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comparison cuffdata.py @ 7:b5562b9a55c7

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Use same bias_correction cached param as devteam cuffdiff
author Jim Johnson <jj@umn.edu>
date Mon, 13 Oct 2014 09:12:47 -0500
parents 137aab1d9ac1
children
comparison
equal deleted inserted replaced
6:137aab1d9ac1 7:b5562b9a55c7
133 return 133 return
134 try: 134 try:
135 ## Create a tmpdir 135 ## Create a tmpdir
136 ## create an Rscript to write out info about the CuffData, e.g. samples replicates gene_ids 136 ## create an Rscript to write out info about the CuffData, e.g. samples replicates gene_ids
137 ## define file names to use as sinks for each type of data 137 ## define file names to use as sinks for each type of data
138 # tmp_dir = tempfile.mkdtemp() 138 tmp_dir = tempfile.mkdtemp()
139 tmp_dir = '/tmp/gx/cuffdb'
140 if not os.path.isdir(tmp_dir): 139 if not os.path.isdir(tmp_dir):
141 os.makedirs(tmp_dir) 140 os.makedirs(tmp_dir)
142 rscript = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.r' ).name 141 rscript = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.r' ).name
143 rscript_fh = open( rscript, 'wb' ) 142 rscript_fh = open( rscript, 'wb' )
144 rscript_fh.write('library(cummeRbund)\n') 143 rscript_fh.write('library(cummeRbund)\n')