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Update doc with the recent changes.
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@ArnaudBelcour
ArnaudBelcour committed Mar 1, 2024
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -4,7 +4,7 @@

WARNING: change for individual and community scopes:
* for individual scope: only seeds that are producible, ie associated with activated reactions are now shown in the results. Additional information on producible, non-producible and absent seeds are available in the json output. This requires MeneTools version >= `3.4.0`.
* for community scope: use of `miscoto focus` for computation in order to retrieve the metabolite producers in community. This requires MeneTools version >= `3.2.0`.
* for community scope: use of `miscoto focus` for computation in order to retrieve the metabolite producers in community. This requires MiSCoTo version >= `3.2.0`.

## Add

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226 changes: 104 additions & 122 deletions docs/command.rst
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Expand Up @@ -21,15 +21,12 @@ Features
There is NO WARRANTY, to the extent permitted by law.
usage: m2m [-h] [-v]
{recon,iscope,cscope,addedvalue,mincom,seeds,workflow,metacom,test}
...
usage: m2m [-h] [-v] {recon,iscope,cscope,addedvalue,mincom,seeds,workflow,metacom,test} ...
From metabolic network reconstruction with annotated genomes to metabolic
capabilities screening to identify organisms of interest in a large
microbiota. For specific help on each subcommand use: m2m {cmd} --help
From metabolic network reconstruction with annotated genomes to metabolic capabilities screening to identify organisms of interest in a large microbiota.
For specific help on each subcommand use: m2m {cmd} --help
optional arguments:
options:
-h, --help show this help message and exit
-v, --version show program's version number and exit
Expand All @@ -40,8 +37,7 @@ Features
recon metabolic network reconstruction
iscope individual scope computation
cscope community scope computation
addedvalue added value of microbiota's metabolism over
individual's
addedvalue added value of microbiota's metabolism over individual's
mincom minimal communtity selection
seeds creation of seeds SBML file
workflow whole workflow
Expand All @@ -56,27 +52,24 @@ m2m recon

.. code::
usage: m2m recon [-h] -g GENOMES -o OUPUT_DIR [-c CPU] [-q] [-l {2,3}]
[--noorphan] [-p] [--clean] [--pwt-xml]
Run metabolic network reconstruction for each annotated genome of the input
directory, using Pathway Tools
optional arguments:
-h, --help show this help message and exit
-g GENOMES, --genomes GENOMES
annotated genomes directory
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-c CPU, --cpu CPU cpu number for multi-process
-q, --quiet quiet mode
-l {2,3}, --level {2,3}
Level for SBML creation, 2 or 3
--noorphan use this option to ignore reactions without gene or
protein association
-p, --padmet create padmet files
--clean clean PGDBs if already present
--pwt-xml use this option to use Pathway Tools xml (incompatible with -p)
usage: m2m recon [-h] -g GENOMES -o OUPUT_DIR [-c CPU] [-q] [-l {2,3}] [--noorphan] [-p] [--clean] [--pwt-xml]
Run metabolic network reconstruction for each annotated genome of the input directory, using Pathway Tools
options:
-h, --help show this help message and exit
-g GENOMES, --genomes GENOMES
annotated genomes directory
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-c CPU, --cpu CPU cpu number for multiprocessing
-q, --quiet quiet mode
-l {2,3}, --level {2,3}
Level for SBML creation, 2 or 3
--noorphan use this option to ignore reactions without gene or protein association
-p, --padmet create padmet files
--clean clean PGDBs if already present
--pwt-xml use this option to use Pathway Tools xml (incompatible with -p)
m2m iscope
Expand All @@ -86,55 +79,52 @@ m2m iscope
usage: m2m iscope [-h] -n NETWORKS_DIR -s SEEDS -o OUPUT_DIR [-q] [-c CPU]
Compute individual scopes (reachable metabolites from seeds) for each
metabolic network of the input directory
Compute individual scopes (reachable metabolites from seeds) for each metabolic network of the input directory
optional arguments:
-h, --help show this help message and exit
-n NETWORKS_DIR, --networksdir NETWORKS_DIR
metabolic networks directory
-s SEEDS, --seeds SEEDS
seeds (growth medium) for metabolic analysis
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-q, --quiet quiet mode
-c CPU, --cpu CPU cpu number for multi-process
options:
-h, --help show this help message and exit
-n NETWORKS_DIR, --networksdir NETWORKS_DIR
metabolic networks directory
-s SEEDS, --seeds SEEDS
seeds (growth medium) for metabolic analysis
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-q, --quiet quiet mode
-c CPU, --cpu CPU cpu number for multiprocessing
m2m cscope
==========

