import sys
import h5py

infiles = sys.argv[1:]

for infile in infiles:
    with h5py.File(infile, 'a') as h5:
        print(infile)
        if 'format-version' in h5.attrs and h5.attrs['format-version'] < 1:

            if 'matrix' in h5 and not 'pixels' in h5:
                print('renaming matrix --> pixels')
                h5['pixels'] = h5['matrix']

            if 'scaffolds' in h5 and not 'chroms' in h5:
                print('renaming scaffolds --> chroms')
                h5['chroms'] = h5['scaffolds']

            h5.attrs['format-version'] = 1


import sys
import h5py

infiles = sys.argv[1:]

for infile in infiles:
    with h5py.File(infile, 'a') as h5:
        print(infile)
        if 'format-version' in h5.attrs and h5.attrs['format-version'] < 1:

            if 'matrix' in h5 and not 'pixels' in h5:
                print('renaming matrix --> pixels')
                h5['pixels'] = h5['matrix']
                del h5['matrix']

            if 'scaffolds' in h5 and not 'chroms' in h5:
                print('renaming scaffolds --> chroms')
                h5['chroms'] = h5['scaffolds']
                del h5['scaffolds']

            h5.attrs['format-version'] = 1


Drop old names from v0
Drop old names from v0

  import sys
  import h5py
  
  infiles = sys.argv[1:]
  
  for infile in infiles:
      with h5py.File(infile, 'a') as h5:
          print(infile)
          if 'format-version' in h5.attrs and h5.attrs['format-version'] < 1:
  
              if 'matrix' in h5 and not 'pixels' in h5:
                  print('renaming matrix --> pixels')
                  h5['pixels'] = h5['matrix']
+                 del h5['matrix']
  
              if 'scaffolds' in h5 and not 'chroms' in h5:
                  print('renaming scaffolds --> chroms')
                  h5['chroms'] = h5['scaffolds']
+                 del h5['scaffolds']
  
              h5.attrs['format-version'] = 1
  
  
Drop old names from v0
## Code Before:
import sys
import h5py

infiles = sys.argv[1:]

for infile in infiles:
    with h5py.File(infile, 'a') as h5:
        print(infile)
        if 'format-version' in h5.attrs and h5.attrs['format-version'] < 1:

            if 'matrix' in h5 and not 'pixels' in h5:
                print('renaming matrix --> pixels')
                h5['pixels'] = h5['matrix']

            if 'scaffolds' in h5 and not 'chroms' in h5:
                print('renaming scaffolds --> chroms')
                h5['chroms'] = h5['scaffolds']

            h5.attrs['format-version'] = 1


## Instruction:
Drop old names from v0
## Code After:
import sys
import h5py

infiles = sys.argv[1:]

for infile in infiles:
    with h5py.File(infile, 'a') as h5:
        print(infile)
        if 'format-version' in h5.attrs and h5.attrs['format-version'] < 1:

            if 'matrix' in h5 and not 'pixels' in h5:
                print('renaming matrix --> pixels')
                h5['pixels'] = h5['matrix']
                del h5['matrix']

            if 'scaffolds' in h5 and not 'chroms' in h5:
                print('renaming scaffolds --> chroms')
                h5['chroms'] = h5['scaffolds']
                del h5['scaffolds']

            h5.attrs['format-version'] = 1

