#!/usr/bin/env python
# coding: utf-8

# # Reading and Writing Models

# Cobrapy supports reading and writing models in SBML (with and without FBC), JSON, YAML, MAT, and pickle formats. Generally, SBML with FBC version 2 is the preferred format for general use. The JSON format may be more useful for cobrapy-specific functionality.
# 
# The package also ships with test models in various formats for testing purposes.

# In[1]:


import cobra.test
import os
from os.path import join

data_dir = cobra.test.data_dir

print("mini test files: ")
print(", ".join(i for i in os.listdir(data_dir) if i.startswith("mini")))

textbook_model = cobra.test.create_test_model("textbook")
ecoli_model = cobra.test.create_test_model("ecoli")
salmonella_model = cobra.test.create_test_model("salmonella")


# ## SBML

# The [Systems Biology Markup Language](http://sbml.org) is an XML-based standard format for distributing models which has support for COBRA models through the [FBC extension](http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_%28flux%29) version 2.
# 
# Cobrapy has native support for reading and writing SBML with FBCv2. Please note that all id's in the model must conform to the SBML SID requirements in order to generate a valid SBML file.

# In[2]:


cobra.io.read_sbml_model(join(data_dir, "mini_fbc2.xml"))


# In[3]:


cobra.io.write_sbml_model(textbook_model, "test_fbc2.xml")


# There are other dialects of SBML prior to FBC 2 which have previously been use to encode COBRA models. The primary ones is the "COBRA" dialect which used the "notes" fields in SBML files.
# 
# Cobrapy can use [libsbml](http://sbml.org/Software/libSBML), which must be installed separately (see installation instructions) to read and write these files. When reading in a model, it will automatically detect whether FBC was used or not. When writing a model, the use_fbc_package flag can be used can be used to write files in this legacy "cobra" format.
# 
# Consider having the [lxml](http://lxml.de/) package installed as it can speed up parsing considerably.

# In[4]:


cobra.io.read_sbml_model(join(data_dir, "mini_cobra.xml"))


# In[5]:


cobra.io.write_sbml_model(
    textbook_model, "test_cobra.xml", use_fbc_package=False)


# ## JSON

# Cobrapy models have a [JSON](https://en.wikipedia.org/wiki/JSON) (JavaScript Object Notation) representation. This format was created for interoperability with [escher](https://escher.github.io).

# In[6]:


cobra.io.load_json_model(join(data_dir, "mini.json"))


# In[7]:


cobra.io.save_json_model(textbook_model, "test.json")


# ## YAML

# Cobrapy models have a [YAML](https://en.wikipedia.org/wiki/YAML) (YAML Ain't Markup Language) representation. This format was created for more human readable model representations and automatic diffs between models.

# In[8]:


cobra.io.load_yaml_model(join(data_dir, "mini.yml"))


# In[9]:


cobra.io.save_yaml_model(textbook_model, "test.yml")


# ## MATLAB

# Often, models may be imported and exported solely for the purposes of working with the same models in cobrapy and the [MATLAB cobra toolbox](http://opencobra.github.io/cobratoolbox/). MATLAB has its own ".mat" format for storing variables. Reading and writing to these mat files from python requires scipy.
# 
# A mat file can contain multiple MATLAB variables. Therefore, the variable name of the model in the MATLAB file can be passed into the reading function:

# In[10]:


cobra.io.load_matlab_model(
    join(data_dir, "mini.mat"), variable_name="mini_textbook")


# If the mat file contains only a single model, cobra can figure out which variable to read from, and the variable_name parameter is unnecessary.

# In[11]:


cobra.io.load_matlab_model(join(data_dir, "mini.mat"))


# Saving models to mat files is also relatively straightforward

# In[12]:


cobra.io.save_matlab_model(textbook_model, "test.mat")


# ## Pickle

# Cobra models can be serialized using the python serialization format, [pickle](https://docs.python.org/2/library/pickle.html).
# 
# Please note that use of the pickle format is generally not recommended for most use cases. JSON, SBML, and MAT are generally the preferred formats.