NAME

       gthbssmtrain - train splice site model

SYNOPSIS

       gthbssmtrain [option ...] GFF3_file

DESCRIPTION

       Create BSSM training data from annotation given in GFF3_file.

OPTIONS

       -outdir
           set name of output directory to which the training files are written default:
           training_data

       -gcdonor
           extract training data for GC donor sites default: yes

       -filtertype
           set type of features to used for filtering (usually 'exon' or 'CDS') default: exon

       -goodexoncount
           set the minimum number of good exons a feature must have to be included into the
           training data default: 1

       -cutoff
           set the minimum score an exon must have to count towards the ``good exon count''
           (exons without a score count as good) default: 1.00

       -extracttype
           set type of features to be extracted as exons (usually 'exon' or 'CDS') default: CDS

       -seqfile
           set the sequence file from which to take the sequences default: undefined

       -encseq
           set the encoded sequence indexname from which to take the sequences default: undefined

       -seqfiles
           set the sequence files from which to extract the features use '--' to terminate the
           list of sequence files

       -matchdesc
           search the sequence descriptions from the input files for the desired sequence IDs (in
           GFF3), reporting the first match default: no

       -matchdescstart
           exactly match the sequence descriptions from the input files for the desired sequence
           IDs (in GFF3) from the beginning to the first whitespace default: no

       -usedesc
           use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence
           entries. If a description contains a sequence range (e.g., III:1000001..2000000), the
           first  part is used as sequence ID ('III') and the first range position as offset
           ('1000001') default: no

       -regionmapping
           set file containing sequence-region to sequence file mapping default: undefined

       -seed
           set seed for random number generator manually 0 generates a seed from the current time
           and the process id default: 0

       -v
           be verbose default: no

       -gzip
           write gzip compressed output files default: no

       -bzip2
           write bzip2 compressed output files default: no

       -force
           force writing to output files default: no

       -help
           display help and exit

       -version
           display version information and exit

                                                                                  GTHBSSMTRAIN(1)