Generic Table View

Introduction

Genome Workbench implements a spreadsheet-like relational view for the data, which can be represented as a table. Generic table view can be used to display:

  1. Genomic Assemblies (Collections)
  2. SNPs
  3. Imported Tabular Data
  4. Phylogenetic Trees

Generic Tabular View can be used to search and query the data. It can also export data to use in third-party programs, like MS Excel.

Viewing Genomic Assemblies (Collections) with Generic Table View

Use Open Dialog to find and load the Genomic Assembly to your project.

open assembly

Once assembly is loaded select it in the Project Tree and use Open View dialog -> Generic Table View.

open table view on assembly

Genome Workbench will display the assembly as a relational table.

generic table assembly

Viewing SNPs as tables

Add a GenBank molecule (say AC021670.2) to your project, then Open it as a Graphical Sequence View.

GSV with Selected Range

In Graphical Sequence View, zoom the area of your interest and select that area. Use context menu to open a view.

Open SNP Table View

Use “SNP Table View” for this.

SNP Table view shows SNPs in the same tabular forms as Generic Table View, but you will see a different nomenclature of columns.

SNP Table view with column selector

Use context menu to change columns you need to display.

Imported Tabular Data

For detailed information on imported tabular data please see the Loading Tabular Data tutorial.

Vieweing Phylogenetic Trees with Generic Table View

Obtaining the Test File

Pleas download test ASN.1 file to be used in this tutorial.

Opening the tree's ASN.1 file

From the File menu choose Open and select File Import from the left side:

tree tabular view 1

Select NCBI ASN.1 files from the drop down list File Format. Navigate to the folder where the file is located and click Open. Then click Finish.

Opening Generic Table View

Now there is a 'New Project' in the Project Tree View.

tree tabular view 2

Double click the tree to open the Open View dialog and select Generic Table View from the list:

tree tabular view 3

A new Generic Table View will open:

tree tabular view 4

Each node is represented by one line in the table and its id, parent, and a set of properties are shown.

Showing/hiding columns

You can select the columns (properties) that are displayed by right clicking the table’s header:

tree tabular view 5

If the table has more than 20 columns, the context menu will display 20 and show item "More...".

Clicking it opens a new Filter Columns dialog, that lets the user set columns visibility:

tree tabular view 6

In this dialog:

  • individual columns can be selected
  • all columns can be selected or deselected
  • a range of visible columns can be defined

The range field is flexible and can hold column numbers, column ranges (from number - to number) and a comma separated combinations of the two. The columns list box is updated to reflect the selection in the range field.

Press Select to save your selection.

Exporting tabular data to CSV

The CSV ("Comma Separated Values") file format is often used to exchange data between different applications. CSV stores tabular data in plain text. Each record is stored on one line and consists of one or more fields, separated by commas. The CSV format is described in RFC 4180.

In order to export a tree’s tabular data to CSV, right click inside the table and select Export to CSV…:

tree tabular view 7

Export To CSV dialog lets you control what data is exported:

tree tabular view 8

You can choose:

  • whether the first row in the output CSV file will contain the names (headers) of the columns
  • to export only the selected cells only
  • which columns will be exported (Select columns to export list box)

When you are done with the configuration, press OK to generate the output CSV file. It will be stored in the path defined in the File Name field.

You can open the generated CSV file using Microsoft Excel or other compatible application:

tree tabular view 9

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Last updated: 2019-09-16T20:01:40Z