Camacho

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.