Pulling Template/Predictor

[1]:

import modelseedpy

[2]:

from modelseedpy.helpers import get_classifier, get_template, get_file

[3]:

get_file('template_core.json', 'data', 'template_folder')
get_file('template_gram_neg.json', 'data', 'template_folder')
get_file('template_gram_pos.json', 'data', 'template_folder')
get_file('knn_filter.pickle', 'data', 'classifier_folder')
get_file('knn_filter_features.json', 'data', 'classifier_folder')

[3]:

'/usr/local/lib/python3.8/site-packages/modelseedpy//data/ml/knn_filter_features.json'

load classifier

options

  • knn_filter

[4]:

genome_cls = get_classifier('knn_filter')

load template

options

  • template_core

  • template_gram_neg

  • template_gram_pos

[5]:

core_template = get_template('template_core')
core_template['id']

[5]:

'CoreModelTemplateV2'

[7]:

from modelseedpy.core.mstemplate import MSTemplateBuilder
template = MSTemplateBuilder.from_dict(core_template).build()

[8]:

template

[8]:
ID CoreModelTemplateV2
Memory address 0x07ff7918e46d0
Number of metabolites 161
Number of species 187
Number of reactions 197
Number of biomasses 2
Number of roles 20552
Number of complexes 9423 
[13]:

template_reaction = template.reactions[0]
template_reaction

[13]:
Reaction identifierrxn01975_c
Namebeta-D-Glucose-6-phosphate:NADP+ 1-oxoreductase
Memory address 0x07ff790433310
Stoichiometry

cpd00006_c + cpd00863_c --> cpd00005_c + cpd00067_c + cpd00911_c

NADP + beta-D-Glucose 6-phosphate --> NADPH + H+ + 6-phospho-D-glucono-1-5-lactone
GPRcpx00354 or cpx30278
Lower bound0
Upper bound1000 
[14]:

template_reaction.to_reaction()

[14]:
Reaction identifierrxn01975_c0
Namebeta-D-Glucose-6-phosphate:NADP+ 1-oxoreductase [c0]
Memory address 0x07ff7901ef220
Stoichiometry

cpd00006_c0 + cpd00863_c0 --> cpd00005_c0 + cpd00067_c0 + cpd00911_c0

NADP [c0] + beta-D-Glucose 6-phosphate [c0] --> NADPH [c0] + H+ [c0] + 6-phospho-D-glucono-1-5-lactone [c0]
GPR
Lower bound0
Upper bound1000 
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