# HG changeset patch
# User fubar
# Date 1315544868 14400
# Node ID 1959becd059294ed7070f28940553f51bddfb68b
Initial upload of files for DGE tool
diff -r 000000000000 -r 1959becd0592 rgDGE.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rgDGE.py Fri Sep 09 01:07:48 2011 -0400
@@ -0,0 +1,338 @@
+# Copyright ross lazarus
+# september 2011
+# all rights reserved
+# for the Rgenetics project
+# all rights reserved
+# licensed to you under the terms of the LGPL as documented at http://www.gnu.org/copyleft/lesser.html
+
+import sys
+import shutil
+import subprocess
+import os
+import time
+import tempfile
+import optparse
+
+progname = os.path.split(sys.argv[0])[1]
+myversion = 'V000.2 September 2011'
+verbose = False
+debug = False
+
+
+galhtmlprefix = """
+
+
+
+
+
+
+
+
+
+"""
+galhtmlattr = """
Galaxy Rgenetics tool output %s run at %s"""
+galhtmlpostfix = """
Galaxy DGE outputs run at %sClick on the images below to download high quality PDF versions\n' % timenow())
+ if len(flist) > 0:
+ html.append('
\n')
+ for fname in flist:
+ dname,e = os.path.splitext(fname)
+ if e.lower() == '.pdf' : # compress and make a thumbnail
+ thumb = '%s.%s' % (dname,self.thumbformat)
+ pdff = os.path.join(self.opts.output_dir,fname)
+ retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
+ if retval == 0:
+ s= ' |
' \
+ % (fname,thumb,fname)
+ else:
+ dname = '%s (thumbnail image not_found)' % fname
+ s= '| %s |
' % (fname,dname)
+ html.append(s)
+ else:
+ html.append('| %s |
' % (fname,fname))
+ html.append('
\n')
+ else:
+ html.append('### Error - R returned no files - please confirm that parameters are sane')
+ html.append('R log follows below
\n')
+ rlog = open(self.tlog,'r').readlines()
+ html += rlog
+ html.append('%s CL = %s\n' % (self.myName,' '.join(sys.argv)))
+ html.append('DGE.R CL = %s\n' % (' '.join(self.cl)))
+ html.append('\n')
+ html.append(galhtmlattr % (progname,timenow()))
+ html.append(galhtmlpostfix)
+ htmlf = file(self.opts.output_html,'w')
+ htmlf.write('\n'.join(html))
+ htmlf.write('\n')
+ htmlf.close()
+
+
+def main():
+ u = """
+ This is a Galaxy wrapper. It expects to be called by DGE.xml as:
+ rgDGE.py --output_html "$html_file.files_path" --input_matrix "$input1" --treatcols "$Treat_cols" --treatname "$treatment_name"
+--ctrlcols "$Control_cols"
+ --ctrlname "$control_name" --output_tab "$outtab" --output_html "$html_file" --output_dir "$html_file.files_path" --method "edgeR"
+
+ """
+ op = optparse.OptionParser()
+ a = op.add_option
+ a('--input_matrix',default=None)
+ a('--output_tab',default=None)
+ a('--output_html',default=None)
+ a('--treatcols',default=None)
+ a('--treatname',default='Treatment')
+ a('--ctrlcols',default=None)
+ a('--ctrlname',default='Control')
+ a('--output_dir',default=None)
+ a('--method',default='edgeR')
+ opts, args = op.parse_args()
+ assert opts.input_matrix and opts.output_html,u
+ assert os.path.isfile(opts.input_matrix),'## DGE runner unable to open supplied input file %s' % opts.input_matrix
+ assert opts.treatcols,'## DGE runner requires a comma separated list of treatment columns eg --treatcols 4,5,6'
+ assert opts.treatcols,'## DGE runner requires a comma separated list of control columns eg --ctlcols 2,3,7'
+ myName=os.path.split(sys.argv[0])[-1]
+ if not os.path.exists(opts.output_dir):
+ os.makedirs(opts.output_dir)
+ m = DGE(myName, opts=opts)
+ retcode = m.runDGE()
+ if retcode:
+ sys.exit(retcode) # indicate failure to job runner
+
+
+
+if __name__ == "__main__":
+ main()
+
+
+