Merge pull request #2 from matthiaskoenig/develop

Changes for v0.0.2

Author: matthiaskoenig

README.md

@@ -10,14 +10,14 @@
 This repository creates standard files for FBC curation based on cobrapy.
 
 ## Reference output
-In the following the reference outputs are described for the [`e_coli_core.xml`](../examples/e_coli_core.xml) model.
+In the following the created reference output files are described and examples provided for the [`e_coli_core.xml`](./examples/models/e_coli_core.xml) model.
 
 ### 01 Objective value
 The objective value file contains the objective value if the model is optimized with the default settings. The file only contains the objective value.
 ```
 0.873921507
 ```
-See for instance: [`e_coli_core_01_objective.tsv`](../results/e_coli_core_01_objective.tsv)
+See for instance: [`e_coli_core_01_objective.tsv`](./examples/results/e_coli_core_01_objective.tsv). For more information: https://cobrapy.readthedocs.io/en/latest/simulating.html
 
 ### 02 Flux variability analysis (FVA)
 The flux variability analysis results contain the SBML reaction identifiers and the minimum and maximum values of the FVA. The file is a tab separated file (TSV) with the three columns `reaction`, `minimum` and `maximum`.
@@ -33,7 +33,7 @@ ADK1	0.0	0.0
 AKGDH	5.0643756615	5.0643756615
 ...
 ```
-See for instance: [`e_coli_core_02_fva.tsv`](../results/e_coli_core_02_fva.tsv)
+See for instance: [`e_coli_core_02_fva.tsv`](./examples/results/e_coli_core_02_fva.tsv). For more information: https://cobrapy.readthedocs.io/en/latest/simulating.html#Running-FVA
 
 ### 03 Gene deletions 
 The gene deletions results contain the SBML reaction identifiers, the optimal value under the given gene deletion and the status of the optimization. The file is a tab separated file (TSV) with the three columns `gene`, `value` and `status`. The status can be either `optimal` or `infeasible`. In case of an `infeasible` status no solution could be found and no optimal value is provided.
@@ -51,7 +51,7 @@ b2417	0.873921507	optimal
 b2458	0.873921507	optimal
 ...
 ```
-See for instance: [`e_coli_core_03_gene_deletion.tsv`](../results/03_gene_deletion.tsv)
+See for instance: [`e_coli_core_03_gene_deletion.tsv`](./examples/results/e_coli_core_03_gene_deletion.tsv). For more information: https://cobrapy.readthedocs.io/en/latest/deletions.html
 
 ### 04 Reaction deletions 
 The gene deletions results contain the SBML reaction identifiers, the optimal value under the given gene deletion and the status of the optimization. The file is a tab separated file (TSV) with the three columns `reaction`, `value` and `status`. In case of an `infeasible` status no solution could be found and no optimal value is provided.
@@ -67,7 +67,7 @@ ADK1	0.873921507	optimal
 AKGDH	0.858307408	optimal
 ...
 ```
-See for instance: [`e_coli_core_04_reaction_deletion.tsv`](../results/04_reaction_deletion.tsv)
+See for instance: [`e_coli_core_04_reaction_deletion.tsv`](./examples/results/e_coli_core_04_reaction_deletion.tsv). For more information: https://cobrapy.readthedocs.io/en/latest/deletions.html
 
 ## Installation
 
@@ -95,7 +95,6 @@ Options:
                         path to SBML model with fbc information
   -o OUTPUT_PATH, --out=OUTPUT_PATH
                         path to write the output to
-
 ```
 For instance for the `e_coli_core.xml` example use
 ```

fbc_curation/examples.py

@@ -17,6 +17,7 @@ def example_iJR904(results_dir):
     model_path = EXAMPLE_PATH / "models" / "iJR904.xml.gz"
     create_fbc_files(results_dir=results_dir, model_path=model_path)
 
+
 def run_examples():
     results_dir = EXAMPLE_PATH / "results"
     example_ecoli_core(results_dir)