What is Python?

Python is a clear and powerful object-oriented programming language, comparable to Perl, Ruby, Scheme, or Java. Integrating Python into SVS 7 provides full programmatic access to many of the software's features enabling the augmentation of existing tools, creating entirely new ones, automation of work flows, integration with other programs and more.

Python Learning Resources

» SVS 7 Scripting Reference
» Python.org
» Beginners Guide to Python

Add-On Scripts Repository for SVS

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

The following scripts are for SVS 7.4+
For scripts compatible with older versions, please visit the Scripts Repository for SVS 7.0-7.3.

Share your scripts with the Golden Helix Community

If you have written any scripts and would like to share them with other SVS 7 users, we encourage you to email a *.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 post it on this page for others to download.

Date Modified	Category	Script	Author
11/10/2011	Edit	Convert Binary and Integer Values to Genotypes This script recodes binary and integer genotypes to the standard genotype format of A_A, A_B, and B_B. Prompts for value of A_A, A_B, and B_B. All other numbers are encoded as missing. Thus if there is multi-allelic data in the spreadsheet, all numbers other than those specified will be encoded as "?". More info »	Greta Linse Peterson Golden Helix
11/10/2011	Analysis	Create Pseudo Marker Mapped Spreadsheet From a non-marker mapped spreadsheet this script creates a new marker mapped spreadsheet with a pseudo marker map containing chromosome 1, positions 1 - #Rows. More info »	Greta Linse Peterson Golden Helix
11/10/2011	CNV Analysis	Create Spreadsheet for Segmentation Based on a column from a spreadsheet, this script creates a new spreadsheet with a pseudo marker map and generic column headers making it suitable for running CNAM optimal segmenting. More info »	Greta Linse Peterson Golden Helix
11/10/2011	Analysis	Frequency Table This script will calculate the frequency distribution of two columns in a spreadsheet. The script can be accessed through the scripts menu and will prompt the user to select two non-real columns. More info »	Autumn Laughbaum Golden Helix
11/10/2011	Edit	Split Column on Specified Delimiter This script prompts the user to select a column that needs to be split on a specified delimiter and for the delimiter to use. The delimiter can be more than one character. More info »	Greta Linse Peterson Golden Helix
11/10/2011	Analysis	Genetic Distance between Samples This script is designed to calculate Cochran-Mantel-Haenszel statistics, given several different spreadsheets corresponding to data from several different strata. More info »	Greta Linse Peterson Golden Helix
11/10/2011	Edit	MIP CN Transformation This script creates 5 transposed spreadsheets, one for each column imported from the MIP Array copy number text file: Copy A, Copy B, CopyNumber, AlleleRatio, and AllelicDifference More info »	Greta Linse Peterson Golden Helix
11/10/2011	Filter	Select Subset of Data by XY Coordinates This script takes an upper and lower bound for two numeric columns and creates a subset spreadsheet for the two columns. More info »	Greta Linse Peterson Golden Helix
10/25/2011	Analysis	CMH Test over Several Strata This script is designed to calculate Cochran-Mantel-Haenszel statistics, given several different spreadsheets corresponding to data from several different strata. More info »	Autumn Laughbaum Golden Helix
10/04/2011	Analysis	Genotype Statistics Summary This script takes a spreadsheet that contains a case/control dependent variable and SNPs and runs all of the genotype association tests as well as tests for a heterozygous advantage model (Dd vs DD, dd) and a homozygous comparison model (DD vs dd). Also calculates Chi Squared Scores, Correlation/Trend test scores and completes count tables. More info »	Greta Linse Peterson Golden Helix
9/29/2011	Filter	Activate or Inactivate based on Marker Map Field This function takes a map field from the current spreadsheet as input and activates based on existence in another spreadsheet's column or another spreadsheet's map, or both. More info »	Autumn Laughbaum Golden Helix
7/28/2011	Analysis	Alternate Allele Frequency This script calculates the percentage of alternate alleles over all samples for each variant. The resulting spreadsheet has columns containing the reference count, alternate allele, alternate allele frequency, reference allele count and alternate allele count. More info »	Mike Thiesen Golden Helix
