Coordinometer - Revision history

Mtrevisan at 14:17, 19 February 2018

2018-02-19T14:17:38Z

Mtrevisan: updated to v1.01 with newWay mode

2018-01-24T11:45:01Z

updated to v1.01 with newWay mode

Mtrevisan: Created page with "Coordinometer v0.01 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to calculate the degree o..."

2017-12-13T14:23:19Z

Created page with "Coordinometer v0.01 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to calculate the degree o..."

New page

Coordinometer v0.01 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). Currently only the OldWay mode of
'''[[SanXoTSieve]]''' is supported (NewWay using tags coming soon).

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 oldstyle mode.
-n QCINPUTNOOUTS, --qcinputnoouts QCINPUTNOOUTS
Input outstats file with the q2c integration, NOT
including outliers (using this parameter automatically
implies the oldstyle 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).

← Older revision		Revision as of 14:17, 19 February 2018
Line 47:		Line 47:
	--caseinsensitive Consider case insensitive categories and protein		--caseinsensitive Consider case insensitive categories and protein
	identifiers (by default, they are case sensitive).		identifiers (by default, they are case sensitive).
		+
		+	[[Category:SanXoT software package]]

@@ Line 1: / Line 1: @@
-Coordinometer v0.01 is a program made in the Jesus Vazquez Cardiovascular
+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). Currently only the OldWay mode of
+command prompt and within the logFile). If the -n argument is omitted, the
-'''[[SanXoTSieve]]''' is supported (NewWay using tags coming soon).
+newWay mode for [[SanXoTSieve]] (relations file with outliers tagged as "out")
 Usage:
@@ Line 29: / Line 32: @@
                          new SanXoTSieve files, or, alternatively, it must add
                          the corresponding file with no outliers (see -n
-                         argument) for SanXoTSieve in oldstyle mode.
+                         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 oldstyle option has been used in
+                         implies the oldWay option has been used in
                          SanXoTSieve, i.e. removing outliers from the relations
                          file, instead of just tagging them).