Mercurial > repos > cropgeeks > flapjack

changeset 77:6ace5881c494 draft

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Uploaded
author cropgeeks
date Mon, 26 Feb 2018 04:02:00 -0500
parents 84ce7c332dc4
children 3f84a298c6ca
files FlapjackProject.py
diffstat 1 files changed, 14 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/FlapjackProject.py	Fri Feb 23 10:10:08 2018 -0500
+++ b/FlapjackProject.py	Mon Feb 26 04:02:00 2018 -0500
@@ -38,8 +38,7 @@
 
 parents = {}
 
-samplefiles = {}
-genotypefiles = {}
+filenames = {}
 
 def splitfile(my_file, sample_data, isSample):
     temp_parents = parents
@@ -71,14 +70,13 @@
                         name = my_file + "_" + key
                         if isSample:
                             continue
-                        if name not in samplefiles:
+                        if name not in filenames:
                             filename = tempfile.NamedTemporaryFile(delete=False).name
-                            print("sample file %s has filename %s" % (name, filename))
-                            samplefiles[name] = filename
+                            filenames[name] = filename
                             f = open(filename, "w")
                             f.write('%s' % header)
                         else:
-                            filename = samplefiles.get(name)
+                            filename = filenames.get(name)
                             f=open(filename, "a+")
                         f.write('%s' % line)                        
                         isParent = True
@@ -95,21 +93,22 @@
                     # get file name for genotype data
                     if isinstance(cycle, float) and math.isnan(cycle):
                         # save genotype data to file
-                        if my_file + "_" + group not in genotypefiles:
-                            genotypefiles[my_file + "_" + group] = filename
-                            print("genotype file %s has filename %s" % (my_file + "_" + group, filename))
+                        if my_file + "_" + group not in filenames:
+                            filenames[my_file + "_" + group] = filename
                             f = open(filename, "w")
                             f.write('%s' % header)
                         else :
+                            filename = filenames.get(my_file + "_" + group)
                             f=open(filename, "a+")
                         f.write('%s' % line)
                     else:
                         # save genotype data to file
-                        if group not in genotypefiles:
-                            genotypefiles[my_file + "_" + group+'_'+cycle] = filename
+                        if my_file + "_" + group+'_'+cycle not in filenames:
+                            filenames[my_file + "_" + group+'_'+cycle] = filename
                             f = open(filename, "w")
                             f.write('%s' % header)
                         else :
+                            filename = filenames.get(my_file + "_" + group+'_'+cycle)
                             f=open(filename, "a+")
                         f.write('%s' % line)
                     
@@ -176,8 +175,8 @@
             else:
                 name = key+'_'+sub
             name = str(name)
-            sfile = samplefiles.get(samplefile + "_" + name)
-            gfile = genotypefiles.get(genofile + "_" + name)
+            sfile = filenames.get(samplefile + "_" + name)
+            gfile = filenames.get(genofile + "_" + name)
             gfile += '.tmp'
             cmd = ['java', '-cp',jarfile,'jhi.flapjack.io.cmd.CreateProject','-A','-g',gfile,'-t',sfile,'-p',project,'-n',name,'-S',separator,'-M',missing,'-C']
             if qtlfile:
@@ -203,11 +202,8 @@
             else:
                 name = key+'_'+sub
             name = str(name)
-            print("samplefile %s name %s" % (samplefile, name))
-            sfile = samplefiles.get(samplefile + "_" + name)
-            print("sfile %s" + sfile)
-            gfile = genotypefiles.get(genofile + "_" + name)
-            print("gfile %s" + gfile)
+            sfile = filenames.get(samplefile + "_" + name)
+            gfile = filenames.get(genofile + "_" + name)
 
             cmd = ['java','-jar',headerjar,sfile,gfile,gfile+'.tmp']
             call(cmd)