Cardenio - Revision history

Mtrevisan at 14:18, 19 February 2018

2018-02-19T14:18:29Z

Mtrevisan: adding some details

2017-12-19T11:53:00Z

adding some details

Mtrevisan: Created page with "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..."

2017-10-03T14:35:28Z

Created page with "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..."

New page

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.

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.

← Older revision		Revision as of 14:18, 19 February 2018
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	-v, --verbose To write down extra information about operations		-v, --verbose To write down extra information about operations
	performed.		performed.
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		+	[[Category:SanXoT software package]]

← Older revision		Revision as of 11:53, 19 December 2017
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	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.		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:		Usage: