13.1.1.3. bpforms.xlink package¶

13.1.1.3.1. Submodules¶

13.1.1.3.2. bpforms.xlink.core module¶

Classes to represent an ontology of crosslinks

Author: Jonathan Karr <karr@mssm.edu>
Date: 2019-08-12
Copyright: 2019, Karr Lab
License: MIT

class bpforms.xlink.core.CrosslinksOnto[source]¶: Bases: dict

bpforms.xlink.core.load_onto(filename='/root/project/bpforms/xlink/xlink.yml')[source]¶

Load an ontology of crosslinks from a YAML file

Parameters: filename (str) – path to ontology
Returns: ontology of crosslinks
Return type: CrosslinksOnto

bpforms.xlink.core.parse_atom(atom)[source]¶

Parse description of atom in ontology

Parameters: atom (str) –
Returns: element, position, charge
Return type: tuple

13.1.1.3.3. bpforms.xlink.xlink_xlsx2yml module¶

Read the manually-curated xlink xlsx file and export it to an xlink ontology

Author: Mike Zheng <xzheng20@colby.edu>
Date: 2019-08-05
Copyright: 2019, Karr Lab
License: MIT

bpforms.xlink.xlink_xlsx2yml.main()[source]¶

13.1.1.3.4. Module contents¶