6/23/2011	Analysis	Create Table for Significant Region Creates a spreadsheet with significant regions from a spreadsheet of p-values. This script extracts p-values more extreme than a certain significance value (cutoff) and combines the remaining markers into segments. If two markers are on different chromosomes or more than a certain distance apart (split), a new region is created. More info »	Ingo Helbig UK-SH Kiel
5/20/2011	Marker Maps	Add Gene Names to Marker Map Adds the associated gene name(s) to each marker in a marker map. More info »	Sam Gardner Golden Helix
5/13/2011	Regression	Extract Info from Regression Stats Viewer This script scans the Regression Statistics Viewer output and prints out the p-value after correcting for any covariates. More info »	Greta Linse Peterson Golden Helix
4/21/2011	Filter	Filter by Marker Map Field This function takes a map field from the current spreadsheet as input, then activates or inactivates based on a given threshold or list, or both. More info »	Autumn Laughbaum Golden Helix
4/21/2011	Analysis	KBAC with Permutation Testing The Kernel-Based Adaptive Cluster (KBAC) method by Liu and Leal [Liu and Leal 2010] first catalogs the variant data within each of a number of regions into multi-marker genotypes. Since the variants are rare, only a relatively few different multi-marker genotypes will be found in any given region. More info »	James Grover Golden Helix
4/21/2011	Marker Maps	Apply Additional Marker Map This function will apply an additional marker map to the a currently mapped spreadsheet. The user can choose to apply the new map's data to only unmapped columns or to all columns, preferring either new marker map or old marker map information. More info »	Sam Gardner Golden Helix
4/21/2011	Analysis	LD Pairwise Analysis Scripts This script outputs results from LD analysis, both the EM and CHM methods and both R² and D' values. More info »	Greta Linse Peterson Golden Helix
4/18/2011	Plotting	Highlight Values in XY Scatter Plot This script plots an XY scatter plot with additional graph items to highlight values of interest. An independent column, dependent column and sample list is needed. More info »	Greta Linse Peterson Golden Helix
4/7/2011	Analysis	Run Multiple Genotype Association Tests This script runs genotypic association tests on multiple dependent phenotype columns. More info »	Christophe Lambert, Greta Linse Peterson Golden Helix
3/14/2011	Import	Import PennCNV This script imports PennCNV input signal intensity files, where each file contains data for a single sample. More info »	Sam Gardner Golden Helix
3/11/2011	Edit	Append Several Spreadsheets This function allows the user to append several spreadsheets in one dialog, saving the user from having to append each spreadsheet individually. More info »	Autumn Laughbaum Golden Helix
3/11/2011	Edit	Join or Merge Several Spreadsheets This function allows the user to merge several spreadsheets in one dialog, saving the user from having to merge each spreadsheet individually. More info »	Autumn Laughbaum Golden Helix
3/3/2011	Analysis	ANOVA with Phenotype and SNPs This function makes use of the scipy package, specifically the scipy.stats.f_oneway and scipy.stats.kruskal functions. This requires a numeric phenotype column and several genotype columns which provide the grouping structure in each test. More info »	Autumn Laughbaum Golden Helix
3/3/2011	Analysis	ANOVA on Numeric Columns This function makes use of the scipy package, specifically the scipy.stats.f_oneway and scipy.stats.kruskal functions. This requires a categorical dependent column that provides the grouping structure and several numeric columns. More info »	Autumn Laughbaum Golden Helix
3/3/2011	Import	Import Affymetrix CN Segment Files This script will import Affymetrix CN Segment files containing copy number segment data as outputted from Affymetrix. More info »	Sam Gardner Golden Helix
3/3/2011	Filter	Filter by SIFT Synonymous Classification This function scans a marker-mapped spreadsheet with several genotypic columns and investigates the corresponding SIFT marker map synonymous or non-synonymous classifications.This script requires the purchase of the Sequence Module to function. More info »	Gabe Rudy Golden Helix
1/26/2011	Edit	Activate ATCG SNPs to flip strand or to exclude SNPs These scripts can be used to identify SNPs that have ambivalent orientation by comparing a genotype dataset with a reference dataset, such as HapMap data. More info »	Joost W. Morsink and Sander W. van der Laan University Medical Center Utrecht
1/26/2011	CNV Analysis	Affymetrix B Allele Frequency Calculation Using Affymetrix CEL files as its source, this script combines quantile normalized SNP A and B probe intensities for each marker into a theta value, then calculates B-Allele Frequencies for each marker. More info »	Greta Linse Peterson Golden Helix
