This manual page is provisionary. It is a simple copy / paste of the manual of the command line tool.
NAME
convert-classes
DESCRIPTION
Interconversions between different formats of class/cluster files.
AUTHORS
Jacques van Helden
Sylvain Brohée
CATEGORY
util
USAGE
convert-classes [-i inputfile] [-o outputfile] [-v]
INPUT/OUTPUT FORMATS
mcl
The output format of the MCL algorithm. MCL is a graph-based clustering
algorithm developed by Stijn Van Dongen (http://micans.org/mcl/).
The output format has one row per cluster, each row giving a list of
elements, separated by tabulations.
mcode
The output format of the MCODE algorithm. MCODE is a graph-based
clustering algorithm developed by Bader and Hogue (Bader and Hogue, BMC
Bioinformatics, 2003)
http://baderlab.org/Software/MCODE
tab
A tab-delimited text file with 2 columns (+1 optional). The first column
indicates the element, the second column the class (cluster). The third
column is optional, it can be used to indicate the score for the
assignation of the element to the class (e.g. a posterior probability).
Any real value is accepted as score.
profiles
A tab-delimited text file with a table containing one row per element,
and one column per class. The first row starting with a '#' (the header
row) indicates the class names. The first column contains the element
names. The cells of the table contain either boolean or real values.
Boolean values indicate the membership (1 if the element is member of
the class, 0 otherwise). Real values can specify a score for the
membership of the element to the class (e.g. posterior probability).
ermg
Erdros-Renyi Mixture of Graphs. format defined by Stephane Robin for his
ERMG algorithm (submitted).
rnsc
RNSC format. format defined by Andrew King for his RNSC clustering
algorithm. Each line of the file represents a clusters contains a list
of integer representing the member. The end of the classification is
indicated by '-1'.
To convert from RNSC to another format, two files must thus be given : a
cluster file (-i option) and a name file (-names option) which is a two
colum tab delimited file containing the name of each corresponding id
(See King et al, 2004).
OPTIONS
-v #
Level of verbosity (detail in the warning messages during execution)
-h
Display full help message
-help
Same as -h
-i inputfile
If no input file is specified, the standard input is used. This
allows to use the command within a pipe.
-o outputfile
If no output file is specified, the standard output is used. This
allows to use the command within a pipe.
-names file_name
Two column file specifying the labels of the members of the
classification given in the classification file. First column
contains the identifier and second column the corresponding label.
-from input_format
Input format. Supported: tab, mcl, profiles, mcode, rnsc
-to output_format
Output format. Supported: tab, mcl,profiles
-mcol
Member column. Column containing the member names in the tab format
(default 1).
-ccol
Class column. Column containing the class names in the tab format
(default 1).
-scol
Score column. Column containing the scores in tab format. If not
specified, scores are not defined.
-null
Null string used as score in the profile output for the undefined
class memberships (default 0).
-all_scores
Assign each node to all the clusters with the ERMG format, with the
posterior probability as score.
-min_score
Minimal score value for member to class assignation.
SEE ALSO