Modernize exception handling for devteam tools

tool_collections/taxonomy/find_diag_hits/find_diag_hits.py

@@ -136,7 +136,7 @@ def stop_err(msg):
         val_string = val_string.strip(', ')
         val_string = "insert into tax values(" + val_string + ")"
         cur.execute(val_string)
-except Exception, e:
+except Exception as e:
     stop_err('%s\n' % e)
 
 tax_file.close()    
@@ -165,6 +165,6 @@ def stop_err(msg):
                 out_string = '%s\t%s\t' % ( item[0], item[1] )
                 out_string += rankName
                 print >>out_file, out_string
-except Exception, e:
+except Exception as e:
     stop_err("%s\n" % e)
 

tool_collections/taxonomy/find_diag_hits/find_diag_hits.xml

@@ -1,4 +1,4 @@
-<tool id="find_diag_hits" name="Find diagnostic hits" version="1.0.0">
+<tool id="find_diag_hits" name="Find diagnostic hits" version="1.0.1">
     <description></description>
     <requirements>
         <requirement type="package" version="1.0.0">taxonomy</requirement>

tool_collections/taxonomy/lca_wrapper/lca.py

@@ -65,7 +65,7 @@ class       :10,
         if POS2 is not specified, the newer versions of sort will consider the entire line for sorting. To prevent this, we set POS2=POS1.
         """
         command_line = "sort -f -k " + str(group_col+1) +"," + str(group_col+1) + " -o " + tmpfile.name + " " + inputfile
-    except Exception, exc:
+    except Exception as exc:
         stop_err( 'Initialization error -> %s' %str(exc) )
 
     error_code, stdout = commands.getstatusoutput(command_line)
@@ -190,4 +190,4 @@ class       :10,
         print "Skipped %d invalid lines." % ( skipped_lines )
 
 if __name__ == "__main__":
-    main()
+    main()

tool_collections/taxonomy/lca_wrapper/lca.xml

@@ -1,4 +1,4 @@
-<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.1">
+<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.2">
   <description></description>
     <requirements>
         <requirement type="package" version="1.0.0">taxonomy</requirement>

tool_collections/taxonomy/t2ps/t2ps_wrapper.py

@@ -42,7 +42,7 @@ def stop_err(msg):
     retcode = subprocess.call( t2t_cmd, shell=True )
     if retcode < 0:
         print >>sys.stderr, "Execution of taxonomy2tree terminated by signal", -retcode
-except OSError, e:
+except OSError as e:
     print >>sys.stderr, "Execution of taxonomy2tree failed:", e
 
 
@@ -53,7 +53,7 @@ def stop_err(msg):
     retcode = subprocess.call( t2ps_cmd, shell=True )
     if retcode < 0:
         print >>sys.stderr, "Execution of tree2PS-fast terminated by signal", -retcode
-except OSError, e:
+except OSError as e:
     print >>sys.stderr, "Execution of tree2PS-fast failed:", e
 
 # Convert PS to PDF
@@ -63,5 +63,5 @@ def stop_err(msg):
     retcode = subprocess.call( ps2pdf_cmd, shell=True )
     if retcode < 0:
         print >>sys.stderr, "Execution of ps2pdf terminated by signal", -retcode
-except OSError, e:
+except OSError as e:
     print >>sys.stderr, "Execution of ps2pdf failed:", e

tool_collections/taxonomy/t2ps/t2ps_wrapper.xml

@@ -1,4 +1,4 @@
-<tool id="Draw_phylogram" name="Draw phylogeny" version="1.0.0">
+<tool id="Draw_phylogram" name="Draw phylogeny" version="1.0.1">
   <description></description>
     <requirements>
         <requirement type="package" version="1.0.0">taxonomy</requirement>

tools/annotation_profiler/annotation_profiler.xml

@@ -1,4 +1,4 @@
-<tool id="Annotation_Profiler_0" name="Profile Annotations" version="1.0.0">
+<tool id="Annotation_Profiler_0" name="Profile Annotations" version="1.0.1">
   <description>for a set of genomic intervals</description>
   <requirements>
     <requirement type="package" version="0.7.1">bx-python</requirement>

