Exporting data from ISA formats¶

We have provided a number of modules that allow you to export data from ISA formats to formats ready for consumption by well-known databases or services in the following conversion modules found in the isatools.convert package:

Converting from ISA-Tab to SRA XML¶

To convert from a directory ./tabdir/ containing valid ISA-Tab files to a write the SRA XML files to a target directory ./outdir/, validating against a given configuration in ./isaconfig-default_v2015-07-02/:

from isatools.convert import isatab2sra

sra_settings={
         "sra_broker": "MYORG",
         "sra_center": "MYORG",
         "sra_project": "MYORG",
         "sra_broker_inform_on_status": "support@myorg.org",
         "sra_broker_inform_on_error": "support@myorg.org",
         "sra_broker_contact_name": "Support"
     }

isatab2sra.convert('./tabdir/', './outdir/', sra_settings=sra_settings)

This method writes the SRA files out to ./outdir/.

Note that when subitting SRA XML to ENA, you need to supply broker information as shown above in the sra_settings JSON, customised to your own organisation’s settings.

Converting from ISA JSON file to SRA XML¶

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

from isatools.convert import json2sra

sra_settings={
         "sra_broker": "MYORG",
         "sra_center": "MYORG",
         "sra_project": "MYORG",
         "sra_broker_inform_on_status": "support@myorg.org",
         "sra_broker_inform_on_error": "support@myorg.org",
         "sra_broker_contact_name": "Support"
     }

json2sra.convert(open('isa.json'), './outdir/', sra_settings=sra_settings)

This method writes the SRA files out to ./outdir/.

Note that when subitting SRA XML to ENA, you need to supply broker information as shown above in the sra_settings JSON, customised to your own organisation’s settings.

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

Converting ISA content to SampleTab¶

Warning

As of July 2020, EBI Biosample has decommissioned SampleTab format and now only accepts submission via a REST API. Future releases of the ISA-API will support this mode of data deposition.

To export metadata from SampleTab files (e.g. for EBI BioSamples database), you can do the following to export a ISA-Tab to SampleTab:

from isatools.convert import isatab2sampletab

with open('your/path/to/i_investigation.txt', 'r') as input_investigation_file:
    with open('your/path/to/sampletab.txt', 'w') as output_sampletab_file:
        isatab2sampletab.convert(input_investigation_file, output_sampletab_file)

To export an ISA JSON file to SampleTab, you can do:

from isatools.convert import isatab2sampletab

with open('your/path/to/i_investigation.txt', 'r') as input_investigation_file:
    with open('your/path/to/sampletab.txt', 'w') as output_sampletab_file:
        isatab2sampletab.convert(input_investigation_file, output_sampletab_file)

You can also dump SampleTab content directly from ISA Python objects:

from isatools import sampletab

with open('your/path/to/sampletab.txt', 'w') as output_sampletab:
    # Note: ISA would be a previously loaded or constructed root Investigation object
    sampletab.dump(ISA, output_sampletab)

Exporting ISA content to MAGE-TAB¶

To export metadata to MAGE-TAB files (e.g. for EBI ArrayExpress database), you can do the following to export a ISA-Tab to MAGE-TAB:

from isatools.convert import isatab2magetab

with open('your/path/to/i_investigation.txt', 'r') as input_investigation_file:
    isatab2magetab.convert(input_investigation_file, 'your/output/path/')