Update docs

docs/guide/guide.md

@@ -1,4 +1,4 @@
-# **Meneco** User Guide (version 2.0.1-dev)
+# **Meneco** User Guide (version 2.0.1)
 
 Sven Thiele
 
@@ -207,34 +207,34 @@ and to specify the seeds and targets.
 
 ```text
 7 unproducible targets:
-        M_so4_c
-        M_cl_c
-        M_cu2_c
-        M_pe161_c
-        M_thf_c
-        M_ribflv_c
-        M_utp_c
+    M_so4_c
+    M_cl_c
+    M_cu2_c
+    M_pe161_c
+    M_thf_c
+    M_ribflv_c
+    M_utp_c
 ```
 
 In this section Meneco outputs which target metabolite are producible given the seeds and the reactions of the draft network.
 In this case the result shows 7 target metabolites which are not producible.
 
-Given that unproducible target metabolites exist the next sections documents which of the targets remain unproducible even with the reactions from the repair database `repairdb.sbml` 
+Given that unproducible target metabolites exist the next sections documents which of the targets remain unproducible even with the reactions from the repair database `repairdb.sbml`
 and for which targets the metabolic pathways can be reconstructed.
 
 ```text
 Repair db file: repairdb.sbml
 
 Still 5 unreconstructable targets:
-        M_so4_c
-        M_pe161_c
-        M_utp_c
-        M_ribflv_c
-        M_thf_c
+    M_so4_c
+    M_pe161_c
+    M_utp_c
+    M_ribflv_c
+    M_thf_c
 
 2 reconstructable targets:
-        M_cu2_c
-        M_cl_c
+    M_cu2_c
+    M_cl_c
 ```
 
 In this example 5 metabolites remain unproducible,
@@ -246,14 +246,14 @@ This intermediate result is reused in the subsequent computations as a solution
 
 ```text
 1 essential reactions for target M_cu2_c:
-        R_CU2tpp
+    R_CU2tpp
 
 1 essential reactions for target M_cl_c:
-        R_CLt3_2pp
+    R_CLt3_2pp
 
 Overall 2 essential reactions found:
-        R_CU2tpp
-        R_CLt3_2pp
+    R_CU2tpp
+    R_CLt3_2pp
 ```
 
 In this example for each single target metabolite exist one essential reaction.
@@ -262,9 +262,9 @@ The section shows one minimal completion to produce all targets.
 
 ```text
 One minimal completion of size 3:
-        R_O2Stex
-        R_CU2tpp
-        R_CLt3_2pp
+    R_O2Stex
+    R_CU2tpp
+    R_CLt3_2pp
 ```
 
 In this example the first minimal completion contains 3 reactions.
@@ -274,14 +274,14 @@ Meneco outputs the intersection and union of all minimal completion
 
 ```text
 Intersection of cardinality minimal completions:
-        R_CU2tpp
-        R_CLt3_2pp
+    R_CU2tpp
+    R_CLt3_2pp
 
 Union of cardinality minimal completions:
-        R_O2tex
-        R_O2Stex
-        R_CU2tpp
-        R_CLt3_2pp
+    R_O2tex
+    R_O2Stex
+    R_CU2tpp
+    R_CLt3_2pp
 ```
 
 In our case we get 2 reactions in the intersection and 4 reactions in the union.
@@ -291,15 +291,14 @@ all minimal completions are enumerated.
 
 ```text
 Completion 1:
-        R_O2Stex
-        R_CU2tpp
-        R_CLt3_2pp
+    R_O2Stex
+    R_CU2tpp
+    R_CLt3_2pp
 
 Completion 2:
-        R_O2tex
-        R_CU2tpp
-        R_CLt3_2pp
-
+    R_O2tex
+    R_CU2tpp
+    R_CLt3_2pp
 ```
 
 Fortunately, our example has only two solutions.

docs/guide/guide.tex

@@ -13,7 +13,7 @@
 
 \title{ \meneco  \\
 User Guide \\
-version 1.5.2
+version 2.0.1
 }
 
 \author{Sven Thiele}
@@ -49,74 +49,24 @@ \section{Prerequisites}
 
 \section{Installation}
 
-\subsection{Installation using \texttt{pip}}
-You can install the \meneco\ package by running:
-
 \begin{Verbatim}[frame=single]
 $ pip install --user meneco
 \end{Verbatim}
 
