gthbssmtrain1

Usage

Overview

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