tools/annotation_profiler/annotation_profiler_for_interval.py

@@ -34,7 +34,7 @@ def __getitem__( self, i ):
         try:
             start = struct.unpack( self.fmt, self.file.read( self.fmt_size ) )[0]
             end = struct.unpack( self.fmt, self.file.read( self.fmt_size ) )[0]
-        except Exception, e:
+        except Exception as e:
             raise IndexError, e
         self._cached_ranges[i] = ( start, end )
         return start, end
@@ -45,12 +45,12 @@ class RegionCoverage:
     def __init__( self, filename_base, profiler_info ):
         try:
             self._coverage = CachedRangesInFile( "%s.covered" % filename_base, profiler_info )
-        except Exception, e:
+        except Exception as e:
             #print "Error loading coverage file %s: %s" % ( "%s.covered" % filename_base, e )
             self._coverage = []
         try: 
             self._total_coverage = int( open( "%s.total_coverage" % filename_base ).read() )
-        except Exception, e:
+        except Exception as e:
             #print "Error loading total coverage file %s: %s" % ( "%s.total_coverage" % filename_base, e )
             self._total_coverage = 0
     def get_start_index( self, start ):

tools/annotation_profiler/scripts/build_profile_indexes.py

@@ -257,7 +257,7 @@ def __main__():
                 chrom_lengths[ fields[0] ] = int( fields[ 1 ] )
             chroms = chrom_lengths.keys()
             print 'Chrom info taken from chromInfo.txt.gz.'
-        except Exception, e:
+        except Exception as e:
             print 'Error loading chrom info from chromInfo.txt.gz, trying FTP method.'
             chrom_lengths = {} #zero out chrom_lengths
             chroms = []

tools/best_regression_subsets/best_regression_subsets.py

@@ -42,13 +42,13 @@ def stop_err(msg):
             fields = line.split("\t")
             try:
                 yval = float(fields[y_col])
-            except Exception, ey:
+            except Exception as ey:
                 yval = r('NA')
             y_vals.append(yval)
             for k, col in enumerate(x_cols):
                 try:
                     xval = float(fields[col])
-                except Exception, ex:
+                except Exception as ex:
                     xval = r('NA')
                 x_vals[k].append(xval)
         except:
@@ -65,7 +65,7 @@ def stop_err(msg):
 set_default_mode(NO_CONVERSION)
 try:
     leaps = r.regsubsets(r("y ~ x"), data= r.na_exclude(dat))
-except RException, rex:
+except RException as rex:
     stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain no numeric values.")
 set_default_mode(BASIC_CONVERSION)
 

tools/best_regression_subsets/best_regression_subsets.xml

@@ -1,4 +1,4 @@
-<tool id="BestSubsetsRegression1" name="Perform Best-subsets Regression" version="1.0.0">
+<tool id="BestSubsetsRegression1" name="Perform Best-subsets Regression" version="1.0.1">
   <description> </description>
   <requirements>
     <requirement type="package" version="1.7.1">numpy</requirement>

tools/blat_coverage_report/blat_coverage_report.py

@@ -74,7 +74,7 @@ def __main__():
                 if not diff_hash.has_key((chrom, cur_index)):
                     try:
                         diff_hash[(chrom, cur_index)] = [0,0,0,0,sub_b.upper()]    # a, t, c, g, ref. nuc.
-                    except Exception, e:
+                    except Exception as e:
                         stop_err( str( e ) )
                 if sub_a in ['a','t','c','g']:
                     diff_hash[(chrom, cur_index)][nuc_index[(sub_a)]] += 1
@@ -104,4 +104,4 @@ def __main__():
     if invalid_chars:
         print 'Skipped %d invalid characters in the alignment. ' % (invalid_chars)
 
