1. Davide Cittaro
  2. utils

Commits

Davide Cittaro  committed 017f10b

bugfixes

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  • Parent commits d314609
  • Branches default

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Files changed (2)

File pcavcf.py

View file
 
   # perform the pca
   results = mlab.PCA(t_data)
-  
-  sys.stderr.write("Plotting PCA charts...\n")
-  if cli_options.label:
-    labels = parser.samples
-  else:
-    labels = []  
-  plot_pca(results, ncomp=cli_options.ncomp, samples=labels, classes=cli_options.classes, prefix=cli_options.vcf)
 
   if cli_options.vcfout:
     sys.stderr.write("Writing VCF file...\n")
       dump_file = "PCAdata"
     np.savez(dump_file, results.Wt, results.Y)    
   
+  sys.stderr.write("Plotting PCA charts...\n")
+  if cli_options.label:
+    labels = parser.samples
+  else:
+    labels = []  
+  plot_pca(results, ncomp=cli_options.ncomp, samples=labels, classes=cli_options.classes, prefix=cli_options.vcf)
 
 
 if __name__ == '__main__':
-  analyze()
+  analyze()

File vcf2xls.py

View file
       header.append("DESCRIPTION")  
       for d_line in cli_options.description:
         tmp_f = d_line.strip().split('\t')
-        description[tmp_f[0]] = tmp_f[1]
+        try:
+          description[tmp_f[0]] = tmp_f[1]
+        except:
+          description[tmp_f[0]] = ''
     
     
   # initialize workbook