-
-On Linux the executable scripts can then be found in \texttt{~/.local/bin}
-
-and on Mac OS the scripts are under \texttt{/Users/YOURUSERNAME/Library/Python/3.2/bin}.
-
-
-\subsection{Installation of \texttt{pip}}
-If \texttt{pip} is not installed one can install \texttt{pip} without admin rights.
-Therefore one has to first download \texttt{getpip.py} via:
-\begin{Verbatim}[frame=single]
-$ wget https://raw.github.com/pypa/pip/master/contrib/get-pip.py
-\end{Verbatim}
-and then install pip locally:
-\begin{Verbatim}[frame=single]
-$ python get-pip.py --user
-\end{Verbatim}
-Now it is possible to use the local pip and proceed with the section \emph{Installation of \texttt{pip}}.
-
-\subsection{Installation without \texttt{pip}}
-Although we do not recommend it, it is possible to install \meneco\ without \texttt{pip}.
-But then one has to take care of the dependencies oneself.
-Therefore one has to first download \texttt{pyasp-1.4.2}.
-
-\begin{Verbatim}[frame=single]
-$ wget https://pypi.python.org/packages/source/p/pyasp/pyasp-1.4.2.tar.gz
-\end{Verbatim}
-Next one has to extract and install \texttt{PyASP}:
-\begin{Verbatim}[frame=single]
-$ gzip -d pyasp-1.4.2.tar.gz
-$ tar -xvf pyasp-1.4.2.tar
-$ cd pyasp-1.4.2
-$ python setup.py install --user
-\end{Verbatim}
-Then one needs to download \texttt{meneco-1.5.2}:
-\begin{Verbatim}[frame=single]
-$ wget https://pypi.python.org/packages/source/m/meneco/meneco-1.5.2.tar.gz
-\end{Verbatim}
-and to extract and install meneco:
-\begin{Verbatim}[frame=single]
-$ gzip -d meneco-1.5.2.tar.gz
-$ tar -xvf meneco-1.5.2.tar
-$ cd meneco-1.5.2
-$ python setup.py install --user
-\end{Verbatim}
-
 On Linux the executable scripts can then be found in \texttt{~/.local/bin}
 
-and on Mac OS the scripts are under \texttt{/Users/YOURUSERNAME/Library/Python/3.2/bin}.
-
-
+and on Mac OS the scripts are under \texttt{/Users/YOURUSERNAME/Library/Python/3.7/bin}.
 
 \section{Usage}
 
 Typical usage is:
 \begin{Verbatim}[frame=single]
-$ meneco.py -d draftnet.sbml -s seeds.sbml -t targets.sbml -r repairdb.sbml
+$ meneco -d draftnet.sbml -s seeds.sbml -t targets.sbml -r repairdb.sbml
 \end{Verbatim}
 For more options you can ask for help as follows:
 \begin{Verbatim}[frame=single]
-$ meneco.py --h
-meneco.py [-h] -d DRAFTNET -s SEEDS -t TARGETS [-r REPAIRNET]
+$ meneco --h
+meneco [-h] -d DRAFTNET -s SEEDS -t TARGETS [-r REPAIRNET]
                  [--enumerate]
 
 optional arguments:
@@ -222,116 +172,124 @@ \section{Output}
 For example to write the results shown below into the file \texttt{myfile.txt} type:
 
 \begin{Verbatim}[frame=single]
-$ meneco.py -d draftnet.sbml -s seeds.sbml -t targets.sbml -r repairdb.sbml --enumerate > myfile.txt
+$ meneco -d draftnet.sbml -s seeds.sbml -t targets.sbml -r repairdb.sbml --enumerate > myfile.txt
 \end{Verbatim}
 
 In the following we will dissect the output generated by \meneco.
 The first 3 lines document which files have been used as representation of the metabolic reaction network (line 1)
 and which files to specify the seed (line 2) and targets (line 3).
 \begin{Verbatim}[frame=single,numbers=left]
-Reading draft network from  data/draftnet.sbml ... done.
-Reading seeds from  data/seeds.sbml ... done.
-Reading targets from  data/targets.sbml ... done.
+Reading draft network ...
+Draft network file: draft.sbml
+Reading seeds ...
+Seeds file: seeds.sbml
+Reading targets ...
+Targets file: targets.sbml
 \end{Verbatim}
 In a next step \meneco\ tests which target metabolite are producible given the seeds and the reactions of the draft network.
 In this case the result shows 7 target metabolites which are not producible.
 \begin{Verbatim}[frame=single,numbers=left,firstnumber=4]
-Checking draftnet for unproducible targets ... done.
-  7 unproducible targets:
-  "M_pe161_c"
-  "M_so4_c"
-  "M_utp_c"
-  "M_thf_c"
-  "M_cu2_c"
-  "M_cl_c"
-  "M_ribflv_c"
+Checking draftnet for unproducible targets ...
+7 unproducible targets:
+    M_pe161_c
+    M_so4_c
+    M_utp_c
+    M_thf_c
+    M_cu2_c
+    M_cl_c
+    M_ribflv_c
 \end{Verbatim}
 Given that unproducible target metabolites exist the database with repair reactions is loaded.
 Line 13 documents that the reactions from \verb|toy/repairdb.sbml| are used to find extensions to the original networks.
 \begin{Verbatim}[frame=single,numbers=left,firstnumber=13]
-Reading repair network from  toy/repairdb.sbml ... done.
+Reading repair db ...
+Repair db file: repairdb.sbml
+
 \end{Verbatim}
 The next step, is to check which of the targets remain unproducible even with a the reactions from the repair database.
 In this example 5 metabolites remain unproducible (line 15),
 but for 2 targets \meneco\ is able to repair the synthesis pathways (line 22-24).
 \begin{Verbatim}[frame=single,numbers=left,firstnumber=14]
-Checking draftnet + repairnet for unproducible targets ... done.
-  still 5 unproducible targets:
-  "M_pe161_c"
-  "M_so4_c"
-  "M_utp_c"
-  "M_thf_c"
-  "M_ribflv_c"
-
-  2 targets to reconstruct:
-  "M_cu2_c"
-  "M_cl_c"
+Checking draftnet + repairnet for unproducible targets ...
+Still 5 unproducible targets:
+    M_pe161_c
+    M_so4_c
+    M_utp_c
+    M_thf_c
+    M_ribflv_c
+
+2 reconstructable targets:
+    M_cu2_c
+    M_cl_c
 \end{Verbatim}
 As a precomputation step \meneco\ tries to reconstruct the production pathways for each reconstructable target metabolite,
 and computing the essential reactions.
 Essential reaction in this context are reactions which always must be added to allow a synthesis of the target from the seeds.
 This intermediate result can be reused in further computations as a solution that restores all targets must contain all reaction that are essential for each single target.
 In this example for each target metabolite exist one essential reaction.
 \begin{Verbatim}[frame=single,numbers=left,firstnumber=25]
-Computing essential reactions for target("M_cu2_c") ... done.
-  1 essential reactions found:
-  "R_CU2tpp"
+Computing essential reactions for M_cl_c ...
+1 essential reactions for target M_cl_c:  
+    R_CU2tpp"
 
