Mercurial > repos > stemcellcommons > spp_tool
changeset 1:23b22c1692fa draft default tip
Replace simplejson with json.
| author | hackdna |
|---|---|
| date | Tue, 20 May 2014 10:53:35 -0400 |
| parents | b15734276ca3 |
| children | |
| files | run_spp.R spp_wrapper.py spp_wrapper.xml |
| diffstat | 3 files changed, 6 insertions(+), 8 deletions(-) [+] |
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--- a/run_spp.R Thu Oct 17 12:39:45 2013 -0400 +++ b/run_spp.R Tue May 20 10:53:35 2014 -0400 @@ -120,7 +120,7 @@ sep.peak <- NA # user-defined peak shift exclude.min <- 10 # lowerbound of strand shift exclusion region exclude.max <- NaN # upperbound of strand shift exclusion region - n.nodes <- NA # number of parallel processing nodes + n.nodes <- 32 # number of parallel processing nodes fdr <- 0.01 # false discovery rate threshold for peak calling npeak <- NA # threshold on number of peaks to call temp.dir <- tempdir() # temporary directory
--- a/spp_wrapper.py Thu Oct 17 12:39:45 2013 -0400 +++ b/spp_wrapper.py Tue May 20 10:53:35 2014 -0400 @@ -5,14 +5,12 @@ import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip from galaxy import eggs -import pkg_resources -pkg_resources.require( "simplejson" ) -import simplejson +import json CHUNK_SIZE = 1024 def main(): - options = simplejson.load( open( sys.argv[1] ) ) + options = json.load( open( sys.argv[1] ) ) output_narrow_peak = sys.argv[2] output_region_peak = sys.argv[3] output_peakshift_file = sys.argv[4] @@ -99,4 +97,4 @@ os.unlink( stderr_name ) #os.rmdir( tmp_dir ) -if __name__ == "__main__": main() \ No newline at end of file +if __name__ == "__main__": main()
--- a/spp_wrapper.xml Thu Oct 17 12:39:45 2013 -0400 +++ b/spp_wrapper.xml Tue May 20 10:53:35 2014 -0400 @@ -99,7 +99,7 @@ <configfiles> <configfile name="options_file"><% -import simplejson +import json %> #set $__options ={ 'experiment_name':str($experiment_name), 'chip_file':str($major_command.input_chipseq_file1) } @@ -165,7 +165,7 @@ #set $__options['savp'] = str( $major_command.save_plot_file ) #end if -${ simplejson.dumps( __options ) } +${ json.dumps( __options ) } </configfile> </configfiles> <tests>