Scroll to navigation

GT-INLINESEQ_ADD(1) GenomeTools Manual GT-INLINESEQ_ADD(1)

NAME

gt-inlineseq_add - Adds inline sequences from external source to GFF3 input.

SYNOPSIS

gt inlineseq_add [options] [GFF3_file ...]

DESCRIPTION

-seqfile [filename]
set the sequence file from which to take the sequences (default: undefined)
-encseq [filename]
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 [yes|no]
search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)
-matchdescstart [yes|no]
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 [yes|no]
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 [string]
set file containing sequence-region to sequence file mapping (default: undefined)
-o [filename]
redirect output to specified file (default: undefined)
-gzip [yes|no]
write gzip compressed output file (default: no)
-bzip2 [yes|no]
write bzip2 compressed output file (default: no)
-force [yes|no]
force writing to output file (default: no)
-help
display help and exit
-version
display version information and exit

REPORTING BUGS

Report bugs to <gt-users@genometools.org>.
07/29/2016 GenomeTools 1.5.9