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| Create a working directory and unzip the zip file in that directory. Two subdirectories will be created, ''programs'' and ''sample_data''. Typing | Create a working directory and unzip the zip file in that directory. Two subdirectories will be created, ''programs'' and ''sample_data''. Typing, for example, |
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| . `python trendtest1.py --help` | . `python26 trendtest1.py --help` |
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| python ttconvert1.py -v hol abc ../sample_data | python ttconvert1.py -v -s'.abc' hol abc ../sample_data |
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TrendTest Software
The trend validation procedures are described in the Interbull Code of Practice, https://wiki.interbull.org/public/CoPAppendixIII?action=print.
This software consists of two programs to convert legacy file formats to new formats (ttconvert1/3.py), three programs to perform trend validation by methods 1 - 3 (trendtest1-3.py), a program to combine the results across methods and prepare a zip file ready for submission to the Interbull Center (ttzip.py), and utility module used by those programs (ibutils.py). The conversion programs will process sets of legacy files (file01x and file04x) for all trait groups for a single breed and population of evalution and create a single set of files in a trait independent format. The remaining programs will perform the trend validation tests for all traits for one breed and population and then create a zip file with the input and output files, ready for submission to the Interbull Centre.
Note: In the future, organizations may prefer to prepare the data for the trendtest1-3.py programs directly, bypassing the creation of the legacy file formats and the use of the ttconvert1/3.py programs.
Installation and testing
The programs have been tested under Python 2.6, 2.7, 3.2 and 3.3. As a minimum you will need to have these extra python modules installed on your system: NumPy and, just for Python 2.6, argparse.
Download the attached trendtest20131017.zip file.
Create a working directory and unzip the zip file in that directory. Two subdirectories will be created, programs and sample_data. Typing, for example,
python26 trendtest1.py --help
from a command line prompt, from within the programs directory, should print a brief help message if the installation has been successful.
Some sample data for breed HOL and population ABC are available in the sample_data directory. The two programs for method 1 can be run from the programs directory as follows:
python ttconvert1.py -v -s'.abc' hol abc ../sample_data python trendtest1.py -v -m hol abc ../sample_data
In this example data, parameters and output are all in the sample_data directory. Files can be read from other locations and output written to other locations as well. Please see the following sections for further information.
The outputs should match those in the source zip file.
Detailed descriptions of the single programs are given in the following sections.
More to come ...
Joao/Vale: you could follow the example of the GEBVtest documentation ...