Scripts: Management¶
Description:
#TODO
manual_curation¶
- Description:
Update a padmetSpec by filling specific forms.
1./ Create new reaction(s) to padmet file.
- Get the template form with –template_new_rxn
- Fill the template
- set –data as path to the filled template
2./ Add reaction(s) from padmetRef or remove reactions(s).
- Get the template form with –template_add_delete_rxn
- Fill the template
- set –date as path to the filled template
Update padmetSpec and create a new padmet (new_padmet) or overwrite the input
usage:
manual_curation.py --padmetSpec=FILE --data=FILE [--padmetRef=FILE] [--output=FILE] [--tool=STR] [--category=STR] [-v]
manual_curation.py --template_new_rxn=FILE
manual_curation.py --template_add_delete_rxn=FILE
option:
-h --help Show help.
--padmetSpec=FILE path to the padmet to update
--padmetRef=FILE path of the padmet representing the reference database
--data=FILE path to the form with data for curation
--output=FILE path to the output. if None. Overwriting padmetSpec
--tool=STR specification of the tool used to allow this curation: ex a tool of gapfilling (meneco)
--category=STR specification of the category of curation: ex if a reaction is added based on annotation info, use 'annotation'
--template_new_rxn=FILE create a form used to create new reaction, use this form as input for 'data' option
--template_add_delete_rxn=FILE create a form used to add or delete reaction, use this form as input for 'data' option
-v print info
padmet_compart¶
- Description:
For a given padmet file, check and update compartment.
1./ Get all compartment with 1st usage
2./ Remove a compartment with 2nd usage. Remove all reactions acting in the given compartment
3./ change compartment id with 3rd usage
usage:
padmet_compart.py --padmet=FILE
padmet_compart.py --padmet=FILE --remove=STR [--output=FILE] [-v]
padmet_compart.py --padmet=FILE --old=STR --new=STR [--output=FILE] [-v]
options:
-h --help Show help.
--padmet=FILE pathname of the padmet file
--remove=STR compartment id to remove
--old=STR compartment id to change to new id
--new=STR new compartment id
--output=FILE new padmet pathname, if none, overwritting the original padmet
-v print info
padmet_medium¶
- Description:
For a given set of compounds representing the growth medium (or seeds). Create 2 reactions for each compounds to maintain consistency of the network for flux analysis. For each compounds create:
An exchange reaction: this reaction consumes the compound in the compartment ‘C-BOUNDARY’ and produces the compound in the compartment ‘e’ extracellular
A transport reaction: this reaction consumes the compound in the compartment ‘e’ extracellular’ and produces the compound in the compartment ‘c’ cytosol ex: for seed ‘cpd-a’
1/ check if cpd-a in padmetSpec, if not, copy from padmetRef.
2/ create exchange reaction: ExchangeSeed_cpd-a_b: 1 cpd-a (C-BOUNDARAY) <=> 1 cpd-a (e)
3/ create transport reaction: TransportSeed_cpd-a_e: 1 cpd-a (e) => 1 cpd-a (c)
4/ create a new file if output not None, or overwrite padmetSpec
usage:
padmet_medium.py --padmetSpec=FILE
padmet_medium.py --padmetSpec=FILE -r [--output=FILE] [-v]
padmet_medium.py --padmetSpec=FILE --seeds=FILE [--padmetRef=FILE] [--output=FILE] [-v]
options:
-h --help Show help.
--padmetSpec=FILE path to the padmet file to update
--padmetRef=FILE path to the padmet file representing to the database of reference (ex: metacyc_18.5.padmet)
--seeds=FILE the path to the file containing the compounds ids and the compart, line = cpd-id compart.
--output=FILE If not None, pathname to the padmet file updated
-r Use to remove all medium from padmet
-v print info