icaprint - print DNA cluster index
icaprint [-index filename ] [-ini filename ] [-screen n
] [-families n ] [-parents n ] [-children n ] [-patterns
n ] [-orphans n ]
ICAprint takes an index file produced by the ICAtool program
and prints an ascii text version of the index to the
screen(stdout). This index file includes references to
necessary other files containing the DNA sequences. All
these files must be exactly as they were when the index was
Defines the name of the index file. Default is
"cluster.index" in the current directory.
Defines the name of the file which holds the user's initial
configuration file. Default is "ICAtool.ini" in the current
This determines the number of characters per printed line.
Default is 80.
Only prints out sequences if they are a member of a cluster,
that is, they share a subsequence with some other sequence
in the dataset used. This option is useful if only matched
sequences are of interest.
Only prints out a single member of each cluster of
sequences. This option is especially useful when investigat-
ing the reasons why sequences were clustered together. The
sequences listed by this option should be submitted to ica-
tool as query sequences. The output of icatool is a list of
alignments showing the regions of local similarity shared
between the parent sequence and the children in its cluster.
Only prints out child sequences.
Only prints out pattern sequences. The pattern sequences are
a superset of the parent sequences and orphan sequences.
This option is useful in the preparation of a list of
sequence names where every sequence is different from every
other, a kind of basic, unique set of sequences.
Only prints out the names of sequences which didn't match
If this file is present or another ini file has been
defined, then all startup details present in the file will
be read. An example showing only relevant lines would be:
This cluster index file, or its replacement, must be
N2tool(1), ICAass(1), ICAtool(1), ICAstats(1), ICAmatches