Commands
Outputs and logs
By default, m2m writes into the console (stdout) and into a log file located at the root of the results directory and named after the subcommand that was executed. The option -q can be given to any m2m subcommand to write in the log file and to stdout only the warnings, errors and critical issues, together with the path to the log file.
m2m Commands
Features
Copyright (C) Dyliss & Pleiade License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> m2m is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. 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 options: -h, --help show this help message and exit -v, --version show program's version number and exit subcommands: valid subcommands: {recon,iscope,cscope,addedvalue,mincom,seeds,workflow,metacom,test} recon metabolic network reconstruction iscope individual scope computation cscope community scope computation addedvalue added value of microbiota's metabolism over individual's mincom minimal communtity selection seeds creation of seeds SBML file workflow whole workflow metacom whole metabolism community analysis test test on sample data from rumen experiments Requires: Pathway Tools installed and in $PATH, and NCBI Blast
m2m recon
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
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 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
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 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
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 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
m2m mincom
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 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
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
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 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 -m MODELHOST, --modelhost MODELHOST host metabolic model for community analysis -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 -q, --quiet quiet mode -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
usage: m2m seeds [-h] -o OUPUT_DIR [-q] --metabolites METABOLITES 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)
m2m test
usage: m2m test [-h] [-q] [-c CPU] -o OUPUT_DIR Test the whole workflow on a data sample options: -h, --help show this help message and exit -q, --quiet quiet mode -c CPU, --cpu CPU cpu number for multiprocessing -o OUPUT_DIR, --out OUPUT_DIR output directory path