Cardenio

Cardenio v0.03 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to generate joined integration data and relations files from different experiments.

For this program you need two types of input:

1) a set of lowerNormV files, produced during a SanXoT integration.

2) a "tag file", which is a tag separated file containing information this way:

tag file
experiment1	D:\dataFolder\data1_lowerNormV.xls
experiment2	D:\dataFolder\data2_lowerNormV.xls
experiment3	D:\dataFolder\data3_lowerNormV.xls

Where "experiment1"... are the suffixes Cardenio is going to use to tag the higher level elements (in most cases, proteins identifiers), to identify in which analysis their fold-changes have been calculcated. Note that the separation between the suffixes and file locations is a tabulator. Take into account also that a header row (containing any text) is needed (it will be ignored by Cardenio).

And produces three output files:

prefix_newData.txt
prefix_newRels.txt
logFile.txt

The two first of which can be used in a SanXoT integration as usual, where the lower level are the identifiers (usually proteins) in each experiment with the suffix assigned, while the higher level are the same identifiers (proteins) without suffix (because the information associated to each element is not associated to a specific experiment, but to the global analysis).

Usage:

cardenio.py [-h] -a ANALYSIS -p PLACE [-L LOGFILE] -t TAGFILE
                  [-d DATAFILE] [-r RELFILE] [-s SEPARATOR] [-v]

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.
 -t TAGFILE, --tagfile TAGFILE
                       The file containing the tags used for the different
                       experiments to be joined.
 -d DATAFILE, --datafile DATAFILE
                       To use a non-default merged data file name.
 -r RELFILE, --relfile RELFILE
                       To use a non-default merged relations file name.
 -s SEPARATOR, --separator SEPARATOR
                       To use a non-default suffix separator (default is
                       "_").
 -v, --verbose         To write down extra information about operations
                       performed.