ISA Conversions

The ISA API includes a set of functions to allow you to convert between ISA formats, as well as between ISA formats and other formats such as SRA. These converters can be found in the isatools.convert package.

Converting from ISA-Tab to ISA JSON

To convert from a directory ./tabdir/ containing valid ISA-Tab files (e.g. i_investigation.txt, s_...txt and a_...txt files):

from isatools.convert import isatab2json
isa_json = isatab2json.convert('./tabdir/')

Hint

The conversions by default run the ISA validator to check for correctness of the input content. To skip the validation step, set the validate_first parameter to False by doing something like converter.convert('./my/path/', validate_first=False).

Hint

The conversions by default use a legacy ISA-Tab parser, which has now been replaced with a faster version. To specify using the new parser, set the use_new_parser parameter to True by doing something like isatab2json.convert('./my/path/', use_new_parser=True).

Converting from ISA JSON to ISA-Tab

To convert from a ISA JSON file isa.json directory to write out ISA-Tab files to a target directory ./outdir/:

from isatools.convert import json2isatab
with open('isa.json')) as file_pointer:
    json2isatab.convert(file_pointer, './outdir/')

To turn off pre-conversion validation, use validate_first=False. By default it is set to validate_first=True.