**What it does**

This tool runs the trained content predictor, supplied as a TCP file,
on the given genomic sequences, as encoded in the GIO file.  It
operates as follows:

Around each location in the given genomic sequence, a sequence window
(the extent of which is specified in the TCP file) is copied from the
genomic sequence.  This window serves as input for the trained SVM,
which computes a corresponding output score.  The higher the score,
the more likely that the location is indeed part of a segment of the
given content type.

------

**Output**

The output is a file in signal prediction format (SPF) which contains
a prediction score for each location in the genomic input sequence.
(Note that this is not a mistake: no extra "content prediction format"
is required, as SPF is perfectly suitable for contents as well.)

The output may typically serve as input for 'GeneTrain'.  It can also
be analyzed with 'ContentEval'.

------

**Example**

A content predictor for acceptor splice sites may provided the following outputs::

   CHR1	acc	Conf_cum	731	+	0.239
   CHR1	acc	Conf_cum	734	+	0.264
   CHR1	acc	Conf_cum	764	+	0.857
   CHR1	acc	Conf_cum	766	+	0.115
   CHR1	acc	Conf_cum	784	+	0.085

--------

**About formats**

**CPF format** Content Prediction format was designed for providing
information such as labels or predictions for specific genomic
locations (with strand information). It has requires exactly six
fields::

    1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
    2. contentName - possible choices include intergenic, utr5exon, cds_exon, intron utr3exon.
    3. scoreName - possible choices include label, output.
    4. chromPos - The position in the chromosome. (The first base in a chromosome is numbered 1.)
    5. strand - Defines the strand - either '+' or '-'.
    6. score - The score between -infinity and infinity. If scoreName is 'label', then the score should be either -1 or 1.