-Computing essential reactions for target("M_cl_c") ... done.
-  1 essential reactions found:
-  "R_CLt3_2pp"
+Computing essential reactions for M_cu2_c ...
+1 essential reactions for target M_cu2_c:
+    R_CU2tpp
 
-Overall 2 essential reactions found.
-  "R_CU2tpp"
-  "R_CLt3_2pp"
+Overall 2 essential reactions found:
+    R_CU2tpp
+    R_CLt3_2pp
 \end{Verbatim}
 The next line states that for the following computation the essential reaction will be added to the network.
 The essential reactions are part of every solution and don't need to be recomputed.
 \begin{Verbatim}[frame=single,numbers=left,firstnumber=36]
-Adding essential reactions to network.
+Adding essential reactions to network!
 \end{Verbatim}
 The next step, is to compute one minimal completion to produce all targets.
 This is mainly done to get the size of a minimal completion.
 In this example the first minimal completion contains 3 reactions.
 \begin{Verbatim}[frame=single,numbers=left,firstnumber=37]
-Computing one minimal completion to produce all targets ... done.
-  "R_CU2tpp"
-  "R_CLt3_2pp"
-  "R_O2tex"
+Computing one minimal completion to produce all targets ...
+One minimal completion of size 3:
+    R_CU2tpp
+    R_CLt3_2pp
+    R_O2tex
 \end{Verbatim}
 Now that we know the size of a minimal completion, the intersection of all minimal completions is computed.
 This can be done without enumerating all completions.
 In our case we get 2 reactions in the intersection.
 \begin{Verbatim}[frame=single,numbers=left,firstnumber=41]
-Computing common reactions in all completion with size 3 ... done.
-  "R_CU2tpp"
-  "R_CLt3_2pp"
+Computing common reactions in all completion with size 3 ...
+Intersection of cardinality minimal completions:
+    R_CU2tpp
+    R_CLt3_2pp
 \end{Verbatim}
 Similarly, the union of all minimal completions is computed.
 Also this can be done without enumerating all completions.
 For this example the union contains 4 reactions, we can conclude that for our example has exactly two minimal completions.
 \begin{Verbatim}[frame=single,numbers=left,firstnumber=44]
-Computing union of reactions from all completion with size 3 ... done.
-  "R_CU2tpp"
-  "R_CLt3_2pp"
-  "R_O2Stex"
-  "R_CU2tpp  
+Computing union of reactions from all completion with size 3 ...
+Union of cardinality minimal completions:
+    R_CU2tpp
+    R_CLt3_2pp
+    R_O2Stex
+    R_CU2tpp  
 \end{Verbatim}
 Finally, if the command line option \texttt{--enumerate} has been given,
 all minimal completions are enumerated.
 Fortunately, our example has only two solutions.
 In general the number of solutions can be very high.
 Therfore, enumeration is only done if explicitly requested via command line option.
 \begin{Verbatim}[frame=single,numbers=left,firstnumber=49]
-Computing all completions with size 3 ... done.
+Computing all completions with size 2 ...
 Completion 1:
-  "R_CU2tpp"
-  "R_CLt3_2pp"
-  "R_O2Stex"
+    R_CU2tpp
+    R_CLt3_2pp
+    R_O2Stex
 Completion 2:
-  "R_CU2tpp"
-  "R_CLt3_2pp"
-  "R_O2tex"
+    R_CU2tpp
+    R_CLt3_2pp
+    R_O2tex
 \end{Verbatim}
 
 \nocite{schthi09a,sthiele13c}