-if __name__ == '__main__': __main__()
+if __name__ == '__main__': __main__()

tools/blat_coverage_report/blat_coverage_report.xml

@@ -1,4 +1,4 @@
-<tool id="generate_coverage_report" name="Polymorphism of the Reads" version="1.0.0">
+<tool id="generate_coverage_report" name="Polymorphism of the Reads" version="1.0.1">
 	<description>the percentage of reads supporting each nucleotide at each location</description>
 	<command interpreter="python">blat_coverage_report.py $input1 $output1</command>
 	<inputs>	

tools/canonical_correlation_analysis/cca.py

@@ -106,7 +106,7 @@ def stop_err(msg):
     ycolnames = ["c%d" %(el+1) for el in y_cols]
     cc = r.cca(x=x_dat, y=y_dat, xlab=xcolnames, ylab=ycolnames, xcenter=r(x_center), ycenter=r(y_center), xscale=r(x_scale), yscale=r(y_scale), standardize_scores=r(std_scores))
     ftest = r.F_test_cca(cc)
-except RException, rex:
+except RException as rex:
     stop_err("Encountered error while performing CCA on the input data: %s" %(rex))
 
 set_default_mode(BASIC_CONVERSION)
@@ -155,4 +155,4 @@ def stop_err(msg):
 #r.plot(cc)
 for i in range(ncomps):
     r.helio_plot(cc, cv = i+1, main = r.paste("Explained Variance for CV",i+1), type = "variance")
-r.dev_off()
+r.dev_off()

tools/canonical_correlation_analysis/cca.xml

@@ -1,9 +1,9 @@
-<tool id="cca1" name="Canonical Correlation Analysis" version="1.0.0">
+<tool id="cca1" name="Canonical Correlation Analysis" version="1.0.1">
   <description> </description>
   <requirements>
     <requirement type="package" version="2.11.0">R</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
-    <requirement type="package" version="1.0">yacca</requirement>
+    <requirement type="package" version="1.0">r-yacca</requirement>
     <requirement type="package" version="1.0.3">rpy</requirement>
   </requirements>
   <command interpreter="python">

tools/ccat/ccat_wrapper.py

@@ -34,7 +34,7 @@ def main():
         shutil.move( os.path.join( tmp_dir, "%s.significant.peak" % project_name ), output_peak_file )
         shutil.move( os.path.join( tmp_dir, "%s.significant.region" % project_name ), output_region_file )
         shutil.move( os.path.join( tmp_dir, "%s.top%i.peak" % ( project_name, output_num ) ), output_top_file )
-    except Exception, e:
+    except Exception as e:
         return stop_err( tmp_dir, e )
     os.rmdir( tmp_dir ) #clean up empty temp working directory
 

tools/ccat/ccat_wrapper.xml

@@ -1,7 +1,6 @@
-<tool id="peakcalling_ccat" name="CCAT" version="0.0.1">
+<tool id="peakcalling_ccat" name="CCAT" version="0.0.2">
   <description>Control-based ChIP-seq Analysis Tool</description>
   <requirements>
-    <requirement type="package" version="3.0">CCAT</requirement>
     <requirement type="package" version="3.0">ccat</requirement>
   </requirements>
   <command>

tools/correlation/cor.py

@@ -71,7 +71,7 @@ def main():
         # Run correlation
         try:
             value = r.cor( array( matrix ), use="pairwise.complete.obs", method=method )
-        except Exception, exc:
+        except Exception as exc:
             out.close()
             stop_err("%s" %str( exc ))
         for row in value:

tools/correlation/cor.xml

@@ -1,4 +1,4 @@
-<tool id="cor2" name="Correlation" version="1.0.0">
+<tool id="cor2" name="Correlation" version="1.0.1">
   <description>for numeric columns</description>
   <requirements>
     <requirement type="package" version="1.0.3">rpy</requirement>

tools/featurecounter/featureCounter.py

@@ -128,7 +128,7 @@ def main():
                 out_file.write( "%s\n" % "\t".join( line.fields ) )
             else:
                 out_file.write( "%s\n" % line )
-    except ParseError, exc:
+    except ParseError as exc:
         out_file.close()
         fail( str( exc ) )
 

