Extend. Customize. Innovate.

Here you will find a collection of Python scripts submitted by Golden Helix and its customers. All scripts are provided for no additional cost. So feel free to download, use, and even enhance!
›› Learn more about Python scripting

Share your scripts with the Golden Helix community!

If you have written any scripts and would like to share them with other SNP & Variation Suite users, we encourage you to do so. Please email your *.txt or *.py file to community@goldenhelix.com with any accompanying documentation or special instructions. Once we test your script and check its validity, we'll put it on this page for others to download.

Learn how to script

Want to become a scripting innovator? Sign up for a free training session and we'd be happy to teach you! For more information, please contact Josh Forsythe at 406-585-8137 x202.

Added/ Updated	Download	Script Name	Author	Documentation
7/29/08		Log of Eigenvalues Takes the eigenvalues from PCA correction and creates a new spreadsheet with three columns, an index, the untransformed eigenvalues and a column for the log transformed eigenvalues.	Greta Linse Golden Helix
7/14/08		Discretize CN Segment Covariates Discretizes continuous LogR segment covariates created upon running copy number segmentation in CNAM as two state (0,1) or three state (-1,0,1) covariates based upon user specified tolerance level thresholds.	Greta Linse Golden Helix
7/3/08		Column Concordance Tests to see if the values of two columns in the same spreadsheet are identical.	Greta Linse Golden Helix
7/3/08		Gender Concordance Tests to see if the reported gender matches the imputed gender as calculated using the Row Mean Threshold script.	Greta Linse Golden Helix
7/3/08		Row Mean Threshold Calculates the mean of each row, creating a new spreadsheet with a column of row means, and a column indicating whether the mean is greater than a specified threshold.	Greta Linse Golden Helix
7/3/08		Export Univariate Segment Means to WIG Files Exports the segment means spreadsheet as a series of Wiggle files that can be opened an viewed in supported genome browsers.	James Grover Golden Helix
7/3/08		Export Multivariate Segment Means to WIG File Exports the segment means spreadsheet as a single Wiggle file that can be opened an viewed in supported genome browsers.	James Grover Golden Helix
4/11/08		Export LogRs to CNT Exports LogRs as a series of CNT files, one for each sample in a LogR spreadsheet, which can then be viewed in Affymetrix’s GTC Browser - part of Genotyping Console 2.	Jesse Dupre Golden Helix
3/25/08		Import Illumina iControl DB Data Imports Illumina data exported from the iControl database.	Jesse Dupre Golden Helix
3/14/08		Transpose LogR Spreadsheet Transposes the LogR spreadsheet created upon importing LogR values into HelixTree via the Copy Number Segmentation window and adds an index column, making it possible to visualize LogRs and corresponding copy number segments in HelixTree.	Christophe Lambert Golden Helix
3/13/08		Convert to Binary Creates a new spreadsheet that converts all real-valued (R) and integer (I) columns in original spreadsheet to binary (B) columns containing only ones and zeros, based on a user-specified threshold.	Jesse Dupre Golden Helix
2/29/08		Median Smooth For real-valued columns, calculates a moving median centered about a given observation plus/minus the window size.	Christophe Lambert Golden Helix
1/28/08		Inactivate Rows by Row Labels Inactivate only the rows in a spreadsheet whose row labels are in another spreadsheet specified by the user.	Gabe Rudy Golden Helix
1/25/08		Activate Rows by Row Labels Activate only the rows in a spreadsheet whose row labels are in another spreadsheet specified by the user.	Gabe Rudy Golden Helix
12/18/07		Genotype Gender Check Quality control script that predicts gender by looking at the rate of heterozygosity in chromosome X genotype data.	Bo Peng MD Anderson Cancer Center
12/18/07		Integer to Categorical Convert columns automatically imported as integers to categorical variables.	Christophe Lambert Golden Helix
12/18/07		Mean LD in Window (Haynes, 2005)¹ Outputs the mean LD log (p-value) over various positions (inside one chromosome) of a moving window over a specified genetic distance.	James Grover Golden Helix
12/18/07		Recode Affymetrix Genotypes Recodes Affymetrix genotypes from the A,B format to the A,C,G,T format.	Jesse Dupre Golden Helix
12/18/07		Change SNP Names to RSID Converts SNP column names to corresponding RSID #'s using associated marker map info.	Carole Holl Golden Helix
12/18/07		Transpose Spreadsheet Transposes the data within any open spreadsheet so that all the rows will be columns and the columns will be rows.	Christophe Lambert Golden Helix
12/18/07		Allele Frequencies Calculates the number of alleles and their respective frequencies for each SNP.	Josh Forsythe Golden Helix
12/18/07		Calculate Call Rates Calculates call rates for each SNP in a spreadsheet by sample and by SNP.	Josh Forsythe Golden Helix
12/18/07		Transpose File Takes a comma-delimited text file and create a new comma-delimited text file where the rows are columns and the columns are rows.	Christophe Lambert Golden Helix
12/18/07		Import Transposed Imports a comma-delimited text file into HelixTree where the rows are SNPs and the columns are observations.	Christophe Lambert Golden Helix

References

1. M. Hayes, et al. Brief Genetics Report, Patterns of Linkage Disequilibrium in the Type-2 Diabetes Gene Calpain-10, Diabetes, Vol. 54, Dec. 2005 pg. 3573-3576.

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