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| Original file line number | Diff line number | Diff line change |
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| @@ -1,6 +1,6 @@ | ||
| [run] | ||
| branch = True | ||
| include = genipe* | ||
| source = genipe | ||
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| [report] | ||
| exclude_lines = | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,79 @@ | ||
| #!/usr/bin/env bash | ||
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| # Getting genipe's version to build | ||
| genipe_version=$1 | ||
| if [ -z $genipe_version ] | ||
| then | ||
| echo "usage: $0 VERSION" 1>&2 | ||
| exit 1 | ||
| fi | ||
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| # Creating a directory for the build module | ||
| mkdir -p conda_dist | ||
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| # Creating a directory for the skeleton | ||
| mkdir -p skeleton | ||
| pushd skeleton | ||
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| # Creating the skeleton | ||
| conda skeleton pypi genipe --version $genipe_version | ||
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| # Checking that fetching genipe was successful | ||
| if [ $? -ne 0 ] | ||
| then | ||
| echo "Error when creating skeleton for genipe version $genipe_version" 1>&2 | ||
| exit 1 | ||
| fi | ||
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| # The different python versions and platforms | ||
| python_versions="3.4 3.5" | ||
| platforms="linux-32 linux-64 osx-64" | ||
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| # Building | ||
| for python_version in $python_versions | ||
| do | ||
| # Building | ||
| conda build --python $python_version genipe &> log.txt | ||
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| # Checking the build was completed | ||
| if [ $? -ne 0 ] | ||
| then | ||
| cat log.txt | ||
| echo "Error when building genipe $genipe_version (python" \ | ||
| "$python_version)" 1>&2 | ||
| exit 1 | ||
| fi | ||
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| # Fetching the file name of the build | ||
| filename=$(egrep "^# [$] anaconda upload \S+$" log.txt | cut -d " " -f 5) | ||
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| # Checking the file exists | ||
| if [ -z $filename ]||[ ! -e $filename ] | ||
| then | ||
| echo "Problem fetching file $filename" 1>&2 | ||
| exit 1 | ||
| fi | ||
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| # Converting to the different platforms | ||
| for platform in $platforms | ||
| do | ||
| conda convert -p $platform $filename -o ../conda_dist | ||
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| # Checking the conversion was completed | ||
| if [ $? -ne 0 ] | ||
| then | ||
| echo "Problem converting genipe $genipe_version (python" \ | ||
| "$python_version) to $platform" 1>&2 | ||
| exit 1 | ||
| fi | ||
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| done | ||
| done | ||
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| popd | ||
| rm -rf skeleton | ||
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| # Indexing | ||
| pushd conda_dist | ||
| conda index * | ||
| popd |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,45 @@ | ||
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| .. _stats-exec-time: | ||
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| Statistical Analysis Execution Time | ||
| ==================================== | ||
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| GWAS analysis of imputed markers is computationally intensive. While it is | ||
| feasible to run such analyses on some simple models like linear and logistic | ||
| regression, more complex models like Cox regression and mixed linear models | ||
| require more computing power or specialized implementations. | ||
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| We have optimized the mixed linear model analysis to significantly decrease | ||
| computation time. Using a two-step approach (as described by Sikorska *et al.*, | ||
| 2015 [doi: `10.1038/ejhg.2015.1 | ||
| <http://www.nature.com/ejhg/journal/v23/n10/abs/ejhg20151a.html>`_]), the | ||
| execution time is comparable to a simple linear regression. Prior to | ||
| optimization, the analysis of chromosome 2 was performed in 53 hours for 33 | ||
| sub-analysis with 6 threads each (which corresponds to 198 threads). | ||
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| The following figure shows the execution time for a typical imputation analysis | ||
| of chromosome 2, imputed for 5,045 samples. Chromosome 2 was composed a total | ||
| of 1,170,797 loci, where 961,019 were of sufficient quality, and 528,932 had a | ||
| MAF higher than 1%. The black dashed line is the execution time for Plink. | ||
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| .. figure:: _static/images/execution_time.png | ||
| :align: center | ||
| :width: 70% | ||
| :alt: Statistical analysis exection time. | ||
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| .. note:: | ||
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| On some installation, when executing the analysis with *n* threads, | ||
| *OPENBLAS* automatically uses all the CPUs for each thread, such that the | ||
| load quickly increases to *n* times the number of CPUs. Such high load slows | ||
| down the analysis considerably. | ||
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| To avoid this, always export the following environment variable and specify | ||
| the total number of threads using the ``--nb-process`` option. | ||
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| .. code-block:: bash | ||
| export OPENBLAS_NUM_THREADS=1 | ||
| We are planning to optimize the Cox's proportional hazard regression in the | ||
| near future. |
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