1/26/2011	Import/Export	BEAGLE/BEAGLECALL Scripts Package These scripts are for importing and exporting files from the BEAGLE and BEAGLECALL Genetic Analysis Software Packages. More info »	Various GHI Staff Golden Helix
1/26/2011	Analysis	Calculate Expected P-value This script takes spreadsheet that contains a p-value column and calculates expected p-values for the specified column. It is also optional to export expected –log10 p-values as well. More info »	Greta Linse Peterson Golden Helix
1/26/2011	SNP Analysis	Chi-Squared Contingency Table This script computes the Pearson’s Chi-Squared Statistic for a contingency table with m groups and n observations (m rows and n columns). For 2x2 tables the p-value, –log10 p-value, Bonferroni p-value and –log10 Bonferroni p-value are also computed. More info »	Greta Linse Peterson Golden Helix
1/26/2011	CNV Analysis	CNV PCA Search Given a spreadsheet, prompt for a principal components spreadsheet, a lower and upper bound on the number of components and a step size. Runs association tests using each components setting, does a linear regression on the least significant 90% of the data and reports the slope of the line and a goodness of fit statistic. This script can be used in conjunction with the CNV PCA Search Tutorial. More info »	Christophe Lambert Golden Helix
1/26/2011	Analysis	Compute Odds Ratio CI This script takes a logistic regression results spreadsheet and calculates 90, 95 or 99% confidence intervals for the Odds Ratio. More info »	Greta Linse Peterson Golden Helix
1/26/2011	Analysis	Create Table for Significant Regions This script creates a spreadsheet with significant regions from a spreadsheet of p-values (in the first column). It also extracts p-values more extreme than a certain significance value (cutoff) and combines the remaining markers into segments. If two markers are on different chromosomes or more than a certain distance apart (split), a new region is created. More info »	Ingo Helbig UK-SH Kiel
1/26/2011	Export	Export MACH PED_DAT Files This script exports MACH/Merlin PED and DAT formatted files. Run this script from a pedigree spreadsheet that can contain as many phenotypes as desired. The user will be provided with the option to create one file per chromosome if a marker map is applied to the pedigree spreadsheet. More info »	Greta Linse Peterson Golden Helix
1/26/2011	CNV Analysis	Log Ratio Tails This script calculates percentile values for the upper and lower tails of log ratios using two user-specified thresholds. Missing values are skipped. A log ratio call rate is returned with the results. This script may also be used to identify percentiles for real-value data other than log ratios. More info »	Christophe Lambert, Bryce Christensen Golden Helix
1/26/2011	Analysis	Nonparametric Association Tests (Binary Dependent) This function makes use of the scipy package, specifically the scipy.stats.ranksums and scipy.stats.mannwhitneyu functions. With one binary dependent column, the user can perform nonparametric association tests on all numeric columns. More info »	Autumn Laughbaum Golden Helix
1/26/2011	Analysis	Nonparametric Correlation This function makes use of the scipy package, specifically the scipy.stats.spearmanr and scipy.stats.kendalltau functions. With one numeric dependent column, the user can perform nonparametric correlation tests on all numeric columns. More info »	Autumn Laughbaum Golden Helix
1/26/2011	CNV Analysis	Row Averages with Histogram This script will create a column subset from a numeric spreadsheet, then take the row averages and create a histogram of those averages. The subset is specified with a column chooser. This function is useful for LogR spreadsheets to investigate for possible CNVs. More info »	Autumn Laughbaum Golden Helix
1/26/2011	Quality Assurance	Sample Pair Mismatch This script compares genotype calls from NSP and STY files and calculates the correlation between the nearest markers in the two sets. If there is a high correlation, the NSP and STY markers correspond to the same person, otherwise there is a mismatch. More info »	Christophe Lambert, Greta Linse Peterson Golden Helix
1/26/2011	Plotting	SNP Cluster Plots This script creates scatter plots based on A and B allele intensities that can be split on SNP genotypes to create tri-colored cluster plots. The script will work for up to 100 SNPs at a time. More info »	Greta Linse Peterson Golden Helix

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Add-On Scripts Repository for SVS

Share your scripts with the Golden Helix Community