.. code::
usage: m2m cscope [-h] -n NETWORKS_DIR -s SEEDS -o OUPUT_DIR [-m MODELHOST]
[-q]
usage: m2m cscope [-h] -n NETWORKS_DIR -s SEEDS -o OUPUT_DIR [-m MODELHOST] [-q] [-t TARGETS]
Compute the community scope of all metabolic networks
optional arguments:
-h, --help show this help message and exit
-n NETWORKS_DIR, --networksdir NETWORKS_DIR
metabolic networks directory
-s SEEDS, --seeds SEEDS
seeds (growth medium) for metabolic analysis
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-m MODELHOST, --modelhost MODELHOST
host metabolic model for community analysis
-q, --quiet quiet mode
options:
-h, --help show this help message and exit
-n NETWORKS_DIR, --networksdir NETWORKS_DIR
metabolic networks directory
-s SEEDS, --seeds SEEDS
seeds (growth medium) for metabolic analysis
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-m MODELHOST, --modelhost MODELHOST
host metabolic model for community analysis
-q, --quiet quiet mode
-t TARGETS, --targets TARGETS
Optional targets for metabolic analysis, if not used metage2metabo will use the addedvalue of the community
m2m addedvalue
==============

.. code::
usage: m2m addedvalue [-h] -n NETWORKS_DIR -s SEEDS -o OUPUT_DIR
[-m MODELHOST] [-q]
usage: m2m addedvalue [-h] -n NETWORKS_DIR -s SEEDS -o OUPUT_DIR [-m MODELHOST] [-q]
Compute metabolites that are reachable by the community/microbiota and not by
individual organisms
Compute metabolites that are reachable by the community/microbiota and not by individual organisms
optional arguments:
options:
-h, --help show this help message and exit
-n NETWORKS_DIR, --networksdir NETWORKS_DIR
metabolic networks directory
Expand All @@ -152,71 +142,64 @@ m2m mincom

.. code::
usage: m2m mincom [-h] -n NETWORKS_DIR -s SEEDS -o OUPUT_DIR [-m MODELHOST]
[-q] -t TARGETS
usage: m2m mincom [-h] -n NETWORKS_DIR -s SEEDS -o OUPUT_DIR [-m MODELHOST] [-q] -t TARGETS
Select minimal-size community to make reachable a set of metabolites
optional arguments:
-h, --help show this help message and exit
-n NETWORKS_DIR, --networksdir NETWORKS_DIR
metabolic networks directory
-s SEEDS, --seeds SEEDS
seeds (growth medium) for metabolic analysis
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-m MODELHOST, --modelhost MODELHOST
host metabolic model for community analysis
-q, --quiet quiet mode
-t TARGETS, --targets TARGETS
options:
-h, --help show this help message and exit
-n NETWORKS_DIR, --networksdir NETWORKS_DIR
metabolic networks directory
-s SEEDS, --seeds SEEDS
seeds (growth medium) for metabolic analysis
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-m MODELHOST, --modelhost MODELHOST
host metabolic model for community analysis
-q, --quiet quiet mode
-t TARGETS, --targets TARGETS
targets for metabolic analysis
m2m workflow
============

