gt-inlineseq_add1
Adds inline sequences from external source to gff3 input.
Usage
gt inlineseq_add
[options]
[GFF3_file ...]
Overview
-
-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
Releases
5 releases since Debian 9 (Stretch); the text changed 4 times.