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Migrate older EMDB-SFF files to newer versions

Project description PyPI - Python Version Documentation Status


sfftk-migrate is a utility for migrating EMDB-SFF files from older to the latest version of the data model (see for the latest version). It currently only supports migrations of XML (.sff) files from EMDB-SFF v0.7.0.dev0.


The main entry point for this utility is the sff-migrate command. Please consult the command-line help using:

~$ sff-migrate -h
usage: sff-migrate [-h] [-t TARGET_VERSION] [-o OUTFILE] [-v] [-l] [-s]

Upgrade EMDB-SFF files to more recent schema

positional arguments:
  infile                input XML file

optional arguments:
  -h, --help            show this help message and exit
  -t TARGET_VERSION, --target-version TARGET_VERSION
                        the target version to migrate to [default: 0.8.0.dev1]
  -o OUTFILE, --outfile OUTFILE
                        outfile file [default: <infile>_<target>.xml]
  -v, --verbose         verbose output [default: False]
  -l, --list-versions   list supported versions [default: False]
  -s, --show-version    show the version of the input file [default: False]

Migrating is simple:

~$ sff-migrate file.sff

List supported versions:

~$ sff-migrate -l
versions migratable to 0.8.0.dev1:
* 0.7.0.dev0

Show the file’s version:

~$ sff-migrate -s sfftk_migrate/data/xml/emd_1547.sff
file sfftk_migrate/data/xml/emd_1547.sff is of version 0.7.0.dev0

~$ sff-migrate -s sfftk_migrate/data/xml/emd_1547_v0.8.0.dev1.sff
file sfftk_migrate/data/xml/emd_1547_v0.8.0.dev1.sff is of version v0.8.0.dev0


sfftk-migrate is free and open source software released under the terms of the Apache License, Version 2.0. Source code is copyright EMBL-European Bioinformatics Institute (EMBL-EBI) 2020.

Source code is available from the Github repository:

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