tools/featurecounter/featureCounter.xml

@@ -1,4 +1,4 @@
-<tool id="featureCoverage1" name="Feature coverage" version="2.0.0">
+<tool id="featureCoverage1" name="Feature coverage" version="2.0.1">
   <description></description>
   <requirements>
     <requirement type="package" version="0.7.1">bx-python</requirement>

tools/getindelrates_3way/getIndelRates_3way.py

@@ -130,7 +130,7 @@ def main():
                 elif elems[1].endswith('delete'):
                     deletes[sp_ind] += 1
                 prev_bnum = new_bnum
-            except Exception, ei:
+            except Exception as ei:
                 #print >>sys.stderr, ei
                 continue
         irate = []

tools/getindelrates_3way/getIndelRates_3way.xml

@@ -1,4 +1,4 @@
-<tool id="indelRates_3way" name="Estimate Indel Rates" version="1.0.0">
+<tool id="indelRates_3way" name="Estimate Indel Rates" version="1.0.1">
   <description> for 3-way alignments</description>
   <requirements>
     <requirement type="package" version="0.7.1">bx-python</requirement>

tools/kernel_canonical_correlation_analysis/kcca.py

@@ -122,7 +122,7 @@ def stop_err(msg):
 
 try:
     kcc = r.kcca(x=x_dat, y=y_dat, kernel=kernel, kpar=pars, ncomps=ncomps)
-except RException, rex:
+except RException as rex:
     raise
     log.exception( rex )
     stop_err("Encountered error while performing kCCA on the input data: %s" %(rex))

tools/kernel_canonical_correlation_analysis/kcca.xml

@@ -1,4 +1,4 @@
-<tool id="kcca1" name="Kernel Canonical Correlation Analysis" version="1.0.0">
+<tool id="kcca1" name="Kernel Canonical Correlation Analysis" version="1.0.1">
   <description> </description>
   <requirements>
     <requirement type="package" version="1.0.3">rpy</requirement>

tools/kernel_principal_component_analysis/kpca.py

@@ -101,7 +101,7 @@ def stop_err(msg):
 
 try:
     kpc = r.kpca(x=r.na_exclude(dat), kernel=kernel, kpar=pars, features=ncomps)
-except RException, rex:
+except RException as rex:
     stop_err("Encountered error while performing kPCA on the input data: %s" %(rex))
 set_default_mode(BASIC_CONVERSION)
 
@@ -131,4 +131,4 @@ def stop_err(msg):
     r.pairs(rotated,labels=r.list(range(1,ncomps+1)),main="Scatterplot of rotated values")
 else:
     r.plot(rotated, ylab='Comp.1', main="Scatterplot of rotated values")
-r.dev_off()
+r.dev_off()

tools/kernel_principal_component_analysis/kpca.xml

@@ -1,9 +1,9 @@
-<tool id="kpca1" name="Kernel Principal Component Analysis" version="1.0.0">
+<tool id="kpca1" name="Kernel Principal Component Analysis" version="1.0.1">
   <description> </description>
   <requirements>
     <requirement type="package" version="1.0.3">rpy</requirement>
-    <requirement type="package" version="2.11.0">R</requirement>
-    <requirement type="package" version="0.1-4">kernlab</requirement>
+    <requirement type="package" version="2.11.0">r-base</requirement>
+    <requirement type="package" version="0.1-4">r-kernlab</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
     <requirement type="package" version="0.7.1">bx-python</requirement>
   </requirements>

tools/linear_regression/linear_regression.py

@@ -61,7 +61,7 @@ def stop_err(msg):
 set_default_mode(NO_CONVERSION)
 try:
     linear_model = r.lm(r("y ~ x"), data = r.na_exclude(dat))
-except RException, rex:
+except RException as rex:
     stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain only non-numeric or invalid values.")
 set_default_mode(BASIC_CONVERSION)