphicalBamViewer
      • GraphicalBamViewer.add_widgets()
      • GraphicalBamViewer.load_data()
      • GraphicalBamViewer.redraw()
      • GraphicalBamViewer.set_chrom()
      • GraphicalBamViewer.staticMetaObject
      • GraphicalBamViewer.update_chrom()
      • GraphicalBamViewer.value_changed()
      • GraphicalBamViewer.zoom_in()
      • GraphicalBamViewer.zoom_out()
    • MergeDialog
      • MergeDialog.apply()
      • MergeDialog.createWidgets()
      • MergeDialog.staticMetaObject
      • MergeDialog.updateColumns()
    • MultipleInputDialog
      • MultipleInputDialog.accept()
      • MultipleInputDialog.staticMetaObject
    • PlainTextEditor
      • PlainTextEditor.contextMenuEvent()
      • PlainTextEditor.staticMetaObject
      • PlainTextEditor.zoom()
    • PlotViewer
      • PlotViewer.clear()
      • PlotViewer.create_figure()
      • PlotViewer.redraw()
      • PlotViewer.set_figure()
      • PlotViewer.staticMetaObject
      • PlotViewer.zoom()
    • PreferencesDialog
      • PreferencesDialog.apply()
      • PreferencesDialog.createButtons()
      • PreferencesDialog.createWidgets()
      • PreferencesDialog.reset()
      • PreferencesDialog.setDefaults()
      • PreferencesDialog.staticMetaObject
      • PreferencesDialog.updateWidgets()
    • SimpleBamViewer
      • SimpleBamViewer.add_widgets()
      • SimpleBamViewer.find_gene()
      • SimpleBamViewer.goto()
      • SimpleBamViewer.load_data()
      • SimpleBamViewer.next_page()
      • SimpleBamViewer.prev_page()
      • SimpleBamViewer.redraw()
      • SimpleBamViewer.set_chrom()
      • SimpleBamViewer.staticMetaObject
      • SimpleBamViewer.update_chrom()
      • SimpleBamViewer.value_changed()
      • SimpleBamViewer.zoom_in()
      • SimpleBamViewer.zoom_out()
    • TableViewer
      • TableViewer.setDataFrame()
      • TableViewer.staticMetaObject
    • TextViewer
      • TextViewer.add_widgets()
      • TextViewer.staticMetaObject
    • ToolBar
      • ToolBar.addButton()
      • ToolBar.createButtons()
      • ToolBar.staticMetaObject
    • addToolBarItems()
    • dialogFromOptions()
    • getWidgetValues()
    • setWidgetValues()
  • snipgenie.tools module
    • bam_to_fastq()
    • batch_iterator()
    • blast_fasta()
    • blast_sequences()
    • checkDict()
    • clustal_alignment()
    • concat_seqrecords()
    • core_alignment_from_vcf()
    • dataframe_to_fasta()
    • diffseqs()
    • fasta_to_dataframe()
    • fastq_quality_report()
    • fastq_random_seqs()
    • fastq_to_dataframe()
    • fastq_to_fasta()
    • fastq_to_rec()
    • features_summary()
    • fetch_sra_reads()
    • genbank_to_dataframe()
    • get_attributes()
    • get_blast_results()
    • get_chrom()
    • get_cmd()
    • get_fasta_length()
    • get_fastq_info()
    • get_fastq_read_lengths()
    • get_fastq_size()
    • get_gc()
    • get_mean_depth()
    • get_sb_number()
    • get_snp_matrix()
    • get_spoligotype()
    • get_spoligotypes()
    • get_subsample_reads()
    • get_unique_snps()
    • get_vcf_samples()
    • gff_bcftools_format()
    • gff_to_records()
    • gunzip()
    • kraken()
    • local_blast()
    • make_blast_database()
    • move_files()
    • normpdf()
    • pdf_qc_reports()
    • plot_fastq_gc_content()
    • plot_fastq_qualities()
    • records_to_dataframe()
    • remote_blast()
    • resource_path()
    • samtools_coverage()
    • samtools_depth()
    • samtools_flagstat()
    • samtools_tview()
    • set_attributes()
    • snp_dist_matrix()
    • trim_reads()
    • trim_reads_default()
    • vcf_to_dataframe()
  • snipgenie.app module
    • Logger
      • Logger.flush()
      • Logger.write()
    • WorkFlow
      • WorkFlow.run()
      • WorkFlow.setup()
    • align_reads()
    • blast_contaminants()
    • check_platform()
    • check_samples_aligned()
    • check_samples_unique()
    • clean_bam_files()
    • copy_ref_genomes()
    • csq_call()
    • fetch_binaries()
    • fetch_contam_file()
    • get_aa_snp_matrix()
    • get_files_from_paths()
    • get_pivoted_samples()
    • get_samples()
    • get_samples_from_bam()
    • main()
    • mapping_stats()
    • mask_filter()
    • mpileup()
    • mpileup_multiprocess()
    • mpileup_parallel()
    • mpileup_region()
    • overwrite_vcf()
    • read_csq_file()
    • relabel_vcfheader()
    • run_bamfiles()
    • site_proximity_filter()
    • test_run()
    • trim_files()
    • variant_calling()
    • worker()
    • write_samples()
  • snipgenie.aligners module
    • bowtie_align()
    • build_bowtie_index()
    • build_bwa_index()
    • build_subread_index()
    • bwa_align()
    • minimap2_align()
    • subread_align()
  • snipgenie.plotting module
    • create_grid()
    • create_hex_grid()
    • display_igv()
    • draw_pie()
    • gen_colors()
    • get_bam_aln()
    • get_chrom_from_bam()
    • get_color_mapping()
    • get_coverage()
    • get_fasta_length()
    • get_fasta_names()
    • get_fasta_sequence()
    • heatmap()
    • make_legend()
    • plot_bam_alignment()
    • plot_coverage()
    • plot_features()
    • random_colors()
    • show_colors()
  • snipgenie.trees module
    • biopython_draw_tree()
    • color_leaves()
    • colors_from_labels()
    • convert_branch_lengths()
    • create_tree()
    • delete_nodes()
    • format_nodes()
    • get_clusters()
    • get_colormap()
    • remove_nodes()
    • remove_tiplabels()
    • run_RAXML()
    • run_fasttree()
    • run_treecluster()
    • set_nodesize()
    • set_tiplabels()
    • toytree_draw()
  • snipgenie.simulate module
    • artificial_fastq_generator()
    • generate_fastqs()
    • run_phastsim()
  • Module contents