biom convert to json writes the type as a byte literal

[corburn]

In python 3, biom convert will write the type as a byte literal. As a result, the type is not recognize by scripts expecting a string literal. This can be reproduced with the biom-format test data where, unlike the data this was encountered in, the id is also written as a byte literal:

biom convert -i  tests/test_data/test.biom -o test.json --to-json

{
  "id": "b'No Table ID'",
  "type": "b'Unspecified'"
  ...
}

Including the table-type flag will replace the byte literal with a string literal.
biom convert -i tests/test_data/test.biom -o test.json --to-json --table-type "OTU table"

System information

     Platform:	linux

Python version: 3.4.2 (default, Oct 8 2014, 10:45:20) [GCC 4.9.1]
Python executable: /biom-format/env/bin/python3

Dependency versions

click version: 6.7
NumPy version: 1.12.0
SciPy version: 0.18.1
h5py version: 2.6.0

biom-format package information

biom-format version: 2.1.5-dev

[wasade]

Good catch. Am surprised this hasn't popped up or was caught by the test harness. Will investigate today, thank you for creating the issue!

…

On Feb 2, 2017 06:46, "Jason Travis" ***@***.***> wrote: In python 3, biom convert will write the type as a byte literal. As a result, the type is not recognize by scripts expecting a string literal. This can be reproduced with the biom-format test data where, unlike the data this was encountered in, the id is also written as a byte literal: biom convert -i tests/test_data/test.biom -o test.json --to-json { "id": "b'No Table ID'", "type": "b'Unspecified'" ... } Including the table-type flag will replace the byte literal with a string literal. biom convert -i tests/test_data/test.biom -o test.json --to-json --table-type "OTU table" System information Platform: linux Python version: 3.4.2 (default, Oct 8 2014, 10:45:20) [GCC 4.9.1] Python executable: /biom-format/env/bin/python3 Dependency versions click version: 6.7 NumPy version: 1.12.0 SciPy version: 0.18.1 h5py version: 2.6.0 biom-format package information biom-format version: 2.1.5-dev — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#731>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAc8sr96SJH0u6b-n-O4uxZSO7Jwh8reks5rYexDgaJpZM4L1MiU> .