gthbssmtrain - train splice site model
gthbssmtrain [option ...] GFF3_file
Create BSSM training data from annotation given in GFF3_file.
-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