NAME

     icaprint - print DNA cluster index

SYNOPSIS

     icaprint  [-index  filename ] [-ini  filename ]  [-screen  n
     ]  [-families n ]  [-parents n ]  [-children n ]  [-patterns
     n ]  [-orphans n ]

DESCRIPTION

     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
     created.

OPTIONS

  -index
     Defines  the  name   of   the   index   file.   Default   is
     "cluster.index" in the current directory.

  -ini
     Defines the name of the file which holds the user's  initial
     configuration  file. Default is "ICAtool.ini" in the current
     directory.

  -screen
     This determines the number of characters per  printed  line.
     Default is 80.

  -families
     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.

  -parents
     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.

  -children
     Only prints out child sequences.

  -patterns
     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.

  -orphans
     Only prints out the names of sequences  which  didn't  match
     any other.

FILES

  ICAtool.ini
     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:
     screen=100
     index=cluster.27thNov

  cluster.index
     This  cluster  index  file,  or  its  replacement,  must  be
     present.

SEE ALSO

     N2tool(1), ICAass(1), ICAtool(1), ICAstats(1), ICAmatches