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