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