.. code::
usage: m2m workflow [-h] -g GENOMES -s SEEDS [-m MODELHOST] -o OUPUT_DIR
[-c CPU] [-q] [--noorphan] [-p] [-t TARGETS] [--clean]
[--pwt-xml]
Run the whole workflow: metabolic network reconstruction, individual and
community scope analysis and community selection
optional arguments:
-h, --help show this help message and exit
-g GENOMES, --genomes GENOMES
annotated genomes directory
-s SEEDS, --seeds SEEDS
seeds (growth medium) for metabolic analysis
-m MODELHOST, --modelhost MODELHOST
host metabolic model for community analysis
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-c CPU, --cpu CPU cpu number for multi-process
-q, --quiet quiet mode
--noorphan use this option to ignore reactions without gene or
protein association
-p, --padmet create padmet files
-t TARGETS, --targets TARGETS
Optional targets for metabolic analysis, if not used
metage2metabo will use the addedvalue of the community
--clean clean PGDBs if already present
--pwt-xml use this option to use Pathway Tools xml (incompatible with -p)
usage: m2m workflow [-h] -g GENOMES -s SEEDS [-m MODELHOST] -o OUPUT_DIR [-c CPU] [-q] [--noorphan] [-p] [-t TARGETS] [--clean] [--pwt-xml] [--target-com-scope]
Run the whole workflow: metabolic network reconstruction, individual and community scope analysis and community selection
options:
-h, --help show this help message and exit
-g GENOMES, --genomes GENOMES
annotated genomes directory
-s SEEDS, --seeds SEEDS
seeds (growth medium) for metabolic analysis
-m MODELHOST, --modelhost MODELHOST
host metabolic model for community analysis
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-c CPU, --cpu CPU cpu number for multiprocessing
-q, --quiet quiet mode
--noorphan use this option to ignore reactions without gene or protein association
-p, --padmet create padmet files
-t TARGETS, --targets TARGETS
Optional targets for metabolic analysis, if not used metage2metabo will use the addedvalue of the community
--clean clean PGDBs if already present
--pwt-xml use this option to use Pathway Tools xml (incompatible with -p)
--target-com-scope Instead of the addedvalue, use the community scope as targets for mincom.
m2m metacom
===========

.. code::
usage: m2m metacom [-h] -n NETWORKS_DIR -s SEEDS [-m MODELHOST] -o OUPUT_DIR
[-t TARGETS] [-q] [-c CPU]
usage: m2m metacom [-h] -n NETWORKS_DIR -s SEEDS [-m MODELHOST] -o OUPUT_DIR [-t TARGETS] [-q] [-c CPU] [--target-com-scope]
Run the whole metabolism community analysis: individual and community scope
analysis and community selection
Run the whole metabolism community analysis: individual and community scope analysis and community selection
optional arguments:
options:
-h, --help show this help message and exit
-n NETWORKS_DIR, --networksdir NETWORKS_DIR
metabolic networks directory
Expand All @@ -227,10 +210,10 @@ m2m metacom
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-t TARGETS, --targets TARGETS
Optional targets for metabolic analysis, if not used
metage2metabo will use the addedvalue of the community
Optional targets for metabolic analysis, if not used metage2metabo will use the addedvalue of the community
-q, --quiet quiet mode
-c CPU, --cpu CPU cpu number for multi-process
-c CPU, --cpu CPU cpu number for multiprocessing
--target-com-scope Instead of the addedvalue, use the community scope as targets for mincom.
m2m seeds
Expand All @@ -240,17 +223,16 @@ m2m seeds
usage: m2m seeds [-h] -o OUPUT_DIR [-q] --metabolites METABOLITES
Create a SBML file starting for a simple text file with metabolic compounds
identifiers
Create a SBML file starting for a simple text file with metabolic compounds identifiers
options:
-h, --help show this help message and exit
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-q, --quiet quiet mode
--metabolites METABOLITES
metabolites file: one per line, encoded (XXX as in <species id="XXXX" .../> of SBML files)
optional arguments:
-h, --help show this help message and exit
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
-q, --quiet quiet mode
--metabolites METABOLITES
metabolites file: one per line, encoded (XXX as in
<species id="XXXX" .../> of SBML files)
m2m test
=========
Expand All @@ -261,9 +243,9 @@ m2m test
Test the whole workflow on a data sample
optional arguments:
options:
-h, --help show this help message and exit
-q, --quiet quiet mode
-c CPU, --cpu CPU cpu number for multi-process
-c CPU, --cpu CPU cpu number for multiprocessing
-o OUPUT_DIR, --out OUPUT_DIR
output directory path
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