SRA conversions

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
isatab2sra.create_sra('./tabdir/', './outdir/', './isaconfig-default_v2015-07-02/')

Converting from ISA JSON file to SRA XML

To convert from a a ISA JSON file isa.jsondirectory to write out SRA XML files to a target directory ./outdir/, validating against a given configuration in ./isaconfig-default_v2015-07-02/:

from isatools.convert import json2sra
json2sra.convert(open('isa.json')), './outdir/', './isaconfig-default_v2015-07-02/')

Importing SRA to ISA tab

from isatools.convert import sra2isatab
sra2isatab.sra_to_isatab_batch_convert(...)