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ramez17khaledramez17khaled
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Merge pull request #9 from brsynth/dev
update v0.1.3: add models to manifest
2 parents 0203aef + c795bdc commit fd5fd9b

9 files changed

Lines changed: 352114 additions & 8 deletions

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‎damn/_version.py‎

Lines changed: 1 addition & 1 deletion
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@@ -1 +1 @@
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__version__ = "0.1.1"
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__version__ = "0.1.3"

‎damn/models/ecoli/M28_OD_20.csv‎

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‎damn/models/ecoli/M28_media.csv‎

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‎damn/models/ecoli/iML1515_duplicated.xml‎

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‎damn/models/putida/IJN1463EXP_duplicated.xml‎

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‎damn/models/putida/modul.zip‎

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‎damn/models/putida/putida_OD_81.csv‎

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‎damn/models/putida/putida_media_81.csv‎

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ID,glc__D_e,xyl__D_e,succ_e,ala__L_e,arg__L_e,asn__L_e,asp__L_e,cys__L_e,glu__L_e,gln__L_e,gly_e,his__L_e,ile__L_e,leu__L_e,lys__L_e,met__L_e,phe__L_e,pro__L_e,ser__L_e,thr__L_e,trp__L_e,tyr__L_e,val__L_e,ade_e,gua_e,csn_e,ura_e,thymd_e
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‎damn/train.py‎

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11
import os
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import numpy as np
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import tensorflow as tf
4+
from importlib.resources import files
45
import damn
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from damn import model
67
from damn import plot
78

89
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
9-
DAMN_DIR = os.path.dirname(os.path.abspath(damn.__file__))
10-
PROJECT_ROOT = os.path.dirname(DAMN_DIR)
11-
DOCS_DIR = os.path.join(PROJECT_ROOT, "docs")
10+
#DAMN_DIR = os.path.dirname(os.path.abspath(damn.__file__))
11+
#PROJECT_ROOT = os.path.dirname(DAMN_DIR)
12+
#DOCS_DIR = os.path.join(PROJECT_ROOT, "docs")
13+
14+
15+
def get_default_model(organism):
16+
if organism.lower() == "putida":
17+
return str(files("damn.models.putida").joinpath("IJN1463EXP_duplicated.xml"))
18+
elif organism.lower() == "ecoli":
19+
return str(files("damn.models.ecoli").joinpath("iML1515_duplicated.xml"))
20+
else:
21+
raise ValueError("Custom model must be provided")
1222

1323
def train_damn(
1424
organism="custom",
@@ -48,8 +58,7 @@ def train_damn(
4858
"file_name": "putida_OD_81",
4959
"od_file": "putida_OD_81.csv",
5060
"media_file": "putida_media_81.csv",
51-
"cobra_model_file": os.path.join(
52-
DOCS_DIR, "putida", "IJN1463EXP_duplicated.xml"),
61+
"cobra_model_file": get_default_model('putida'),
5362
"biomass_rxn_id": "BIOMASS_KT2440_WT3",
5463
"seed": 1,
5564
"num_epochs": 500,
@@ -62,8 +71,7 @@ def train_damn(
6271
"file_name": "M28_OD_20",
6372
"od_file": "M28_OD_20.csv",
6473
"media_file": "M28_media.csv",
65-
"cobra_model_file": os.path.join(
66-
DOCS_DIR, "putida","iML1515_duplicated.xml"),
74+
"cobra_model_file": get_default_model('ecoli'),
6775
"biomass_rxn_id": "BIOMASS_Ec_iML1515_core_75p37M",
6876
"seed": 30,
6977
"num_epochs": 1000,

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