Coordinometer

Coordinometer v1.01 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to calculate the degree of coordination for a given q>c and c>a integration. Input files are the outstats files (part of the output of these integrations), and the output is the coordination calculated from them (presented in both the command prompt and within the logFile). If the -n argument is omitted, the newWay mode for SanXoTSieve (relations file with outliers tagged as "out") will be considered; conversely, if the -n argument is used, the oldWay mode for SanXoTSieve (no tags in the resulting relations file, outliers are just removed) will be assumed.

Usage:

coordinometer.py [-h] [-a ANALYSIS] [-p PLACE] [-L LOGFILE] -q QCINPUT
                       [-n QCINPUTNOOUTS] -c CAINPUT [--cafdr CAFDR]
                       [--caseinsensitive]

Arguments:

 -h, --help            show this help message and exit
 -a ANALYSIS, --analysis ANALYSIS
                       Use a prefix for the output files.
 -p PLACE, --place PLACE
                       To use a different common folder for the output files.
                       If this is not provided, the the folder used will be
                       the same as the FASTA file folder.
 -L LOGFILE, --logfile LOGFILE
                       To use a non-default name for the log file.
 -q QCINPUT, --qcinput QCINPUT
                       Input outstats file with the q2c integration,
                       including outliers. It must include outliers tagged in
                       new SanXoTSieve files, or, alternatively, it must add
                       the corresponding file with no outliers (see -n
                       argument) for SanXoTSieve in oldWay mode.
 -n QCINPUTNOOUTS, --qcinputnoouts QCINPUTNOOUTS
                       Input outstats file with the q2c integration, NOT
                       including outliers (using this parameter automatically
                       implies the oldWay option has been used in
                       SanXoTSieve, i.e. removing outliers from the relations
                       file, instead of just tagging them).
 -c CAINPUT, --cainput CAINPUT
                       Input outstats file with the c2a integration, defining
                       in the FDR column which cateogries are considered to
                       be changing.
 --cafdr CAFDR         To consider a non-default FDR value for changing
                       categories in the c2a integration (default is 0.05).
 --caseinsensitive     Consider case insensitive categories and protein
                       identifiers (by default, they are case sensitive).