We are excited to let you know about new scripts to aid in filtering rows/columns and identifying unique values in a column, as well as two updated scripts. Don’t forget about the Technical Support Bulletins which keep you up-to-date on all the latest script news. You can stream this feed via an RSS reader, receive email updates, or see the latest on the SVS splash screen.
Obtaining New and Updated Scripts
The new and updated scripts listed below and others can be obtained from the Golden Helix Add-On Scripts Repository. Simply click on the script that you would like and download the script and documentation. Please follow the directions for each script to install it in the appropriate directory.
New: Copy Values into User Notes
The Copy Values into User Notes script copies all unique values from an integer, binary, categorical or genotypic column into the User Notes for the selected spreadsheet as a comma separated list. This list can be copied from the User Notes pane and pasted elsewhere, including the script below: Select Rows from String of Values. If only a list of unique values from a column is required this can be an alternative to exporting the data as a spreadsheet.
New: Select Rows from String of Values
The Select Rows from String of Values script activates rows that contain values found in a comma separated string for an integer, binary, categorical or genotypic column. This string of values is entered in the prompt dialog, each value should be separated by a comma. If no values match, all rows are inactivated. An option is available to only change the state of active rows. This script can be used in conjunction with the Copy Values into User Notes script to activate all rows that have a value in the selected column that is in the specified list.
New: Activate Variants by Genotype Count Threshold
The Activate Variants by Genotype Count Threshold tool scans genotypic columns and activates columns based on a user-specified count or percentage threshold of selected genotypes. For example, you could use this tool to activate all genotypic columns where at least 4 out of 6 samples have homozygous alternate variants. Note: This script requires the DNA-Seq Analysis package.
Updated: Find de Novo Candidate Variants
This script was updated to fix a python error that was generated when counting homozygous errors. The updated version of this script is dated 2012-12-10 and can be obtained from the SVS Add-on Scripts Repository page.
Updated: Activate or Inactivate based on Marker Map Field
This script was updated to allow for Integer column types for both the second spreadsheet that contains the values used for filtering as well as Integer field types from the Marker Map.
You can add haplotype block information to a marker map and then use this updated script to filter and select all markers in particular haplotype blocks, such as blocks that contain the most significant SNPs.
Please let us know if you have any questions or concerns about the updates to these scripts or would like assistance in understanding how they can be used in your workflows.