Camacho - Revision history

Mtrevisan: Camacho v0.02, cosmetic change respect v0.01

2018-03-14T12:44:24Z

Camacho v0.02, cosmetic change respect v0.01

Mtrevisan at 14:17, 19 February 2018

2018-02-19T14:17:50Z

Mtrevisan: Created page with "Camacho v0.01 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to take a table including prote..."

2017-10-03T14:26:07Z

Created page with "Camacho v0.01 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to take a table including prote..."

New page

Camacho v0.01 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to take a table including proteins and categories (mainly from DAVID), and organise them as relations file ready to be used in the Systems Biology Triangle.

Usage:
camacho.py [-h] -a ANALYSIS -p PLACE [-L LOGFILE] -d DBFILE
[-x PREVIOUSFILE] [-q ACCNUMCOL] [-c CATEGORYCOL]
[-f PREFIX] [--fasta FASTA]

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.
-d DBFILE, --dbfile DBFILE
The input file containing accession numbers and
categories.
-x PREVIOUSFILE, --previousfile PREVIOUSFILE
An optional relation file to which concatenate
resulting relations (if omitted, a new file will be
produced).
-q ACCNUMCOL, --accnumcol ACCNUMCOL
Column where accession numbers of genes/proteins are.
First column is 1. Default is 1.
-c CATEGORYCOL, --categorycol CATEGORYCOL
Column where categories are. First column is 1.
Default is 2.
-f PREFIX, --prefix PREFIX
Prefix to add to all categories found in this parsing
(such as "GO-full_", "Panther_", or
"KEGG=2017-01-10_".
--fasta FASTA FASTA file contaning the identifiers we want to
replace by FASTA headers in the final file. Note that
identifiers not appearing in this FASTA file will be
removed from the final list.

← Older revision		Revision as of 12:44, 14 March 2018
Line 1:		Line 1:
−	Camacho v0.01 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to take a table including proteins and categories (mainly from DAVID), and organise them as relations file ready to be used in the Systems Biology Triangle.	+	Camacho v0.02 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to take a table including proteins and categories (mainly from DAVID), and organise them as relations file ready to be used in the Systems Biology Triangle.

	Usage:		Usage:

← Older revision		Revision as of 14:17, 19 February 2018
Line 38:		Line 38:
	identifiers not appearing in this FASTA file will be		identifiers not appearing in this FASTA file will be
	removed from the final list.		removed from the final list.
		+
		+	[[Category:SanXoT software package]]