changeset 20:797818b4e2f6 draft

planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty

--- a/recursive_agg_onefile.py	Mon Nov 21 10:45:17 2016 -0500
+++ b/recursive_agg_onefile.py	Mon Nov 21 13:00:20 2016 -0500
@@ -33,11 +33,8 @@
     # transfer base matrix
     with h5py.File(outfile, 'w') as dest, \
          h5py.File(infile, 'r') as src:
-        try:
-            zoomLevel = str(n_zooms)
-            src.copy('/', dest, zoomLevel)
-        except RuntimeWarning as e:
-            print("Error: %s" % e)
+        zoomLevel = str(n_zooms)
+        src.copy('/', dest, zoomLevel)
         print(zoomLevel, file=sys.stderr)
 
 
@@ -50,38 +47,35 @@
         for i in range(n_zooms - 1, -1, -1):
             zoomLevel = str(i)
             
-            try:
-                # aggregate
-                new_binsize = binsize * FACTOR
-                new_bins = cooler.util.binnify(chromsizes, new_binsize)
-     
-                reader = CoolerAggregator(c, new_bins, chunksize)
-                
-                grp = f.create_group(zoomLevel)
-                f.attrs[zoomLevel] = new_binsize
-                cooler.io.create(grp, chroms, lengths, new_bins, reader)
+            # aggregate
+            new_binsize = binsize * FACTOR
+            new_bins = cooler.util.binnify(chromsizes, new_binsize)
+ 
+            reader = CoolerAggregator(c, new_bins, chunksize)
+            
+            grp = f.create_group(zoomLevel)
+            f.attrs[zoomLevel] = new_binsize
+            cooler.io.create(grp, chroms, lengths, new_bins, reader)
 
-                # balance
-                #with Pool(N_CPU) as pool:
-                too_close = 20000  # for HindIII
-                ignore_diags = max(int(np.ceil(too_close / new_binsize)), 3)
+            # balance
+            #with Pool(N_CPU) as pool:
+            too_close = 20000  # for HindIII
+            ignore_diags = max(int(np.ceil(too_close / new_binsize)), 3)
 
-                bias = cooler.ice.iterative_correction(
-                    f, zoomLevel,
-                    chunksize=chunksize,
-                    min_nnz=10,
-                    mad_max=3,
-                    ignore_diags=ignore_diags,
-                    map=map)
-                h5opts = dict(compression='gzip', compression_opts=6)
-                grp['bins'].create_dataset('weight', data=bias, **h5opts)
+            bias = cooler.ice.iterative_correction(
+                f, zoomLevel,
+                chunksize=chunksize,
+                min_nnz=10,
+                mad_max=3,
+                ignore_diags=ignore_diags,
+                map=map)
+            h5opts = dict(compression='gzip', compression_opts=6)
+            grp['bins'].create_dataset('weight', data=bias, **h5opts)
 
-                print(zoomLevel, file=sys.stderr)
+            print(zoomLevel, file=sys.stderr)
 
-                c = cooler.Cooler(grp)
-                binsize = new_binsize
-            except RuntimeWarning:
-                pass
+            c = cooler.Cooler(grp)
+            binsize = new_binsize
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(

--- a/recursive_agg_onefile.xml	Mon Nov 21 10:45:17 2016 -0500
+++ b/recursive_agg_onefile.xml	Mon Nov 21 13:00:20 2016 -0500
@@ -1,7 +1,7 @@
 
 <tool id="recursive_agg_cooler" name="Generate Multi-res Cooler File" version="1.0.0">
   <description>Recursively aggregate a single resolution cooler file into a multi-resolution file.</description>
-  <command> /usr/bin/python $__tool_directory__/recursive_agg_onefile.py $input --out $output</command>
+  <command> /usr/bin/python $__tool_directory__/recursive_agg_onefile.py $input --out $output > /dev/null 2>&1</command>
   <inputs>
     <param format="h5" name="input" type="data" label="Source cooler file"/>
   </inputs>